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Problem connecting to server (jersey) #69

Closed josephwb closed 10 years ago

josephwb commented 10 years ago

When trying to "fixNamesFromTrees", we are getting a "PROBLEM CONNECTING TO SERVER" error:

PROBLEM CONNECTING TO SERVER
com.sun.jersey.api.client.ClientHandlerException: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found
    at com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:151)
    at com.sun.jersey.api.client.Client.handle(Client.java:648)
    at com.sun.jersey.api.client.WebResource.handle(WebResource.java:680)
    at com.sun.jersey.api.client.WebResource.access$200(WebResource.java:74)
    at com.sun.jersey.api.client.WebResource$Builder.post(WebResource.java:568)
    at opentree.PhylografterConnector.fixNamesFromTrees(PhylografterConnector.java:228)
    at opentree.MainRunner.loadPhylografterStudy(MainRunner.java:1400)
    at opentree.MainRunner.pg_loading_ind_studies(MainRunner.java:1529)
    at opentree.MainRunner.main(MainRunner.java:1884)
Caused by: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found
    at com.sun.jersey.api.client.RequestWriter.writeRequestEntity(RequestWriter.java:288)
    at com.sun.jersey.client.urlconnection.URLConnectionClientHandler._invoke(URLConnectionClientHandler.java:213)
    at com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:149)
    ... 8 more

As far as I know, the relevant code (https://github.com/OpenTreeOfLife/treemachine/blob/master/src/main/java/opentree/PhylografterConnector.java#L185-229) has not changed recently.

We were able to determine that the service itself is working through using curl:

curl -X POST http://ec2-54-203-194-13.us-west-2.compute.amazonaws.com/taxomachine/ext/TNRS/graphdb/getContextForNames -H "content-type:application/json" -d '{"names":["Barnardius barnardi","Barnardius zonarius","Platycercus adscitus","Platycercus elegans","Psephotus dissimilis","Psephotus varius","Purpureicephalus spurius","Northiella haematogaster","Psephotus haematonotus","Cyanoramphus auriceps","Cyanoramphus novaezelandiae","Eunymphicus uvaeensis","Prosopeia tabuensis","Lathamus discolor","Pezoporus flaviventris","Pezoporus wallicus","Pezoporus occidentalis","Neophema elegans","Neopsephotus bourkii","Agapornis roseicollis","Loriculus galgulus","Bolbopsittacus lunulatus","Chalcopsitta duivenbodei","Melopsittacus undulatus","Cyclopsitta diophthalma","Psittaculirostris edwardsii","Psittacella brehmii","Psittacella picta","Aprosmictus erythropterus","Polytelis alexandrae","Alisterus amboinensis","Polytelis anthopeplus","Micropsitta finschii","Psittacula columboides","Tanygnathus lucionensis","Geoffroyus heteroclitus","Eclectus roratus","Prioniturus luconensis","Poicephalus robustus","Psittacus erithacus","Coracopsis vasa","Myiopsitta monachus","Psittrichas fulgidus","Calyptorhynchus banksii","Calyptorhynchus funereus","Eolophus roseicapillus","Nestor notabilis","Strigops habroptilus"]}'
blackrim commented 10 years ago

Hm, do we know what has changed?

On Wed, Mar 26, 2014 at 5:14 PM, Joseph W. Brown notifications@github.comwrote:

When trying to "fixNamesFromTrees", we are getting a "PROBLEM CONNECTING TO SERVER" error:

PROBLEM CONNECTING TO SERVER com.sun.jersey.api.client.ClientHandlerException: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found at com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:151) at com.sun.jersey.api.client.Client.handle(Client.java:648) at com.sun.jersey.api.client.WebResource.handle(WebResource.java:680) at com.sun.jersey.api.client.WebResource.access$200(WebResource.java:74) at com.sun.jersey.api.client.WebResource$Builder.post(WebResource.java:568) at opentree.PhylografterConnector.fixNamesFromTrees(PhylografterConnector.java:228) at opentree.MainRunner.loadPhylografterStudy(MainRunner.java:1400) at opentree.MainRunner.pg_loading_ind_studies(MainRunner.java:1529) at opentree.MainRunner.main(MainRunner.java:1884) Caused by: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found at com.sun.jersey.api.client.RequestWriter.writeRequestEntity(RequestWriter.java:288) at com.sun.jersey.client.urlconnection.URLConnectionClientHandler._invoke(URLConnectionClientHandler.java:213) at com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:149) ... 8 more

As far as I know, the relevant code ( https://github.com/OpenTreeOfLife/treemachine/blob/master/src/main/java/opentree/PhylografterConnector.java#L185-229) has not changed recently.

We were able to determine that the service itself is working through using curl:

curl -X POST http://ec2-54-203-194-13.us-west-2.compute.amazonaws.com/taxomachine/ext/TNRS/graphdb/getContextForNames -H "content-type:application/json" -d '{"names":["Barnardius barnardi","Barnardius zonarius","Platycercus adscitus","Platycercus elegans","Psephotus dissimilis","Psephotus varius","Purpureicephalus spurius","Northiella haematogaster","Psephotus haematonotus","Cyanoramphus auriceps","Cyanoramphus novaezelandiae","Eunymphicus uvaeensis","Prosopeia tabuensis","Lathamus discolor","Pezoporus flaviventris","Pezoporus wallicus","Pezoporus occidentalis","Neophema elegans","Neopsephotus bourkii","Agapornis roseicollis","Loriculus galgulus","Bolbopsittacus lunulatus","Chalcopsitta duivenbodei","Melopsittacus undulatus","Cyclopsitta diophthalma","Psittaculirostris edwardsii","Psittacella brehmii","Psittacella picta","Aprosmictus erythropterus","Polytelis alexandrae","Alisterus amboinensis","Polytelis anthopeplus","Micropsitta finschii","Psittacula columboides","Tanygn athus lucionensis","Geoffroyus heteroclitus","Eclectus roratus","Prioniturus luconensis","Poicephalus robustus","Psittacus erithacus","Coracopsis vasa","Myiopsitta monachus","Psittrichas fulgidus","Calyptorhynchus banksii","Calyptorhynchus funereus","Eolophus roseicapillus","Nestor notabilis","Strigops habroptilus"]}'

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69 .

josephwb commented 10 years ago

Not a clue.

jar398 commented 10 years ago

I hope it's nothing I did... I would survey the commit log

The new unmanaged connection stuff does mention the JSON media type, but I don't think it does anything that would have an effect on the state of anything related to jersey. If you have any suspicions, try deleting the classes I added.

On Wed, Mar 26, 2014 at 5:22 PM, Stephen Smith notifications@github.comwrote:

Hm, do we know what has changed?

On Wed, Mar 26, 2014 at 5:14 PM, Joseph W. Brown notifications@github.comwrote:

When trying to "fixNamesFromTrees", we are getting a "PROBLEM CONNECTING TO SERVER" error:

PROBLEM CONNECTING TO SERVER com.sun.jersey.api.client.ClientHandlerException: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found at com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:151)

at com.sun.jersey.api.client.Client.handle(Client.java:648) at com.sun.jersey.api.client.WebResource.handle(WebResource.java:680) at com.sun.jersey.api.client.WebResource.access$200(WebResource.java:74) at com.sun.jersey.api.client.WebResource$Builder.post(WebResource.java:568) at opentree.PhylografterConnector.fixNamesFromTrees(PhylografterConnector.java:228)

at opentree.MainRunner.loadPhylografterStudy(MainRunner.java:1400) at opentree.MainRunner.pg_loading_ind_studies(MainRunner.java:1529) at opentree.MainRunner.main(MainRunner.java:1884) Caused by: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found at com.sun.jersey.api.client.RequestWriter.writeRequestEntity(RequestWriter.java:288)

at com.sun.jersey.client.urlconnection.URLConnectionClientHandler._invoke(URLConnectionClientHandler.java:213)

at com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:149)

... 8 more

As far as I know, the relevant code (

https://github.com/OpenTreeOfLife/treemachine/blob/master/src/main/java/opentree/PhylografterConnector.java#L185-229)

has not changed recently.

We were able to determine that the service itself is working through using curl:

curl -X POST http://ec2-54-203-194-13.us-west-2.compute.amazonaws.com/taxomachine/ext/TNRS/graphdb/getContextForNames-H "content-type:application/json" -d '{"names":["Barnardius barnardi","Barnardius zonarius","Platycercus adscitus","Platycercus elegans","Psephotus dissimilis","Psephotus varius","Purpureicephalus spurius","Northiella haematogaster","Psephotus haematonotus","Cyanoramphus auriceps","Cyanoramphus novaezelandiae","Eunymphicus uvaeensis","Prosopeia tabuensis","Lathamus discolor","Pezoporus flaviventris","Pezoporus wallicus","Pezoporus occidentalis","Neophema elegans","Neopsephotus bourkii","Agapornis roseicollis","Loriculus galgulus","Bolbopsittacus lunulatus","Chalcopsitta duivenbodei","Melopsittacus un dulatus& quot;,"Cyclopsitta diophthalma","Psittaculirostris edwardsii","Psittacella brehmii","Psittacella picta","Aprosmictus erythropterus","Polytelis alexandrae","Alisterus amboinensis","Polytelis anthopeplus","Micropsitta finschii","Psittacula columboides","Tanygn athus lucionensis","Geoffroyus heteroclitus","Eclectus roratus","Prioniturus luconensis","Poicephalus robustus","Psittacus erithacus","Coracopsis vasa","Myiopsitta monachus","Psittrichas fulgidus","Calyptorhynchus banksii","Calyptorhynchus funereus","Eolophus roseicapillus","Nestor notabilis","Strigops habroptilus"]}'

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69> .

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38741617 .

chinchliff commented 10 years ago

Was there a version upgrade for neo4j on taxomachine? Perhaps something changed about the web services that jersey doesn't like.

On Wednesday, March 26, 2014, Jonathan A Rees notifications@github.com wrote:

I hope it's nothing I did... I would survey the commit log

The new unmanaged connection stuff does mention the JSON media type, but I don't think it does anything that would have an effect on the state of anything related to jersey. If you have any suspicions, try deleting the classes I added.

On Wed, Mar 26, 2014 at 5:22 PM, Stephen Smith notifications@github.com<javascript:_e(%7B%7D,'cvml','notifications@github.com');>wrote:

Hm, do we know what has changed?

On Wed, Mar 26, 2014 at 5:14 PM, Joseph W. Brown notifications@github.com<javascript:_e(%7B%7D,'cvml','notifications@github.com');>wrote:

When trying to "fixNamesFromTrees", we are getting a "PROBLEM CONNECTING TO SERVER" error:

PROBLEM CONNECTING TO SERVER com.sun.jersey.api.client.ClientHandlerException: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found at

com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:151)

at com.sun.jersey.api.client.Client.handle(Client.java:648) at com.sun.jersey.api.client.WebResource.handle(WebResource.java:680) at com.sun.jersey.api.client.WebResource.access$200(WebResource.java:74) at com.sun.jersey.api.client.WebResource$Builder.post(WebResource.java:568) at

opentree.PhylografterConnector.fixNamesFromTrees(PhylografterConnector.java:228)

at opentree.MainRunner.loadPhylografterStudy(MainRunner.java:1400) at opentree.MainRunner.pg_loading_ind_studies(MainRunner.java:1529) at opentree.MainRunner.main(MainRunner.java:1884) Caused by: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found at

com.sun.jersey.api.client.RequestWriter.writeRequestEntity(RequestWriter.java:288)

at

com.sun.jersey.client.urlconnection.URLConnectionClientHandler._invoke(URLConnectionClientHandler.java:213)

at

com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:149)

... 8 more

As far as I know, the relevant code (

https://github.com/OpenTreeOfLife/treemachine/blob/master/src/main/java/opentree/PhylografterConnector.java#L185-229)

has not changed recently.

We were able to determine that the service itself is working through using curl:

curl -X POST

http://ec2-54-203-194-13.us-west-2.compute.amazonaws.com/taxomachine/ext/TNRS/graphdb/getContextForNames-H"content-type:application/json" -d '{"names":["Barnardius barnardi","Barnardius zonarius","Platycercus adscitus","Platycercus elegans","Psephotus dissimilis","Psephotus varius","Purpureicephalus spurius","Northiella haematogaster","Psephotus haematonotus","Cyanoramphus auriceps","Cyanoramphus novaezelandiae","Eunymphicus uvaeensis","Prosopeia tabuensis","Lathamus discolor","Pezoporus flaviventris","Pezoporus wallicus","Pezoporus occidentalis","Neophema elegans","Neopsephotus bourkii","Agapornis roseicollis","Loriculus galgulus","Bolbopsittacus lunulatus","Chalcopsitta duivenbodei","Melopsittacus un dulatus& quot;,"Cyclopsitta diophthalma","Psittaculirostris edwardsii","Psittacella brehmii","Psittacella picta","Aprosmictus erythropterus","Polytelis alexandrae","Alisterus amboinensis","Polytelis anthopeplus","Micropsitta finschii","Psittacula columboides","Tanygn

athus lucionensis","Geoffroyus heteroclitus","Eclectus roratus","Prioniturus luconensis","Poicephalus robustus","Psittacus erithacus","Coracopsis vasa","Myiopsitta monachus","Psittrichas fulgidus","Calyptorhynchus banksii","Calyptorhynchus funereus","Eolophus roseicapillus","Nestor notabilis","Strigops habroptilus"]}'

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69> .

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38741617>

.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38753203 .

jar398 commented 10 years ago

Hmm... I've been upgrading everything to neo4j 1.9.5 as I go along. I updated treemachine and ot-base but not taxomachine. Since this is a treemachine problem maybe that's the problem. Perhaps the converter to json has become less liberal and rejects strings, which it handled in the older version?

On Wed, Mar 26, 2014 at 8:37 PM, chinchliff notifications@github.comwrote:

Was there a version upgrade for neo4j on taxomachine? Perhaps something changed about the web services that jersey doesn't like.

On Wednesday, March 26, 2014, Jonathan A Rees notifications@github.com wrote:

I hope it's nothing I did... I would survey the commit log

The new unmanaged connection stuff does mention the JSON media type, but I don't think it does anything that would have an effect on the state of anything related to jersey. If you have any suspicions, try deleting the classes I added.

On Wed, Mar 26, 2014 at 5:22 PM, Stephen Smith <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');>wrote:

Hm, do we know what has changed?

On Wed, Mar 26, 2014 at 5:14 PM, Joseph W. Brown <notifications@github.com<javascript:_e(%7B%7D,'cvml',' notifications@github.com');>>wrote:

When trying to "fixNamesFromTrees", we are getting a "PROBLEM CONNECTING TO SERVER" error:

PROBLEM CONNECTING TO SERVER com.sun.jersey.api.client.ClientHandlerException: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found at

com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:151)

at com.sun.jersey.api.client.Client.handle(Client.java:648) at com.sun.jersey.api.client.WebResource.handle(WebResource.java:680) at com.sun.jersey.api.client.WebResource.access$200(WebResource.java:74) at

com.sun.jersey.api.client.WebResource$Builder.post(WebResource.java:568)

at

opentree.PhylografterConnector.fixNamesFromTrees(PhylografterConnector.java:228)

at opentree.MainRunner.loadPhylografterStudy(MainRunner.java:1400) at opentree.MainRunner.pg_loading_ind_studies(MainRunner.java:1529) at opentree.MainRunner.main(MainRunner.java:1884) Caused by: com.sun.jersey.api.client.ClientHandlerException: A message body writer for Java type, class java.lang.String, and MIME media type, application/json, was not found at

com.sun.jersey.api.client.RequestWriter.writeRequestEntity(RequestWriter.java:288)

at

com.sun.jersey.client.urlconnection.URLConnectionClientHandler._invoke(URLConnectionClientHandler.java:213)

at

com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:149)

... 8 more

As far as I know, the relevant code (

https://github.com/OpenTreeOfLife/treemachine/blob/master/src/main/java/opentree/PhylografterConnector.java#L185-229 )

has not changed recently.

We were able to determine that the service itself is working through using curl:

curl -X POST

http://ec2-54-203-194-13.us-west-2.compute.amazonaws.com/taxomachine/ext/TNRS/graphdb/getContextForNames-H"content-type:application/json" -d '{"names":["Barnardius

barnardi","Barnardius zonarius","Platycercus adscitus","Platycercus elegans","Psephotus dissimilis","Psephotus varius","Purpureicephalus spurius","Northiella haematogaster","Psephotus haematonotus","Cyanoramphus auriceps","Cyanoramphus novaezelandiae","Eunymphicus uvaeensis","Prosopeia tabuensis","Lathamus discolor","Pezoporus flaviventris","Pezoporus wallicus","Pezoporus occidentalis","Neophema elegans","Neopsephotus bourkii","Agapornis roseicollis","Loriculus galgulus","Bolbopsittacus lunulatus","Chalcopsitta duivenbodei","Melopsittacus un dulatus& quot;,"Cyclopsitta diophthalma","Psittaculirostris

edwardsii","Psittacella

brehmii","Psittacella picta","Aprosmictus erythropterus","Polytelis alexandrae","Alisterus amboinensis","Polytelis anthopeplus","Micropsitta finschii","Psittacula columboides","Tanygn

athus lucionensis","Geoffroyus heteroclitus","Eclectus roratus","Prioniturus luconensis","Poicephalus robustus","Psittacus erithacus","Coracopsis vasa","Myiopsitta monachus","Psittrichas fulgidus","Calyptorhynchus banksii","Calyptorhynchus funereus","Eolophus roseicapillus","Nestor notabilis","Strigops habroptilus"]}'

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69> .

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38741617

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38753203

.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38757601 .

jimallman commented 10 years ago

I've found two discussions online that might provide a clue, but I don't really know the tools discussed...

http://stackoverflow.com/questions/17023766/using-jersey-to-post-to-service-a-message-body-writer-was-not-found

https://www.campaignmonitor.com/forums/post/27092/

josephwb commented 10 years ago

FYI, I reset to 1e907741e353ec9b3b11cca49dfdc866368ec6ef, but the error was present then. Thing is, this is only ever encountered if the TNRS is required.

josephwb commented 10 years ago

Ooh, but it was not present in 91f4e8ca337b4271b40a8699acdb1d97a15ec216. Maybe "Add optional security filter" 893f444e13e1f38101b5177f7af6f8304299f1b5 broke it?

josephwb commented 10 years ago

Yup. 893f444e13e1f38101b5177f7af6f8304299f1b5 is where it enters in. The only thing I see immediately is a change in the neo4j version.

jar398 commented 10 years ago

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown notifications@github.comwrote:

Yup. 893f444https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5is where it enters in. The only thing I see immediately is a change in the neo4j version.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977 .

jar398 commented 10 years ago

I am unable to reproduce the problem.

Here is what I did:

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees rees@mumble.net wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown <notifications@github.com

wrote:

Yup. 893f444https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5is where it enters in. The only thing I see immediately is a change in the neo4j version.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977 .

josephwb commented 10 years ago

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees notifications@github.com wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees rees@mumble.net wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444< https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5>is where it enters in. The only thing I see immediately is a change in the neo4j version.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977>

.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259 .

blackrim commented 10 years ago

I am trying this as well now. Sorry to get on this late

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees notifications@github.com wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees rees@mumble.net wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5 is where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015 .

jar398 commented 10 years ago

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees notifications@github.com wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees rees@mumble.net wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5 is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015 .

josephwb commented 10 years ago

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees notifications@github.com wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees notifications@github.com wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees rees@mumble.net wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015>

.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583 .

blackrim commented 10 years ago

Seems the solution may be here https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees notifications@github.com wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees notifications@github.com wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees rees@mumble.net wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015>

.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583 .

Reply to this email directly or view it on GitHub: https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

chinchliff commented 10 years ago

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith notifications@github.comwrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees notifications@github.com wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees notifications@github.com wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees <rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38824752 .

blackrim commented 10 years ago

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith notifications@github.comwrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees notifications@github.com wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees notifications@github.com wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees <rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38824752 .

Reply to this email directly or view it on GitHub: https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38828230

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

jar398 commented 10 years ago

Still can't reproduce the problem. Here's my latest attempt. This is with fresh clone, freshly load maven repo. I'm using 2821 instead of 2823 but hoping that doesn't matter for reproducing the bug.

bash-3.2$ java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind ../../neo4j-treemachine/data/graph.db ../../2821.nexson 6570 test things will happen here 13:09:54.666 [main] WARN o.neo4j.kernel.EmbeddedGraphDatabase - You are using an unsupported version of the Java runtime. Please use Oracle(R) Java(TM) Runtime Environment 7. not entering into the database, just testing file ../../2821.nexson pgloadind OTUs number 236 pgloadind Processing tree @id "6568" pgloadind tree info number nodes 471 pgloadind tree info number edges 470 pgloadind Ingested tree number of external nodes 236 pgloadind property added ot:studyPublicationReference "Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE (2014) Another look at the root of the angiosperms reveals a familiar tale. Systematic Biology" pgloadind property added ot:studyPublication " http://dx.doi.org/10.1093/sysbio/syt108" pgloadind property added ot:curatorName "bryan drew" pgloadind property added ot:studyId "2821" pgloadind property added ot:studyYear "2014" pgloadind property added ot:focalClade "4007209" pgloadind property added ot:focalCladeOTTTaxonName "Magnoliophyta" pgloadind property added ot:branchLengthMode "ot:substitutionCount" pgloadind property added ot:curatedType "ml best tree" loading a specific tree: 6570 skipping tree: 6568

No new trees to add to graph.

bash-3.2$

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith notifications@github.comwrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees notifications@github.com wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38824752

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38828230

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

—

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131 .

josephwb commented 10 years ago

You should use 2823: it was chosen because it has non-mapping OTUs (thereby requiring TNRS). The:

No new trees to add to graph.

means that the tree is already in the graph? You must have run this command twice. Make sure to include "test" as the last argument, so the tree is not added to the DB.

JWB.

On 27 March 2014 13:12, Jonathan A Rees notifications@github.com wrote:

Still can't reproduce the problem. Here's my latest attempt. This is with fresh clone, freshly load maven repo. I'm using 2821 instead of 2823 but hoping that doesn't matter for reproducing the bug.

bash-3.2$ java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind ../../neo4j-treemachine/data/graph.db ../../2821.nexson 6570 test things will happen here 13:09:54.666 [main] WARN o.neo4j.kernel.EmbeddedGraphDatabase - You are using an unsupported version of the Java runtime. Please use Oracle(R) Java(TM) Runtime Environment 7. not entering into the database, just testing file ../../2821.nexson pgloadind OTUs number 236 pgloadind Processing tree @id "6568" pgloadind tree info number nodes 471 pgloadind tree info number edges 470 pgloadind Ingested tree number of external nodes 236 pgloadind property added ot:studyPublicationReference "Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE (2014) Another look at the root of the angiosperms reveals a familiar tale. Systematic Biology" pgloadind property added ot:studyPublication " http://dx.doi.org/10.1093/sysbio/syt108" pgloadind property added ot:curatorName "bryan drew" pgloadind property added ot:studyId "2821" pgloadind property added ot:studyYear "2014" pgloadind property added ot:focalClade "4007209" pgloadind property added ot:focalCladeOTTTaxonName "Magnoliophyta" pgloadind property added ot:branchLengthMode "ot:substitutionCount" pgloadind property added ot:curatedType "ml best tree" loading a specific tree: 6570 skipping tree: 6568

No new trees to add to graph.

bash-3.2$

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith notifications@github.comwrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees notifications@github.com

wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

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Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131>

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blackrim commented 10 years ago

Right, we need to use a tree for testing that has some unmapped taxa (those will call the TNRS)

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

jar398 commented 10 years ago

OK. Hmm, 2823 isn't in phylesystem and I don't know the magic for getting it from phylografter. Can you either mail it to me or send me a URL? Oh, and do I need the full synthetic tree database? I was using the asterales database. Hmm, this is getting difficult. Maybe I will have to do it on norbert, my Mac only has 4G RAM. Thanks.

On Thu, Mar 27, 2014 at 1:15 PM, Joseph W. Brown notifications@github.comwrote:

You should use 2823: it was chosen because it has non-mapping OTUs (thereby requiring TNRS). The:

No new trees to add to graph.

means that the tree is already in the graph? You must have run this command twice. Make sure to include "test" as the last argument, so the tree is not added to the DB.

JWB.

On 27 March 2014 13:12, Jonathan A Rees notifications@github.com wrote:

Still can't reproduce the problem. Here's my latest attempt. This is with fresh clone, freshly load maven repo. I'm using 2821 instead of 2823 but hoping that doesn't matter for reproducing the bug.

bash-3.2$ java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind ../../neo4j-treemachine/data/graph.db ../../2821.nexson 6570 test things will happen here 13:09:54.666 [main] WARN o.neo4j.kernel.EmbeddedGraphDatabase - You are using an unsupported version of the Java runtime. Please use Oracle(R) Java(TM) Runtime Environment 7. not entering into the database, just testing file ../../2821.nexson pgloadind OTUs number 236 pgloadind Processing tree @id "6568" pgloadind tree info number nodes 471 pgloadind tree info number edges 470 pgloadind Ingested tree number of external nodes 236 pgloadind property added ot:studyPublicationReference "Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE (2014) Another look at the root of the angiosperms reveals a familiar tale. Systematic Biology" pgloadind property added ot:studyPublication " http://dx.doi.org/10.1093/sysbio/syt108" pgloadind property added ot:curatorName "bryan drew" pgloadind property added ot:studyId "2821" pgloadind property added ot:studyYear "2014" pgloadind property added ot:focalClade "4007209" pgloadind property added ot:focalCladeOTTTaxonName "Magnoliophyta" pgloadind property added ot:branchLengthMode "ot:substitutionCount" pgloadind property added ot:curatedType "ml best tree" loading a specific tree: 6570 skipping tree: 6568

No new trees to add to graph.

bash-3.2$

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com>wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com>

wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

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.

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.

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josephwb commented 10 years ago

I can't check phylografter for 2821 because it is apparently down ( http://www.reelab.net/phylografter):

Not Found

The requested URL /phylografter was not found on this server.

Apache/2.2.22 (Ubuntu) Server at www.reelab.net Port 80

JWB.

On 27 March 2014 13:21, Stephen Smith notifications@github.com wrote:

Right, we need to use a tree for testing that has some unmapped taxa (those will call the TNRS)

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38833815 .

blackrim commented 10 years ago

you can get it from the bitbucket repo here https://bitbucket.org/blackrim/avatol_nexsons On Thu, Mar 27, 2014 at 10:22:42AM -0700, Jonathan A Rees wrote:

OK. Hmm, 2823 isn't in phylesystem and I don't know the magic for getting it from phylografter. Can you either mail it to me or send me a URL? Oh, and do I need the full synthetic tree database? I was using the asterales database. Hmm, this is getting difficult. Maybe I will have to do it on norbert, my Mac only has 4G RAM. Thanks.

On Thu, Mar 27, 2014 at 1:15 PM, Joseph W. Brown notifications@github.comwrote:

You should use 2823: it was chosen because it has non-mapping OTUs (thereby requiring TNRS). The:

No new trees to add to graph.

means that the tree is already in the graph? You must have run this command twice. Make sure to include "test" as the last argument, so the tree is not added to the DB.

JWB.

On 27 March 2014 13:12, Jonathan A Rees notifications@github.com wrote:

Still can't reproduce the problem. Here's my latest attempt. This is with fresh clone, freshly load maven repo. I'm using 2821 instead of 2823 but hoping that doesn't matter for reproducing the bug.

bash-3.2$ java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind ../../neo4j-treemachine/data/graph.db ../../2821.nexson 6570 test things will happen here 13:09:54.666 [main] WARN o.neo4j.kernel.EmbeddedGraphDatabase - You are using an unsupported version of the Java runtime. Please use Oracle(R) Java(TM) Runtime Environment 7. not entering into the database, just testing file ../../2821.nexson pgloadind OTUs number 236 pgloadind Processing tree @id "6568" pgloadind tree info number nodes 471 pgloadind tree info number edges 470 pgloadind Ingested tree number of external nodes 236 pgloadind property added ot:studyPublicationReference "Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE (2014) Another look at the root of the angiosperms reveals a familiar tale. Systematic Biology" pgloadind property added ot:studyPublication " http://dx.doi.org/10.1093/sysbio/syt108" pgloadind property added ot:curatorName "bryan drew" pgloadind property added ot:studyId "2821" pgloadind property added ot:studyYear "2014" pgloadind property added ot:focalClade "4007209" pgloadind property added ot:focalCladeOTTTaxonName "Magnoliophyta" pgloadind property added ot:branchLengthMode "ot:substitutionCount" pgloadind property added ot:curatedType "ml best tree" loading a specific tree: 6570 skipping tree: 6568

No new trees to add to graph.

bash-3.2$

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com>wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com>

wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

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https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

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.

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Reply to this email directly or view it on GitHub<

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Reply to this email directly or view it on GitHub<

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josephwb commented 10 years ago

I will update phylesystem. JWB.

On 27 March 2014 13:23, Joseph Brown phylo.jwb@gmail.com wrote:

I can't check phylografter for 2821 because it is apparently down ( http://www.reelab.net/phylografter):

Not Found

The requested URL /phylografter was not found on this server.

Apache/2.2.22 (Ubuntu) Server at www.reelab.net Port 80

JWB.

On 27 March 2014 13:21, Stephen Smith notifications@github.com wrote:

Right, we need to use a tree for testing that has some unmapped taxa (those will call the TNRS)

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38833815 .

josephwb commented 10 years ago

Doh. Can't do it with phylografter apparently down:

josephwb@WOPR:~/Work/OToL/phylesystem$ ./bin/refresh_nexsons_from_phylografter.py Traceback (most recent call last): File "./bin/refresh_nexsons_from_phylografter.py", line 243, in to_download, download_db = get_list_of_dirty_nexsons(dd) File "./bin/refresh_nexsons_from_phylografter.py", line 131, in get_list_of_dirty_nexsons resp.raise_for_status() File "/usr/lib/python2.7/dist-packages/requests/models.py", line 683, in raise_for_status raise HTTPError(http_error_msg, response=self) requests.exceptions.HTTPError: 404 Client Error: Not Found

File is attached. JWB.

On 27 March 2014 13:23, Joseph Brown phylo.jwb@gmail.com wrote:

I will update phylesystem. JWB.

On 27 March 2014 13:23, Joseph Brown phylo.jwb@gmail.com wrote:

I can't check phylografter for 2821 because it is apparently down ( http://www.reelab.net/phylografter):

Not Found

The requested URL /phylografter was not found on this server.

Apache/2.2.22 (Ubuntu) Server at www.reelab.net Port 80

JWB.

On 27 March 2014 13:21, Stephen Smith notifications@github.com wrote:

Right, we need to use a tree for testing that has some unmapped taxa (those will call the TNRS)

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38833815 .

josephwb commented 10 years ago

Or, you can use the avatol_nexsonshttps://bitbucket.org/blackrim/avatol_nexsonsrepo which should be completely up to date (refresh late yesterday).

JWB.

On 27 March 2014 13:27, Joseph Brown phylo.jwb@gmail.com wrote:

Doh. Can't do it with phylografter apparently down:

josephwb@WOPR:~/Work/OToL/phylesystem$ ./bin/refresh_nexsons_from_phylografter.py Traceback (most recent call last): File "./bin/refresh_nexsons_from_phylografter.py", line 243, in to_download, download_db = get_list_of_dirty_nexsons(dd) File "./bin/refresh_nexsons_from_phylografter.py", line 131, in get_list_of_dirty_nexsons resp.raise_for_status() File "/usr/lib/python2.7/dist-packages/requests/models.py", line 683, in raise_for_status raise HTTPError(http_error_msg, response=self) requests.exceptions.HTTPError: 404 Client Error: Not Found

File is attached. JWB.

On 27 March 2014 13:23, Joseph Brown phylo.jwb@gmail.com wrote:

I will update phylesystem. JWB.

On 27 March 2014 13:23, Joseph Brown phylo.jwb@gmail.com wrote:

I can't check phylografter for 2821 because it is apparently down ( http://www.reelab.net/phylografter):

Not Found

The requested URL /phylografter was not found on this server.

Apache/2.2.22 (Ubuntu) Server at www.reelab.net Port 80

JWB.

On 27 March 2014 13:21, Stephen Smith notifications@github.com wrote:

Right, we need to use a tree for testing that has some unmapped taxa (those will call the TNRS)

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38833815 .

chinchliff commented 10 years ago

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith notifications@github.comwrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees notifications@github.com wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38824752

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38828230

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131 .

chinchliff commented 10 years ago

What are the treemachine commands that go before the "pgloadind test etc." command to build the taxonomy db to test with?

On Thu, Mar 27, 2014 at 10:41 AM, Joseph W. Brown notifications@github.comwrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees notifications@github.com wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees notifications@github.com wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees rees@mumble.net wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849 .

josephwb commented 10 years ago

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith <notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees notifications@github.com wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38824752

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38828230

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131

.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38834869 .

chinchliff commented 10 years ago

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38824752

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38828230

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38834869

.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835222 .

josephwb commented 10 years ago

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38824752

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38828230

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38834869

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835222

.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835352 .

jar398 commented 10 years ago

Yes... I suppose. I ran it with 2823, but with asterales... is the following uninformative? sure would be nice to be able to get the error with simpler setup. bash-3.2$ java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind ../../neo4j-treemachine/data/graph.db 2823.nexson 6570 test things will happen here 13:28:58.385 [main] WARN o.neo4j.kernel.EmbeddedGraphDatabase - You are using an unsupported version of the Java runtime. Please use Oracle(R) Java(TM) Runtime Environment 7. not entering into the database, just testing file 2823.nexson pgloadind OTUs number 387 pgloadind Processing tree @id "6570" pgloadind tree info number nodes 770 pgloadind tree info number edges 769 pgloadind tree info ingroup "node1142035" pgloadind Setting ingroup root node. pgloadind Ingested tree number of external nodes 385 pgloadind property added ot:studyPublicationReference "test" pgloadind property added ot:curatorName "Chris Owen" pgloadind property added ot:studyId "2823" pgloadind property added ot:studyYear "2014" pgloadind property added ot:focalClade "2534141" pgloadind property added ot:focalCladeOTTTaxonName "Astacidea" pgloadind property added ot:branchLengthMode "ot:substitutionCount" pgloadind property added ot:inGroupClade "node1142035" pgloadind property added ot:curatedType "ML" loading a specific tree: 6570 tree 0: 385 pgloadind conducting TNRS on trees pgloadind name fixing on tree tree id "6570" pgloadind OTT ID missing name "Fallicambarus sp n 2 JWB 2013" nexsonid "node1142214" pgloadind OTT ID missing name "Fallicambarus sp n 1 JWB 2013" nexsonid "node1142216" pgloadind OTT ID missing name "Orconectes sp CCAT 2002" nexsonid "node1142278" pgloadind OTT ID missing name "Orconectes cf virilis sp 2 AP 2009" nexsonid "node1142317" pgloadind OTT ID missing name "Orconectes cf virilis sp 1 AP 2009" nexsonid "node1142322" pgloadind OTT ID missing name "Procambarus sp 3 JEB 2007" nexsonid "node1142409" pgloadind OTT ID missing name "Procambarus sp 1 JEB 2007" nexsonid "node1142410" pgloadind OTT ID missing name "Procambarus sp 2 JEB 2007" nexsonid "node1142412" pgloadind OTT ID missing name "Procambarus sp Aguazarca stream PJGY" nexsonid "node1142445" pgloadind OTT ID missing name "Procambarus sp Chiapas" nexsonid "node1142449" pgloadind OTT ID missing name "Cambarellus sp Pop51" nexsonid "node1142462" pgloadind OTT ID missing name "Cambarellus sp Pop54" nexsonid "node1142463" pgloadind OTT ID missing name "Cambarellus sp Pop57 1" nexsonid "node1142466" pgloadind OTT ID missing name "Cambarellus sp Pop35" nexsonid "node1142468" pgloadind OTT ID missing name "Austropotamobius sp PT 2004" nexsonid "node1142517" pgloadind OTT ID missing name "Geocharax sp 1 MBS 2007" nexsonid "node1142606" pgloadind OTT ID missing name "Geocharax sp 2 MBS 2007" nexsonid "node1142608" pgloadind OTT ID missing name "Gramastacus sp 2 DM 2003" nexsonid "node1142613" pgloadind OTT ID missing name "Gramastacus sp MBS 2007" nexsonid "node1142614" pgloadind OTT ID missing name "Cherax sp New Guinea DM 2003" nexsonid "node1142658" pgloadind OTT ID missing name "Euastacus sp AMB 18 1 FF32SP1" nexsonid "node1142674" pgloadind OTT ID missing name "Euastacus sp KC2705" nexsonid "node1142678" pgloadind OTT ID missing name "Euastacus sp KC2635" nexsonid "node1142679" pgloadind OTT ID missing name "Euastacus sp AMB 38 1" nexsonid "node1142748" pgloadind OTT ID missing name "Euastacus sp AMB IT 5" nexsonid "node1142749" pgloadind OTT ID missing name "Euastacus sp AMB 17 2 BEC2SP1" nexsonid "node1142750" pgloadind OTT ID missing name "Virilastacus sp KAC 2012" nexsonid "node1142782" pgloadind OTT ID missing name "Samastacus nov sp" nexsonid "node1142785" PROBLEM CONNECTING TO SERVER pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus parrishi" nexsonid "node1142055" pgloadind dubious OTT ID 943282 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus hiwasseensis" nexsonid "node1142056" pgloadind dubious OTT ID 81159 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus georgiae" nexsonid "node1142057" pgloadind dubious OTT ID 655341 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus coosae" nexsonid "node1142060" pgloadind dubious OTT ID 1048054 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus speciosus" nexsonid "node1142061" pgloadind dubious OTT ID 133362 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus coosawattae" nexsonid "node1142062" pgloadind dubious OTT ID 1048052 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus fasciatus" nexsonid "node1142065" pgloadind dubious OTT ID 655335 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus scotti" nexsonid "node1142066" pgloadind dubious OTT ID 133358 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus girardianus" nexsonid "node1142067" pgloadind dubious OTT ID 655339 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus sciotensis" nexsonid "node1142070" pgloadind dubious OTT ID 133356 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus longulus" nexsonid "node1142071" pgloadind dubious OTT ID 81149 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus hobbsorum" nexsonid "node1142073" pgloadind dubious OTT ID 81161 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus robustus" nexsonid "node1142074" pgloadind dubious OTT ID 707817 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus cumberlandensis" nexsonid "node1142077" pgloadind dubious OTT ID 1048058 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus manningi" nexsonid "node1142078" pgloadind dubious OTT ID 81151 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus chasmodactylus" nexsonid "node1142079" pgloadind dubious OTT ID 1048056 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus nerterius" nexsonid "node1142085" pgloadind dubious OTT ID 482752 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus longirostris" nexsonid "node1142086" pgloadind dubious OTT ID 81155 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus howardi" nexsonid "node1142087" pgloadind dubious OTT ID 482755 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus acuminatus" nexsonid "node1142089" pgloadind dubious OTT ID 471534 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus reburrus" nexsonid "node1142090" pgloadind dubious OTT ID 707802 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus bartonii bartonii" nexsonid "node1142093" pgloadind dubious OTT ID 1048047 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus carinirostris" nexsonid "node1142094" pgloadind dubious OTT ID 1048043 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus davidi" nexsonid "node1142095" pgloadind dubious OTT ID 655329 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus monongalensis" nexsonid "node1142096" pgloadind dubious OTT ID 638168 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus maculatus" nexsonid "node1142097" pgloadind dubious OTT ID 980735 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus crinipes" nexsonid "node1142105" pgloadind dubious OTT ID 1048060 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus distans" nexsonid "node1142106" pgloadind dubious OTT ID 655333 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus bouchardi" nexsonid "node1142107" pgloadind dubious OTT ID 1048045 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus obeyensis" nexsonid "node1142109" pgloadind dubious OTT ID 707813 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus tuckasegee" nexsonid "node1142110" pgloadind dubious OTT ID 133354 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus unestami" nexsonid "node1142111" pgloadind dubious OTT ID 144843 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus pristinus" nexsonid "node1142112" pgloadind dubious OTT ID 707806 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus truncatus" nexsonid "node1142113" pgloadind dubious OTT ID 133352 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus cryptodytes" nexsonid "node1142114" pgloadind dubious OTT ID 389360 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus reflexus" nexsonid "node1142126" pgloadind dubious OTT ID 707800 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus strigosus" nexsonid "node1142127" pgloadind dubious OTT ID 133350 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus harti" nexsonid "node1142128" pgloadind dubious OTT ID 655343 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus gentryi" nexsonid "node1142129" pgloadind dubious OTT ID 194210 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus cracens" nexsonid "node1142131" pgloadind dubious OTT ID 1048050 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus halli" nexsonid "node1142132" pgloadind dubious OTT ID 655345 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus rusticiformis" nexsonid "node1142136" pgloadind dubious OTT ID 707815 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus hubbsi" nexsonid "node1142137" pgloadind dubious OTT ID 482757 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus tenebrosus" nexsonid "node1142138" pgloadind dubious OTT ID 405645 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus hubrichti" nexsonid "node1142139" pgloadind dubious OTT ID 980748 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus batchi" nexsonid "node1142141" pgloadind dubious OTT ID 965594 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus graysoni" nexsonid "node1142142" pgloadind dubious OTT ID 665176 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus friaufi" nexsonid "node1142145" pgloadind dubious OTT ID 1013806 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus brachydactylus" nexsonid "node1142146" pgloadind dubious OTT ID 299060 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus williami" nexsonid "node1142147" pgloadind dubious OTT ID 133366 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes australis" nexsonid "node1142151" pgloadind dubious OTT ID 454767 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes barri" nexsonid "node1142152" pgloadind dubious OTT ID 768852 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes incomptus" nexsonid "node1142153" pgloadind dubious OTT ID 194218 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes packardi" nexsonid "node1142154" pgloadind dubious OTT ID 194212 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes pellucidus" nexsonid "node1142156" pgloadind dubious OTT ID 90903 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes inermis" nexsonid "node1142157" pgloadind dubious OTT ID 90905 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus latimanus" nexsonid "node1142161" pgloadind dubious OTT ID 81153 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus obstipus" nexsonid "node1142162" pgloadind dubious OTT ID 707811 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus englishi" nexsonid "node1142164" pgloadind dubious OTT ID 655337 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus pyronotus" nexsonid "node1142165" pgloadind dubious OTT ID 707804 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus striatus" nexsonid "node1142166" pgloadind dubious OTT ID 830277 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus pecki" nexsonid "node1142171" pgloadind dubious OTT ID 707808 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus hamulatus" nexsonid "node1142172" pgloadind dubious OTT ID 1013834 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus laconensis" nexsonid "node1142174" pgloadind dubious OTT ID 1083969 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus jonesi" nexsonid "node1142175" pgloadind dubious OTT ID 1083975 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus pecki" nexsonid "node1142176" pgloadind dubious OTT ID 515013 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus speleocoopi" nexsonid "node1142177" pgloadind dubious OTT ID 1083972 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus dubius" nexsonid "node1142179" pgloadind dubious OTT ID 655331 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus asperimanus" nexsonid "node1142180" pgloadind dubious OTT ID 1048048 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus acanthura" nexsonid "node1142184" pgloadind dubious OTT ID 143853 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus deweesae" nexsonid "node1142185" pgloadind dubious OTT ID 655327 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus ludovicianus" nexsonid "node1142187" pgloadind dubious OTT ID 876592 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus diogenes" nexsonid "node1142188" pgloadind dubious OTT ID 665183 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus miltus" nexsonid "node1142189" pgloadind dubious OTT ID 234817 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus aculabrum" nexsonid "node1142193" pgloadind dubious OTT ID 471532 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus setosus" nexsonid "node1142194" pgloadind dubious OTT ID 133360 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus tartarus" nexsonid "node1142195" pgloadind dubious OTT ID 791225 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarus causeyi" nexsonid "node1142196" pgloadind dubious OTT ID 299056 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes etnieri" nexsonid "node1142205" pgloadind dubious OTT ID 142688 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes jonesi" nexsonid "node1142206" pgloadind dubious OTT ID 142690 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes chickasawae" nexsonid "node1142207" pgloadind dubious OTT ID 716936 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes holti" nexsonid "node1142208" pgloadind dubious OTT ID 559787 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes mississippiensis" nexsonid "node1142209" pgloadind dubious OTT ID 142685 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus caesius" nexsonid "node1142213" pgloadind dubious OTT ID 650614 pgloadind Null OTT ID in tree pgloadind null name "Fallicambarus sp n 2 JWB 2013" nexsonid "node1142214" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus gilpini" nexsonid "node1142215" pgloadind dubious OTT ID 2974540 pgloadind Null OTT ID in tree pgloadind null name "Fallicambarus sp n 1 JWB 2013" nexsonid "node1142216" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus danielae" nexsonid "node1142222" pgloadind dubious OTT ID 2974543 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus oryktes" nexsonid "node1142223" pgloadind dubious OTT ID 2974551 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus gordoni" nexsonid "node1142224" pgloadind dubious OTT ID 2974537 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus byersi" nexsonid "node1142225" pgloadind dubious OTT ID 715857 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus burrisi" nexsonid "node1142226" pgloadind dubious OTT ID 2974545 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus fodiens" nexsonid "node1142227" pgloadind dubious OTT ID 550679 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus hortoni" nexsonid "node1142228" pgloadind dubious OTT ID 2974541 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes compressus" nexsonid "node1142233" pgloadind dubious OTT ID 142687 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes cooperi" nexsonid "node1142234" pgloadind dubious OTT ID 142689 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes pagei" nexsonid "node1142235" pgloadind dubious OTT ID 90904 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes validus" nexsonid "node1142237" pgloadind dubious OTT ID 836137 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes rhoadesi" nexsonid "node1142238" pgloadind dubious OTT ID 559786 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes alabamensis" nexsonid "node1142239" pgloadind dubious OTT ID 716935 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes carolinensis" nexsonid "node1142252" pgloadind dubious OTT ID 559790 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes virginiensis" nexsonid "node1142253" pgloadind dubious OTT ID 77970 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes harrisoni" nexsonid "node1142254" pgloadind dubious OTT ID 665180 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes limosus" nexsonid "node1142256" pgloadind dubious OTT ID 705360 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes obscurus" nexsonid "node1142257" pgloadind dubious OTT ID 827730 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes rusticus" nexsonid "node1142258" pgloadind dubious OTT ID 169778 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes jeffersoni" nexsonid "node1142264" pgloadind dubious OTT ID 827726 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes sloanii" nexsonid "node1142265" pgloadind dubious OTT ID 665179 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes juvenilis" nexsonid "node1142266" pgloadind dubious OTT ID 827725 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes cristavarius" nexsonid "node1142267" pgloadind dubious OTT ID 559791 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes durelli" nexsonid "node1142268" pgloadind dubious OTT ID 303587 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes eupunctus" nexsonid "node1142269" pgloadind dubious OTT ID 935322 pgloadind Null OTT ID in tree pgloadind null name "Orconectes sp CCAT 2002" nexsonid "node1142278" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes stannardi" nexsonid "node1142279" pgloadind dubious OTT ID 77972 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes rafinesquei" nexsonid "node1142280" pgloadind dubious OTT ID 827737 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes putnami" nexsonid "node1142281" pgloadind dubious OTT ID 516038 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes kentuckiensis" nexsonid "node1142282" pgloadind dubious OTT ID 827732 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes bisectus" nexsonid "node1142284" pgloadind dubious OTT ID 303567 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes tricuspis" nexsonid "node1142285" pgloadind dubious OTT ID 77971 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes propinquus" nexsonid "node1142286" pgloadind dubious OTT ID 827738 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes ronaldi" nexsonid "node1142288" pgloadind dubious OTT ID 566546 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes indianensis" nexsonid "node1142289" pgloadind dubious OTT ID 665188 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes sanbornii" nexsonid "node1142290" pgloadind dubious OTT ID 77974 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes erichsonianus" nexsonid "node1142295" pgloadind dubious OTT ID 827728 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes wrighti" nexsonid "node1142296" pgloadind dubious OTT ID 665189 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes spinosus" nexsonid "node1142297" pgloadind dubious OTT ID 566548 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes barrenensis" nexsonid "node1142299" pgloadind dubious OTT ID 559789 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes mirus" nexsonid "node1142300" pgloadind dubious OTT ID 516034 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes placidus" nexsonid "node1142302" pgloadind dubious OTT ID 827729 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes shoupi" nexsonid "node1142303" pgloadind dubious OTT ID 77973 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes burri" nexsonid "node1142305" pgloadind dubious OTT ID 303586 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes forceps" nexsonid "node1142306" pgloadind dubious OTT ID 559792 pgloadind Null OTT ID in tree pgloadind null name "Orconectes cf virilis sp 2 AP 2009" nexsonid "node1142317" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes deanae" nexsonid "node1142318" pgloadind dubious OTT ID 90902 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes nais" nexsonid "node1142319" pgloadind dubious OTT ID 142684 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes virilis species complex clade 4" nexsonid "node1142320" pgloadind dubious OTT ID 1073454 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes virilis species complex clade 3" nexsonid "node1142321" pgloadind dubious OTT ID 1073453 pgloadind Null OTT ID in tree pgloadind null name "Orconectes cf virilis sp 1 AP 2009" nexsonid "node1142322" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes virilis species complex clade 1" nexsonid "node1142324" pgloadind dubious OTT ID 1073455 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes virilis" nexsonid "node1142325" pgloadind dubious OTT ID 876593 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes virilis species complex clade 2" nexsonid "node1142326" pgloadind dubious OTT ID 1073456 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes neglectus neglectus" nexsonid "node1142329" pgloadind dubious OTT ID 516033 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes neglectus chaenodactylus" nexsonid "node1142330" pgloadind dubious OTT ID 516032 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes medius" nexsonid "node1142332" pgloadind dubious OTT ID 1042373 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes luteus" nexsonid "node1142333" pgloadind dubious OTT ID 1057924 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes longidigitus" nexsonid "node1142334" pgloadind dubious OTT ID 1057925 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes ozarkae" nexsonid "node1142338" pgloadind dubious OTT ID 692815 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes punctimanus" nexsonid "node1142339" pgloadind dubious OTT ID 1057913 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes marchandi" nexsonid "node1142341" pgloadind dubious OTT ID 827731 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes neglectus" nexsonid "node1142342" pgloadind dubious OTT ID 1057918 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes peruncus" nexsonid "node1142345" pgloadind dubious OTT ID 828547 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes quadruncus" nexsonid "node1142346" pgloadind dubious OTT ID 516035 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes hylas" nexsonid "node1142347" pgloadind dubious OTT ID 559793 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes meeki meeki" nexsonid "node1142353" pgloadind dubious OTT ID 716939 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes meeki brevis" nexsonid "node1142354" pgloadind dubious OTT ID 716938 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes maletae" nexsonid "node1142355" pgloadind dubious OTT ID 90907 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes difficilis" nexsonid "node1142356" pgloadind dubious OTT ID 90909 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes macrus" nexsonid "node1142357" pgloadind dubious OTT ID 1057917 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes hartfieldi" nexsonid "node1142361" pgloadind dubious OTT ID 90908 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes perfectus" nexsonid "node1142362" pgloadind dubious OTT ID 90906 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes hobbsi" nexsonid "node1142363" pgloadind dubious OTT ID 90911 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes palmeri longimanus" nexsonid "node1142364" pgloadind dubious OTT ID 716940 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes saxatilis" nexsonid "node1142369" pgloadind dubious OTT ID 566547 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes acares" nexsonid "node1142370" pgloadind dubious OTT ID 559788 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes menae" nexsonid "node1142371" pgloadind dubious OTT ID 97039 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes immunis" nexsonid "node1142372" pgloadind dubious OTT ID 142691 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Orconectes williamsi" nexsonid "node1142373" pgloadind dubious OTT ID 566549 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Barbicambarus cornutus" nexsonid "node1142375" pgloadind dubious OTT ID 965595 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Barbicambarus simmonsi" nexsonid "node1142376" pgloadind dubious OTT ID 143855 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus dissitus" nexsonid "node1142386" pgloadind dubious OTT ID 2974536 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus petilicarpus" nexsonid "node1142387" pgloadind dubious OTT ID 2974552 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus harpi" nexsonid "node1142389" pgloadind dubious OTT ID 2974548 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus jeanae" nexsonid "node1142390" pgloadind dubious OTT ID 2974542 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus devastator" nexsonid "node1142391" pgloadind dubious OTT ID 2974538 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus strawni" nexsonid "node1142393" pgloadind dubious OTT ID 2974544 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus tenuis" nexsonid "node1142394" pgloadind dubious OTT ID 54565 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus houstonensis" nexsonid "node1142398" pgloadind dubious OTT ID 2974546 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus macneesei" nexsonid "node1142399" pgloadind dubious OTT ID 2974547 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus kountzeae" nexsonid "node1142400" pgloadind dubious OTT ID 2974549 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Fallicambarus wallsi" nexsonid "node1142401" pgloadind dubious OTT ID 5089691 pgloadind Null OTT ID in tree pgloadind null name "Procambarus sp 3 JEB 2007" nexsonid "node1142409" pgloadind Null OTT ID in tree pgloadind null name "Procambarus sp 1 JEB 2007" nexsonid "node1142410" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus liberorum" nexsonid "node1142411" pgloadind dubious OTT ID 54568 pgloadind Null OTT ID in tree pgloadind null name "Procambarus sp 2 JEB 2007" nexsonid "node1142412" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus curdi" nexsonid "node1142413" pgloadind dubious OTT ID 773369 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus reimeri" nexsonid "node1142414" pgloadind dubious OTT ID 773390 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus nigrocinctus" nexsonid "node1142415" pgloadind dubious OTT ID 773393 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus simulans" nexsonid "node1142416" pgloadind dubious OTT ID 813498 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambaridae" nexsonid "node1142424" pgloadind dubious OTT ID 79860 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus fallax" nexsonid "node1142425" pgloadind dubious OTT ID 579001 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus alleni" nexsonid "node1142426" pgloadind dubious OTT ID 456496 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus paeninsulanus" nexsonid "node1142427" pgloadind dubious OTT ID 305572 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus clarkii" nexsonid "node1142428" pgloadind dubious OTT ID 79864 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus leonensis" nexsonid "node1142433" pgloadind dubious OTT ID 79858 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus acutus" nexsonid "node1142434" pgloadind dubious OTT ID 77968 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus geminus" nexsonid "node1142435" pgloadind dubious OTT ID 550676 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus cf. zonangulus AP-2011" nexsonid "node1142436" pgloadind dubious OTT ID 405798 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus ouachitae" nexsonid "node1142437" pgloadind dubious OTT ID 54564 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus spiculifer" nexsonid "node1142441" pgloadind dubious OTT ID 729845 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus gibbus" nexsonid "node1142442" pgloadind dubious OTT ID 428463 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus versutus" nexsonid "node1142443" pgloadind dubious OTT ID 305584 pgloadind Null OTT ID in tree pgloadind null name "Procambarus sp Aguazarca stream PJGY" nexsonid "node1142445" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus toltecae" nexsonid "node1142446" pgloadind dubious OTT ID 523829 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus llamasi" nexsonid "node1142448" pgloadind dubious OTT ID 121652 pgloadind Null OTT ID in tree pgloadind null name "Procambarus sp Chiapas" nexsonid "node1142449" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus chapalanus" nexsonid "node1142460" pgloadind dubious OTT ID 1073407 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus prolixus" nexsonid "node1142461" pgloadind dubious OTT ID 518476 pgloadind Null OTT ID in tree pgloadind null name "Cambarellus sp Pop51" nexsonid "node1142462" pgloadind Null OTT ID in tree pgloadind null name "Cambarellus sp Pop54" nexsonid "node1142463" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus montezumae" nexsonid "node1142464" pgloadind dubious OTT ID 115048 pgloadind Null OTT ID in tree pgloadind null name "Cambarellus sp Pop57 1" nexsonid "node1142466" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus occidentalis" nexsonid "node1142467" pgloadind dubious OTT ID 650637 pgloadind Null OTT ID in tree pgloadind null name "Cambarellus sp Pop35" nexsonid "node1142468" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus zempoalensis" nexsonid "node1142469" pgloadind dubious OTT ID 927937 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus patzcuarensis" nexsonid "node1142470" pgloadind dubious OTT ID 842454 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus ninae" nexsonid "node1142476" pgloadind dubious OTT ID 842452 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus texanus" nexsonid "node1142477" pgloadind dubious OTT ID 842446 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus puer" nexsonid "node1142478" pgloadind dubious OTT ID 842450 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus blacki" nexsonid "node1142481" pgloadind dubious OTT ID 842443 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus lesliei" nexsonid "node1142482" pgloadind dubious OTT ID 842439 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus schmitti" nexsonid "node1142483" pgloadind dubious OTT ID 842448 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus shufeldtii" nexsonid "node1142484" pgloadind dubious OTT ID 876603 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambarellus diminutus" nexsonid "node1142485" pgloadind dubious OTT ID 842441 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus bouvieri" nexsonid "node1142487" pgloadind dubious OTT ID 79863 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus digueti" nexsonid "node1142488" pgloadind dubious OTT ID 523828 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus shermani" nexsonid "node1142491" pgloadind dubious OTT ID 2974423 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Troglocambarus maclanei" nexsonid "node1142492" pgloadind dubious OTT ID 2974576 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus barbatus" nexsonid "node1142493" pgloadind dubious OTT ID 2974390 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Faxonella blairi" nexsonid "node1142497" pgloadind dubious OTT ID 2974534 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Faxonella clypeata" nexsonid "node1142498" pgloadind dubious OTT ID 550672 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Bouchardina robisoni" nexsonid "node1142499" pgloadind dubious OTT ID 2974571 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Hobbseus yalobushensis" nexsonid "node1142502" pgloadind dubious OTT ID 2974350 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Hobbseus prominens" nexsonid "node1142503" pgloadind dubious OTT ID 2974352 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Hobbseus petilus" nexsonid "node1142504" pgloadind dubious OTT ID 2974351 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Procambarus lepidodactylus" nexsonid "node1142505" pgloadind dubious OTT ID 126749 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Austropotamobius italicus" nexsonid "node1142512" pgloadind dubious OTT ID 1087071 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Austropotamobius pallipes" nexsonid "node1142513" pgloadind dubious OTT ID 335542 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Austropotamobius italicus meridionalis" nexsonid "node1142514" pgloadind dubious OTT ID 671874 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Austropotamobius torrentium torrentium" nexsonid "node1142516" pgloadind dubious OTT ID 634761 pgloadind Null OTT ID in tree pgloadind null name "Austropotamobius sp PT 2004" nexsonid "node1142517" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Pontastacus leptodactylus" nexsonid "node1142519" pgloadind dubious OTT ID 601421 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Astacus astacus" nexsonid "node1142520" pgloadind dubious OTT ID 299971 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Pacifastacus connectens" nexsonid "node1142521" pgloadind dubious OTT ID 716389 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Pacifastacus gambelii" nexsonid "node1142522" pgloadind dubious OTT ID 2974330 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Pacifastacus leniusculus trowbridgii" nexsonid "node1142525" pgloadind dubious OTT ID 801454 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Pacifastacus leniusculus klamathensis" nexsonid "node1142526" pgloadind dubious OTT ID 405843 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Pacifastacus leniusculus leniusculus" nexsonid "node1142527" pgloadind dubious OTT ID 405844 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambaroides dauricus" nexsonid "node1142531" pgloadind dubious OTT ID 77218 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambaroides schrenckii" nexsonid "node1142532" pgloadind dubious OTT ID 77219 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambaroides similis" nexsonid "node1142533" pgloadind dubious OTT ID 534086 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cambaroides japonicus" nexsonid "node1142534" pgloadind dubious OTT ID 764422 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus laevis" nexsonid "node1142550" pgloadind dubious OTT ID 787889 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus karnanga" nexsonid "node1142551" pgloadind dubious OTT ID 748174 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus fultoni" nexsonid "node1142552" pgloadind dubious OTT ID 748170 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus tayatea" nexsonid "node1142553" pgloadind dubious OTT ID 478737 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus strictifrons" nexsonid "node1142556" pgloadind dubious OTT ID 620866 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus merosetosus" nexsonid "node1142557" pgloadind dubious OTT ID 787887 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus sericatus" nexsonid "node1142558" pgloadind dubious OTT ID 12272 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus quadrimanus" nexsonid "node1142559" pgloadind dubious OTT ID 787876 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus hemicirratulus" nexsonid "node1142561" pgloadind dubious OTT ID 748168 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus phyllocercus" nexsonid "node1142562" pgloadind dubious OTT ID 748158 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus tuberculatus" nexsonid "node1142567" pgloadind dubious OTT ID 478739 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus victoriensis" nexsonid "node1142568" pgloadind dubious OTT ID 478741 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus affinis" nexsonid "node1142569" pgloadind dubious OTT ID 787877 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus urostrictus" nexsonid "node1142570" pgloadind dubious OTT ID 224574 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus cymus" nexsonid "node1142571" pgloadind dubious OTT ID 787890 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus yabbimunna" nexsonid "node1142577" pgloadind dubious OTT ID 224576 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus lengana" nexsonid "node1142578" pgloadind dubious OTT ID 1055069 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus fossor" nexsonid "node1142579" pgloadind dubious OTT ID 12273 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus cunicularius" nexsonid "node1142582" pgloadind dubious OTT ID 548591 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus disjuncticus" nexsonid "node1142583" pgloadind dubious OTT ID 173887 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus cisternarius" nexsonid "node1142584" pgloadind dubious OTT ID 234316 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus martigener" nexsonid "node1142588" pgloadind dubious OTT ID 748160 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus australis" nexsonid "node1142589" pgloadind dubious OTT ID 1055061 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus spinicaudatus" nexsonid "node1142590" pgloadind dubious OTT ID 748156 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus mairener" nexsonid "node1142592" pgloadind dubious OTT ID 748172 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus granulatus" nexsonid "node1142593" pgloadind dubious OTT ID 1055063 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus nulloporius" nexsonid "node1142594" pgloadind dubious OTT ID 748166 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus mallacoota" nexsonid "node1142596" pgloadind dubious OTT ID 748162 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus orientalis" nexsonid "node1142597" pgloadind dubious OTT ID 748164 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaeus lyelli" nexsonid "node1142598" pgloadind dubious OTT ID 787888 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Geocharax insolitus" nexsonid "node1142604" pgloadind dubious OTT ID 600386 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Geocharax gracilis" nexsonid "node1142605" pgloadind dubious OTT ID 764423 pgloadind Null OTT ID in tree pgloadind null name "Geocharax sp 1 MBS 2007" nexsonid "node1142606" pgloadind Null OTT ID in tree pgloadind null name "Geocharax sp 2 MBS 2007" nexsonid "node1142608" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Geocharax falcata" nexsonid "node1142609" pgloadind dubious OTT ID 27315 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Gramastacus insolitus" nexsonid "node1142612" pgloadind dubious OTT ID 600388 pgloadind Null OTT ID in tree pgloadind null name "Gramastacus sp 2 DM 2003" nexsonid "node1142613" pgloadind Null OTT ID in tree pgloadind null name "Gramastacus sp MBS 2007" nexsonid "node1142614" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Tenuibranchiurus glypticus" nexsonid "node1142615" pgloadind dubious OTT ID 600383 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Engaewa reducta" nexsonid "node1142616" pgloadind dubious OTT ID 570845 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax cairnsensis" nexsonid "node1142625" pgloadind dubious OTT ID 832422 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax depressus" nexsonid "node1142626" pgloadind dubious OTT ID 832421 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax punctatus" nexsonid "node1142627" pgloadind dubious OTT ID 258021 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax parvus" nexsonid "node1142628" pgloadind dubious OTT ID 832419 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax dispar" nexsonid "node1142629" pgloadind dubious OTT ID 548597 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax cuspidatus" nexsonid "node1142630" pgloadind dubious OTT ID 522797 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax setosus" nexsonid "node1142635" pgloadind dubious OTT ID 548594 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax destructor NMAR-2001" nexsonid "node1142636" pgloadind dubious OTT ID 12209 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax rotundus" nexsonid "node1142637" pgloadind dubious OTT ID 522767 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax destructor albidus" nexsonid "node1142638" pgloadind dubious OTT ID 680789 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax destructor destructor" nexsonid "node1142639" pgloadind dubious OTT ID 917791 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax crassimanus" nexsonid "node1142644" pgloadind dubious OTT ID 105221 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax preissii" nexsonid "node1142645" pgloadind dubious OTT ID 988800 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax glaber" nexsonid "node1142646" pgloadind dubious OTT ID 548596 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax tenuimanus" nexsonid "node1142648" pgloadind dubious OTT ID 12245 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax cainii" nexsonid "node1142649" pgloadind dubious OTT ID 555309 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax quadricarinatus" nexsonid "node1142654" pgloadind dubious OTT ID 46784 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax quinquecarinatus" nexsonid "node1142655" pgloadind dubious OTT ID 548595 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax destructor" nexsonid "node1142656" pgloadind dubious OTT ID 79853 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax rhynchotus" nexsonid "node1142657" pgloadind dubious OTT ID 832423 pgloadind Null OTT ID in tree pgloadind null name "Cherax sp New Guinea DM 2003" nexsonid "node1142658" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Cherax robustus" nexsonid "node1142659" pgloadind dubious OTT ID 832420 pgloadind Null OTT ID in tree pgloadind null name "Euastacus sp AMB 18 1 FF32SP1" nexsonid "node1142674" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus australasiensis" nexsonid "node1142675" pgloadind dubious OTT ID 175364 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus spinifer" nexsonid "node1142676" pgloadind dubious OTT ID 27321 pgloadind Null OTT ID in tree pgloadind null name "Euastacus sp KC2705" nexsonid "node1142678" pgloadind Null OTT ID in tree pgloadind null name "Euastacus sp KC2635" nexsonid "node1142679" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus yarraensis" nexsonid "node1142682" pgloadind dubious OTT ID 872789 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus bispinosus" nexsonid "node1142683" pgloadind dubious OTT ID 834397 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus armatus" nexsonid "node1142684" pgloadind dubious OTT ID 872798 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus claytoni" nexsonid "node1142688" pgloadind dubious OTT ID 866255 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus brachythorax" nexsonid "node1142689" pgloadind dubious OTT ID 828521 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus guwinus" nexsonid "node1142691" pgloadind dubious OTT ID 828516 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus yanga" nexsonid "node1142692" pgloadind dubious OTT ID 674956 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus dharawalus" nexsonid "node1142693" pgloadind dubious OTT ID 677194 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus crassus" nexsonid "node1142695" pgloadind dubious OTT ID 828523 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus rieki" nexsonid "node1142696" pgloadind dubious OTT ID 27324 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus diversus" nexsonid "node1142698" pgloadind dubious OTT ID 828517 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus bidawalus" nexsonid "node1142699" pgloadind dubious OTT ID 304430 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus woiwuru" nexsonid "node1142701" pgloadind dubious OTT ID 151853 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus kershawi" nexsonid "node1142702" pgloadind dubious OTT ID 828515 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus dangadi" nexsonid "node1142710" pgloadind dubious OTT ID 828518 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus gumar" nexsonid "node1142711" pgloadind dubious OTT ID 828519 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus valentulus" nexsonid "node1142712" pgloadind dubious OTT ID 151852 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus mirangudjin" nexsonid "node1142713" pgloadind dubious OTT ID 151858 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus neohirsutus" nexsonid "node1142714" pgloadind dubious OTT ID 151860 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus gamilaroi" nexsonid "node1142717" pgloadind dubious OTT ID 828520 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus spinichelatus" nexsonid "node1142718" pgloadind dubious OTT ID 151857 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus polysetosus" nexsonid "node1142720" pgloadind dubious OTT ID 151861 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus" nexsonid "node1142721" pgloadind dubious OTT ID 297663 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus clarkae" nexsonid "node1142724" pgloadind dubious OTT ID 828524 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus suttoni" nexsonid "node1142725" pgloadind dubious OTT ID 27322 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus maidae" nexsonid "node1142726" pgloadind dubious OTT ID 408760 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus urospinosus" nexsonid "node1142728" pgloadind dubious OTT ID 408755 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus hystricosus" nexsonid "node1142729" pgloadind dubious OTT ID 166719 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus monteithorum" nexsonid "node1142734" pgloadind dubious OTT ID 151859 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus eungella" nexsonid "node1142735" pgloadind dubious OTT ID 408753 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus jagara" nexsonid "node1142736" pgloadind dubious OTT ID 408757 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus bindal" nexsonid "node1142738" pgloadind dubious OTT ID 828522 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus setosus" nexsonid "node1142739" pgloadind dubious OTT ID 408758 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus yigara" nexsonid "node1142742" pgloadind dubious OTT ID 408754 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus sulcatus" nexsonid "node1142743" pgloadind dubious OTT ID 408759 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus balanensis" nexsonid "node1142744" pgloadind dubious OTT ID 408751 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus reductus" nexsonid "node1142745" pgloadind dubious OTT ID 151854 pgloadind Null OTT ID in tree pgloadind null name "Euastacus sp AMB 38 1" nexsonid "node1142748" pgloadind Null OTT ID in tree pgloadind null name "Euastacus sp AMB IT 5" nexsonid "node1142749" pgloadind Null OTT ID in tree pgloadind null name "Euastacus sp AMB 17 2 BEC2SP1" nexsonid "node1142750" pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus robertsi" nexsonid "node1142752" pgloadind dubious OTT ID 934798 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Euastacus fleckeri" nexsonid "node1142753" pgloadind dubious OTT ID 408752 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Astacopsis franklinii" nexsonid "node1142756" pgloadind dubious OTT ID 872794 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Astacopsis gouldi" nexsonid "node1142757" pgloadind dubious OTT ID 1074909 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Astacopsis tricornis" nexsonid "node1142758" pgloadind dubious OTT ID 872796 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Paranephrops zealandicus" nexsonid "node1142760" pgloadind dubious OTT ID 534088 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Paranephrops planifrons" nexsonid "node1142761" pgloadind dubious OTT ID 600390 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Parastacus brasiliensis" nexsonid "node1142769" pgloadind dubious OTT ID 58153 pgloadind OTT ID not in database (probably dubious) pgloadind dubious name "Parastacus pilimanus" nexsonid "node

blackrim commented 10 years ago

yeah, you can load the whole thing with inittax if you like or subset On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

Reply to this email directly or view it on GitHub<

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.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835222

.

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josephwb commented 10 years ago

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38824752

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38828230

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38834869

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835222

.

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835352

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835693

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38836200 .

chinchliff commented 10 years ago

I've got it. It's building a with the metazoa taxonomy now.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38824752

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38828230

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38834869

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835222

.

Reply to this email directly or view it on GitHub<

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.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835693

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38836200

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Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38836682 .

jar398 commented 10 years ago

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

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.

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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chinchliff commented 10 years ago

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

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.

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.

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.

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Reply to this email directly or view it on GitHub<

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jimallman commented 10 years ago

On Mar 27, 2014, at 3:29 PM, chinchliff notifications@github.com wrote:

My attempt to get java’s HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl

Have you checked to be sure the java connection matches the curl command?

Jim Allman Interrobang Digital Media http://www.ibang.com/ (919) 649-5760

jar398 commented 10 years ago

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff notifications@github.comwrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38828230

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38834869

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38835222

.

Reply to this email directly or view it on GitHub<

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.

Reply to this email directly or view it on GitHub:

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38849879 .

jar398 commented 10 years ago

Oh sorry, it's treemachine calling out to taxomachine, not to phylografter, so forget what I said about Rick. Which taxomachine instance does it talk to? I haven't made any changes to taxomachine... except the one trivial change setting the main class in the pom... which no one depends on obviously.

On Thu, Mar 27, 2014 at 3:44 PM, Jonathan A Rees rees@mumble.net wrote:

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff notifications@github.comwrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff notifications@github.com wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

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josephwb commented 10 years ago

I was wondering about the switch from neo4j 1.8.M05 too. Was that necessary?

JWB.

On 27 March 2014 15:47, Jonathan A Rees notifications@github.com wrote:

Oh sorry, it's treemachine calling out to taxomachine, not to phylografter, so forget what I said about Rick. Which taxomachine instance does it talk to? I haven't made any changes to taxomachine... except the one trivial change setting the main class in the pom... which no one depends on obviously.

On Thu, Mar 27, 2014 at 3:44 PM, Jonathan A Rees rees@mumble.net wrote:

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff notifications@github.comwrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff < notifications@github.com> wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar

target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar

pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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jar398 commented 10 years ago

Yes- I think so - without that I was unable to synthesize the asterales tree, it was crashing.

-- apologies for brevity / using handheld gizmo --

On Mar 27, 2014, at 15:54, "Joseph W. Brown" notifications@github.com wrote:

I was wondering about the switch from neo4j 1.8.M05 too. Was that necessary?

JWB.

On 27 March 2014 15:47, Jonathan A Rees notifications@github.com wrote:

Oh sorry, it's treemachine calling out to taxomachine, not to phylografter, so forget what I said about Rick. Which taxomachine instance does it talk to? I haven't made any changes to taxomachine... except the one trivial change setting the main class in the pom... which no one depends on obviously.

On Thu, Mar 27, 2014 at 3:44 PM, Jonathan A Rees rees@mumble.net wrote:

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff <notifications@github.com wrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff < notifications@github.com> wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar

target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar

pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38810849

Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

Reply to this email directly or view it on GitHub:

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38830131

.

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.

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Reply to this email directly or view it on GitHub:

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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jar398 commented 10 years ago

OK. I'm able to reproduce the problem and agree based on backtrace that it's a missing converter from the String type to a response content stream.

I tried downgrading to neo4j 1.8.M05. That didn't help.

Then I removed the dependency on neo4j-server from pom.xml. That solved the problem.

So to make progress, make that mod to pom.xml. You also need to delete the class that depends on the library, which is opentree.plugins.TreemachineSecurityFilter.

I'm really pissed about the poor documentation and support for the neo4j security and unmanaged plugin features. I spent days getting them to work, and they do work, but now it turns out that simply LINKING IN the needed library - without even using it - kills existing required functionality.

And this is in the absence of the shade plugin.

I could go back to plan B, which is to do caching with a python script and security using Apache proxypass. I guess I can investigate a bit more before giving up like this - the neo4j native approach almost works and would be faster and more reliable.

Maybe this has to do with some kind of registration needed in some manifest thing somewhere, and can be fixed with some kind of weird pom directive.

On Thu, Mar 27, 2014 at 3:59 PM, Jonathan Rees jonathan.rees@gmail.comwrote:

Yes- I think so - without that I was unable to synthesize the asterales tree, it was crashing.

-- apologies for brevity / using handheld gizmo --

On Mar 27, 2014, at 15:54, "Joseph W. Brown" notifications@github.com wrote:

I was wondering about the switch from neo4j 1.8.M05 too. Was that necessary?

JWB.

On 27 March 2014 15:47, Jonathan A Rees notifications@github.com wrote:

Oh sorry, it's treemachine calling out to taxomachine, not to phylografter, so forget what I said about Rick. Which taxomachine instance does it talk to? I haven't made any changes to taxomachine... except the one trivial change setting the main class in the pom... which no one depends on obviously.

On Thu, Mar 27, 2014 at 3:44 PM, Jonathan A Rees rees@mumble.net wrote:

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff <notifications@github.com wrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff notifications@github.com wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff < notifications@github.com> wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar

target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar

pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

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.

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.

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

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Reply to this email directly or view it on GitHub<

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josephwb commented 10 years ago

Thanks for tracking that down Jonathan.

JWB.

On 27 March 2014 20:47, Jonathan A Rees notifications@github.com wrote:

OK. I'm able to reproduce the problem and agree based on backtrace that it's a missing converter from the String type to a response content stream.

I tried downgrading to neo4j 1.8.M05. That didn't help.

Then I removed the dependency on neo4j-server from pom.xml. That solved the problem.

So to make progress, make that mod to pom.xml. You also need to delete the class that depends on the library, which is opentree.plugins.TreemachineSecurityFilter.

I'm really pissed about the poor documentation and support for the neo4j security and unmanaged plugin features. I spent days getting them to work, and they do work, but now it turns out that simply LINKING IN the needed library - without even using it - kills existing required functionality.

And this is in the absence of the shade plugin.

I could go back to plan B, which is to do caching with a python script and security using Apache proxypass. I guess I can investigate a bit more before giving up like this - the neo4j native approach almost works and would be faster and more reliable.

Maybe this has to do with some kind of registration needed in some manifest thing somewhere, and can be fixed with some kind of weird pom directive.

On Thu, Mar 27, 2014 at 3:59 PM, Jonathan Rees jonathan.rees@gmail.comwrote:

Yes- I think so - without that I was unable to synthesize the asterales tree, it was crashing.

-- apologies for brevity / using handheld gizmo --

On Mar 27, 2014, at 15:54, "Joseph W. Brown" notifications@github.com wrote:

I was wondering about the switch from neo4j 1.8.M05 too. Was that necessary?

JWB.

On 27 March 2014 15:47, Jonathan A Rees notifications@github.com wrote:

Oh sorry, it's treemachine calling out to taxomachine, not to phylografter, so forget what I said about Rick. Which taxomachine instance does it talk to? I haven't made any changes to taxomachine... except the one trivial change setting the main class in the pom... which no one depends on obviously.

On Thu, Mar 27, 2014 at 3:44 PM, Jonathan A Rees rees@mumble.net wrote:

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff < notifications@github.com wrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith notifications@github.com

wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff < notifications@github.com> wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff < notifications@github.com> wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar

target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar

pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

Reply to this email directly or view it on GitHub:

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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blackrim commented 10 years ago

Thanks for tracking this down. Is it pushed? A recent pull didn't seem to have the pom updated but maybe I missed it in there

On Thu, Mar 27, 2014 at 9:14 PM, Joseph W. Brown notifications@github.comwrote:

Thanks for tracking that down Jonathan.

JWB.

On 27 March 2014 20:47, Jonathan A Rees notifications@github.com wrote:

OK. I'm able to reproduce the problem and agree based on backtrace that it's a missing converter from the String type to a response content stream.

I tried downgrading to neo4j 1.8.M05. That didn't help.

Then I removed the dependency on neo4j-server from pom.xml. That solved the problem.

So to make progress, make that mod to pom.xml. You also need to delete the class that depends on the library, which is opentree.plugins.TreemachineSecurityFilter.

I'm really pissed about the poor documentation and support for the neo4j security and unmanaged plugin features. I spent days getting them to work, and they do work, but now it turns out that simply LINKING IN the needed library - without even using it - kills existing required functionality.

And this is in the absence of the shade plugin.

I could go back to plan B, which is to do caching with a python script and security using Apache proxypass. I guess I can investigate a bit more before giving up like this - the neo4j native approach almost works and would be faster and more reliable.

Maybe this has to do with some kind of registration needed in some manifest thing somewhere, and can be fixed with some kind of weird pom directive.

On Thu, Mar 27, 2014 at 3:59 PM, Jonathan Rees <jonathan.rees@gmail.com wrote:

Yes- I think so - without that I was unable to synthesize the asterales tree, it was crashing.

-- apologies for brevity / using handheld gizmo --

On Mar 27, 2014, at 15:54, "Joseph W. Brown" <notifications@github.com

wrote:

I was wondering about the switch from neo4j 1.8.M05 too. Was that necessary?

JWB.

On 27 March 2014 15:47, Jonathan A Rees notifications@github.com wrote:

Oh sorry, it's treemachine calling out to taxomachine, not to phylografter, so forget what I said about Rick. Which taxomachine instance does it talk to? I haven't made any changes to taxomachine... except the one trivial change setting the main class in the pom... which no one depends on obviously.

On Thu, Mar 27, 2014 at 3:44 PM, Jonathan A Rees rees@mumble.net wrote:

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff < notifications@github.com wrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith < notifications@github.com>

wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff < notifications@github.com> wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff < notifications@github.com> wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar

target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar

pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38807259

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808015

.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38808583

.

Reply to this email directly or view it on GitHub:

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Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048

Reply to this email directly or view it on GitHub<

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.

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josephwb commented 10 years ago

I haven't made the edits yet. JWB.

On 28 March 2014 08:39, Stephen Smith notifications@github.com wrote:

Thanks for tracking this down. Is it pushed? A recent pull didn't seem to have the pom updated but maybe I missed it in there

On Thu, Mar 27, 2014 at 9:14 PM, Joseph W. Brown

notifications@github.comwrote:

Thanks for tracking that down Jonathan.

JWB.

On 27 March 2014 20:47, Jonathan A Rees notifications@github.com wrote:

OK. I'm able to reproduce the problem and agree based on backtrace that it's a missing converter from the String type to a response content stream.

I tried downgrading to neo4j 1.8.M05. That didn't help.

Then I removed the dependency on neo4j-server from pom.xml. That solved the problem.

So to make progress, make that mod to pom.xml. You also need to delete the class that depends on the library, which is opentree.plugins.TreemachineSecurityFilter.

I'm really pissed about the poor documentation and support for the neo4j security and unmanaged plugin features. I spent days getting them to work, and they do work, but now it turns out that simply LINKING IN the needed library - without even using it - kills existing required functionality.

And this is in the absence of the shade plugin.

I could go back to plan B, which is to do caching with a python script and security using Apache proxypass. I guess I can investigate a bit more before giving up like this - the neo4j native approach almost works and would be faster and more reliable.

Maybe this has to do with some kind of registration needed in some manifest thing somewhere, and can be fixed with some kind of weird pom directive.

On Thu, Mar 27, 2014 at 3:59 PM, Jonathan Rees < jonathan.rees@gmail.com wrote:

Yes- I think so - without that I was unable to synthesize the asterales tree, it was crashing.

-- apologies for brevity / using handheld gizmo --

On Mar 27, 2014, at 15:54, "Joseph W. Brown" < notifications@github.com

wrote:

I was wondering about the switch from neo4j 1.8.M05 too. Was that necessary?

JWB.

On 27 March 2014 15:47, Jonathan A Rees notifications@github.com wrote:

Oh sorry, it's treemachine calling out to taxomachine, not to phylografter, so forget what I said about Rick. Which taxomachine instance does it talk to? I haven't made any changes to taxomachine... except the one trivial change setting the main class in the pom... which no one depends on obviously.

On Thu, Mar 27, 2014 at 3:44 PM, Jonathan A Rees rees@mumble.net wrote:

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff < notifications@github.com wrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith < notifications@github.com>

wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff < notifications@github.com> wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff < notifications@github.com> wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar

target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar

pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

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josephwb commented 10 years ago

Hey Stephen.

I just got into the office a while ago. Did you make the changes, or should I?

JWB.

On 28 March 2014 08:55, Joseph Brown phylo.jwb@gmail.com wrote:

I haven't made the edits yet. JWB.

On 28 March 2014 08:39, Stephen Smith notifications@github.com wrote:

Thanks for tracking this down. Is it pushed? A recent pull didn't seem to have the pom updated but maybe I missed it in there

On Thu, Mar 27, 2014 at 9:14 PM, Joseph W. Brown

notifications@github.comwrote:

Thanks for tracking that down Jonathan.

JWB.

On 27 March 2014 20:47, Jonathan A Rees notifications@github.com wrote:

OK. I'm able to reproduce the problem and agree based on backtrace that it's a missing converter from the String type to a response content stream.

I tried downgrading to neo4j 1.8.M05. That didn't help.

Then I removed the dependency on neo4j-server from pom.xml. That solved the problem.

So to make progress, make that mod to pom.xml. You also need to delete the class that depends on the library, which is opentree.plugins.TreemachineSecurityFilter.

I'm really pissed about the poor documentation and support for the neo4j security and unmanaged plugin features. I spent days getting them to work, and they do work, but now it turns out that simply LINKING IN the needed library - without even using it - kills existing required functionality.

And this is in the absence of the shade plugin.

I could go back to plan B, which is to do caching with a python script and security using Apache proxypass. I guess I can investigate a bit more before giving up like this - the neo4j native approach almost works and would be faster and more reliable.

Maybe this has to do with some kind of registration needed in some manifest thing somewhere, and can be fixed with some kind of weird pom directive.

On Thu, Mar 27, 2014 at 3:59 PM, Jonathan Rees < jonathan.rees@gmail.com wrote:

Yes- I think so - without that I was unable to synthesize the asterales tree, it was crashing.

-- apologies for brevity / using handheld gizmo --

On Mar 27, 2014, at 15:54, "Joseph W. Brown" < notifications@github.com

wrote:

I was wondering about the switch from neo4j 1.8.M05 too. Was that necessary?

JWB.

On 27 March 2014 15:47, Jonathan A Rees notifications@github.com wrote:

Oh sorry, it's treemachine calling out to taxomachine, not to phylografter, so forget what I said about Rick. Which taxomachine instance does it talk to? I haven't made any changes to taxomachine... except the one trivial change setting the main class in the pom... which no one depends on obviously.

On Thu, Mar 27, 2014 at 3:44 PM, Jonathan A Rees <rees@mumble.net

wrote:

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff < notifications@github.com wrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith < notifications@github.com>

wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff < notifications@github.com> wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff < notifications@github.com> wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar

target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar

pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/treemachine/issues/69#issuecomment-38802977

.

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blackrim commented 10 years ago

You can go ahead. I am working on some other things right now

On Fri, Mar 28, 2014 at 9:58 AM, Joseph W. Brown notifications@github.comwrote:

Hey Stephen.

I just got into the office a while ago. Did you make the changes, or should I?

JWB.

On 28 March 2014 08:55, Joseph Brown phylo.jwb@gmail.com wrote:

I haven't made the edits yet. JWB.

On 28 March 2014 08:39, Stephen Smith notifications@github.com wrote:

Thanks for tracking this down. Is it pushed? A recent pull didn't seem to have the pom updated but maybe I missed it in there

On Thu, Mar 27, 2014 at 9:14 PM, Joseph W. Brown

notifications@github.comwrote:

Thanks for tracking that down Jonathan.

JWB.

On 27 March 2014 20:47, Jonathan A Rees notifications@github.com wrote:

OK. I'm able to reproduce the problem and agree based on backtrace that it's a missing converter from the String type to a response content stream.

I tried downgrading to neo4j 1.8.M05. That didn't help.

Then I removed the dependency on neo4j-server from pom.xml. That solved the problem.

So to make progress, make that mod to pom.xml. You also need to delete the class that depends on the library, which is opentree.plugins.TreemachineSecurityFilter.

I'm really pissed about the poor documentation and support for the neo4j security and unmanaged plugin features. I spent days getting them to work, and they do work, but now it turns out that simply LINKING IN the needed library - without even using it - kills existing required functionality.

And this is in the absence of the shade plugin.

I could go back to plan B, which is to do caching with a python script and security using Apache proxypass. I guess I can investigate a bit more before giving up like this - the neo4j native approach almost works and would be faster and more reliable.

Maybe this has to do with some kind of registration needed in some manifest thing somewhere, and can be fixed with some kind of weird pom directive.

On Thu, Mar 27, 2014 at 3:59 PM, Jonathan Rees < jonathan.rees@gmail.com wrote:

Yes- I think so - without that I was unable to synthesize the asterales tree, it was crashing.

-- apologies for brevity / using handheld gizmo --

On Mar 27, 2014, at 15:54, "Joseph W. Brown" < notifications@github.com

wrote:

I was wondering about the switch from neo4j 1.8.M05 too. Was that necessary?

JWB.

On 27 March 2014 15:47, Jonathan A Rees <notifications@github.com

wrote:

Oh sorry, it's treemachine calling out to taxomachine, not to phylografter, so forget what I said about Rick. Which taxomachine instance does it talk to? I haven't made any changes to taxomachine... except the one trivial change setting the main class in the pom... which no one depends on obviously.

On Thu, Mar 27, 2014 at 3:44 PM, Jonathan A Rees < rees@mumble.net

wrote:

We're talking about treemachine here, not taxomachine, right?

I made three commits: dedd - In pom.xml, changed neo4j version and added dependency on scala-libary (sorry, don't remember why) 893f - In pom.xml added depedency on neo4j-server. Not needed for command line but adding it means we only have a single source tree for both server and command line, so a simplification. Also added a class that isn't referenced anywhere (only comes into play if you add it to neo4j-server.properties). f978 - suppress newick from service call.

Probably the biggest risk is adding the neo4j-server dependency. You (or I) could try removing that, along with the only class that uses it, which is src/main/java/opentree/plugins/TreemachineSecurityRule.java . If I get to the point where I can reproduce the problem, that is probably the next thing I would try. I guess reverting to neo4j 1.8.M05 would be another thing to try, but that breaks something different.

Jonathan

On Thu, Mar 27, 2014 at 3:29 PM, chinchliff < notifications@github.com wrote:

I have no idea what is wrong. But I wonder if there is something going sour in the IO from taxomachine's web services. My attempt to get java's HTTPURLConnection class to connect was met with 500 errors with useless messages like "ERROR CONNECTING TO SERVER", despite the fact that the calls work fine in curl. Jonathan, did anything change about the server configuration or the way taxomachine's services might be transmitting data?

On Thu, Mar 27, 2014 at 1:50 PM, Jonathan A Rees

notifications@github.comwrote:

Metazoa is about 2/3 of the whole tree... http://mumble.net/~jar/tree-sample.png so cropping will help, but not a lot.

Listen, it's fine to back off the security plugin for now if that will help you get your work done. Nothing's depending on it and I can work in a branch.

On Thu, Mar 27, 2014 at 1:43 PM, Joseph W. Brown notifications@github.comwrote:

Right. The idea with the subsetting was just to make it 1) smaller and 2) faster for the testing. Building the whole thing would take annoyingly long just to deal with this particular bug.

@chinchliff -- I can put the entire thing on the shared drive it you like.

JWB.

On 27 March 2014 13:39, Stephen Smith < notifications@github.com>

wrote:

yeah, you can load the whole thing with inittax if you like or subset

On Thu, Mar 27, 2014 at 10:35:50AM -0700, Joseph W. Brown wrote:

You have OTT, right?

python scripts/subset_taxonomy.py Metazoa ott2.4.draft21/taxonomy.tsv Metazoa.txt

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar inittax Metazoa.txt ott2.4.draft21/synonyms.tsv Metazoa.db

JWB.

On 27 March 2014 13:33, chinchliff < notifications@github.com> wrote:

How do I build that taxonomy db?

On Thu, Mar 27, 2014 at 1:32 PM, Joseph W. Brown notifications@github.comwrote:

Great Cody.

Jonathan -- if you want to run the example, you would need a taxonomy DB with Metazoa (the tree contains crustaceans and other leggy things).

JWB.

On 27 March 2014 13:29, chinchliff < notifications@github.com> wrote:

I was using jersey originally because it has cleaner syntax and is less verbose. But I ran into all kinds of problems and ended up switching to java.net in all other cases. I am working on a conversion now, should be ready in a few mins.

On Thu, Mar 27, 2014 at 12:53 PM, Stephen Smith < notifications@github.com

wrote:

I will investigate some. Though you must have checked on some of these other methods before when you were checking out things on this and oti. Any idea why we went this way to begin with instead of java.net? Just wondering if any pros/cons are remembered

On Thu, Mar 27, 2014 at 09:38:50AM -0700, chinchliff wrote:

I wonder if a simpler solution would be to use a different method (not Jersey) to query the web service. It is a standard request, surely there is a simple tool that can handle this that is less finicky than jersey? What about the built-in java.net.* classes?

On Thu, Mar 27, 2014 at 12:12 PM, Stephen Smith < notifications@github.com>wrote:

Seems the solution may be here

https://stackoverflow.com/questions/8039126/missing-standard-message-body-reader-providers-in-my-jar

merging everything to one jar with shade. I am less familiar with this part of the pom. Does someone else know more about transformers or whether this seems to be a problem?

On Thu, Mar 27, 2014 at 07:41:04AM -0700, Joseph W. Brown wrote:

Here is a command that checks a particular tree:

java -jar

target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar

pgloadind Life.2.4.draft21.db ../avatol_nexsons/2823 6570 test

where "Life.2.4.draft21.db" is my taxonomy DB, and "../avatol_nexsons" is where I store my nexsons.

What tipped me off that something was awry was the message:

pgloadind Null OTT ID in tree

something I have never seen before.

HTH. JWB.

On 27 March 2014 10:24, Jonathan A Rees < notifications@github.com> wrote:

Oh, maybe I was confusing this with a different bug.

Can you send me a command that elicits the problem? I've groveled around in the jersey stuff enough now that I might have a chance of debugging this.

On Thu, Mar 27, 2014 at 10:20 AM, Joseph W. Brown notifications@github.comwrote:

It builds fine, it just has the "problem connecting to server" when performing the TNRS. JWB.

On 27 March 2014 10:15, Jonathan A Rees < notifications@github.com> wrote:

I am unable to reproduce the problem.

Here is what I did:

  • Renamed my .m2 to prevent accidental success based on previous repo cache contents.
  • Fresh clone of treemachine master.
  • ./mvn_serverplugins.sh
  • ./mvn_cmdlines.sh No errors.

I am running maven 3.0.4 and java 1.6.0_65 on OS X. Can you email me a transcript of the failing build?

Jonathan

On Thu, Mar 27, 2014 at 10:08 AM, Jonathan A Rees < rees@mumble.net

wrote:

Well I didn't have this problem when I pushed that commit... so I think something must have changed out there at maven central...

I added a dependency on neo4j-server, which might pull in other things.

I'll see if I can reproduce it, and investigate.

On Thu, Mar 27, 2014 at 9:38 AM, Joseph W. Brown < notifications@github.com

wrote:

Yup. 893f444<

https://github.com/OpenTreeOfLife/treemachine/commit/893f444e13e1f38101b5177f7af6f8304299f1b5

is

where it enters in. The only thing I see immediately is a change in the

neo4j version.

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josephwb commented 10 years ago

I made the suggested changes from @jar398, and things appear to work on the example. I am closing this, but @jar398 might want to open a separate issue to get opentree.plugins.TreemachineSecurityFilter working again.