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IXA pipes hackathon #28

Closed ragerri closed 6 years ago

ragerri commented 6 years ago

Mostly I would like to know how to ensure that our component actually works for OMTD. I have shared a component as docker and before I upload the rest of the components I would like to make sure that I am doing things correctly.

Thanks

R

galanisd commented 6 years ago

Hi,

It seems that you have registered IXA several times. https://test.openminted.eu/search;query=IXA Correct?

Which is the latest version? This one? https://test.openminted.eu/landingPage/component/d2d4a389-f243-4378-b0a3-90cf91b8209f ?

ragerri commented 6 years ago

Hello,

Yes, the last one.

Cheers,

R

On Fri, Apr 13, 2018 at 12:06 AM, Dimitrios Galanis < notifications@github.com> wrote:

Hi,

It seems that you have registered IXA several times. https://test.openminted.eu/search;query=IXA Correct?

Which is the latest version? This one? https://test.openminted.eu/landingPage/component/d2d4a389-f243-4378-b0a3- 90cf91b8209f ?

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galanisd commented 6 years ago

I will delete the old versions and have a look to the latest.

galanisd commented 6 years ago

Please can you send me some sample input files for you component just to be sure.

ragerri commented 6 years ago

Hello,

Sure, here it is one.

https://raw.githubusercontent.com/ragerri/ixa-pipes-omtd/master/en/input.xmi

R

On Fri, Apr 13, 2018 at 12:23 PM, Dimitrios Galanis < notifications@github.com> wrote:

Please can you send me some sample input files for you component just to be sure.

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galanisd commented 6 years ago

I had a look into en-ixa-pipes.sh (your executor) ...got it from your image. It seems OK. I do not understand why it does not work; probably it has to do with the code that Galaxy uses to call your executor.

Is it possible to copy the executor (en-ixa-pipes.sh) in /usr/bin/ and provide an updated image? I have successfully tested images with this structure in the past. e.g. https://github.com/openminted/omtd-component-executor/blob/master/omtd-component-executor-gate.dockerfile

Then I will be able to call the executor by just running en-ixa-pipes.sh OR bash en-ixa-pipes.sh.

Thanks

Dimitris

galanisd commented 6 years ago

Also, I just noticed that in some executors that I have created or contributed ...the output directory is created by the executor if it does not exist. E.g. https://github.com/openminted/omtd-component-executor/blob/master/omtd-component-webservice/src/main/java/eu/openminted/component/webservice/WebServiceClient.java

Maybe Galaxy tries to create it and fails. It might has to do with the configuration/setup of Galaxy + Docker. This explains why we get a "ERROR: --output must be a directory" message. The directory does not exist.

Please can you take care of this in the script (executor) and provide an updated image.

Thanks

greenwoodma commented 6 years ago

To make sure we are as well prepared as possible to help during the hackathon sessions could you please add/attach to this issue:

  1. The landing page URL of any component/workflow you have registered
  2. The OMTD-SHARE XML file for each component/workflow
  3. One or two sample documents that you expect to produce sensible output for your component/workflow
ragerri commented 6 years ago

Hello Dimitrios,

Thanks for your help. I have made the changes you suggested and the local tests work fine (e.g., it creates the output dir if it does not exists). Here it is the new version of the component:

https://test.openminted.eu/landingPage/component/6ab57399-1f12-4c9d-9038-c9550db29956

Let's see if that works now in the Galaxy test @ OMTD.

Cheers,

Rodrigo

On Fri, Apr 13, 2018 at 7:02 PM, Dimitrios Galanis <notifications@github.com

wrote:

Also, I just noticed that in some executors that I have created or contributed ...the output directory is created by the executor if it does not exist. E.g. https://github.com/openminted/ omtd-component-executor/blob/master/omtd-component- webservice/src/main/java/eu/openminted/component/ webservice/WebServiceClient.java

Maybe Galaxy tries to create it and fails. It might has to do with the configuration/setup of Galaxy + Docker. This explains why we get a "ERROR: --output must be a directory" message. The directory does not exist.

Please can you take care of this in the script (executor) and provide an updated image.

Thanks

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ragerri commented 6 years ago

Hello Mark.

  1. Landing Page: https://test.openminted.eu/landingPage/component/6ab57399-1f12-4c9d-9038-c9550db29956
  2. Descriptor attached.
  3. Two input files attached.

Best regards,

Rodrigo

On Mon, Apr 16, 2018 at 2:24 PM, Mark A. Greenwood <notifications@github.com

wrote:

To make sure we are as well prepared as possible to help during the hackathon sessions could you please add/attach to this issue:

  1. The landing page URL of any component/workflow you have registered
  2. The OMTD-SHARE XML file for each component/workflow
  3. One or two sample documents that you expect to produce sensible output for your component/workflow

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gkirtzou commented 6 years ago

@ragerri You have forgotten to attach the attachements

galanisd commented 6 years ago

It seems that you provided the same image ragerri/en-ixa-pipes-omtd:0.0.1 same version (0.0.1). This is the correct one? Is it possible to update a tagged image in DockerHub?

Also I did a docker pull...and says that nothing changed.

ragerri commented 6 years ago

Attachments, I did not realize that by email are not included.

corpus_in.tar.gz

The descriptor was not correct, so I have update it.

en-ixa-pipes-omtd-descriptor.xml.gz

ragerri commented 6 years ago

Hello Dimitrios, https://hub.docker.com/r/ragerri/en-ixa-pipes-omtd/tags/

yes, the tagged image is in the Docker Hub:

new tag: 0.1.0 -> old tag 0.0.1

docker pull ragerri/en-ixa-pipes-omtd:0.1.0

The OMTD descriptor has changed accordingly. Now I have two components. The one I uploaded to day that points to the 0.1.0 tag in docker hub and the one I uploaded last week.

Thanks

R

galanisd commented 6 years ago

OK but in OMTD-SHARE of https://test.openminted.eu/landingPage/component/6ab57399-1f12-4c9d-9038-c9550db29956 I see <ns0:distributionLocation>ragerri/en-ixa-pipes-omtd:0.0.1</ns0:distributionLocation> the old tag.

not 0.1.0 See also the en-ixa-pipes-omtd-descriptor.xml.gz that you provided above.

Do I miss something?

Thanks.

ragerri commented 6 years ago

Hello,

I might have messed up with the descriptor :(

It should be correct now.

https://test.openminted.eu/landingPage/component/a448caa2-c1c3-4de1-9fda-c4657893b4be

Cheers,

R

On Mon, Apr 16, 2018 at 5:25 PM, Dimitrios Galanis <notifications@github.com

wrote:

OK but in OMTD-SHARE of https://test.openminted.eu/landingPage/component/ 6ab57399-1f12-4c9d-9038-c9550db29956 I see

ragerri/en-ixa-pipes-omtd:0.0. 1 the old tag. not 0.1.0 See also the en-ixa-pipes-omtd-descriptor.xml.gz that you provided above. Do I miss something? Thanks. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub , or mute the thread .
galanisd commented 6 years ago

Now it is correct. I will delete the old versions from Registry.

Thanks!

galanisd commented 6 years ago

Tested failed. Again ERROR: --output must be a directory I did this to see en-ixa-pipes.sh docker run ragerri/en-ixa-pipes-omtd:0.1.0 /bin/bash -c "cat en-ixa-pipes.sh" | more

if [ ! -d ${output} ]; then mkdir ${output} echo "ERROR: --output must be a directory" exit 1 fi the directory is probably created but then ...exit. :-)

ragerri commented 6 years ago

OK :)

Let's see now. Version 0.1.1

https://test.openminted.eu/landingPage/component/f06baf6a-4000-4afb-88e5-44c85b02cf11

Thanks,

R

On Mon, Apr 16, 2018 at 6:00 PM, Dimitrios Galanis <notifications@github.com

wrote:

Tested failed. Again ERROR: --output must be a directory I did this to see en-ixa-pipes.sh docker run ragerri/en-ixa-pipes-omtd:0.1.0 /bin/bash -c "cat en-ixa-pipes.sh" | more

if [ ! -d ${output} ]; then mkdir ${output} echo "ERROR: --output must be a directory" exit 1 fi the directory is probably created but then ...exit. :-)

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galanisd commented 6 years ago

Problem solved... New one... Creating --output directory /en-ixa-pipes.sh: line 10: ./xmi2naf.py: No such file or directory /en-ixa-pipes.sh: line 16: ./naf2xmi.py: No such file or directory /en-ixa-pipes.sh: line 10: ./xmi2naf.py: No such file or directory /en-ixa-pipes.sh: line 16: ./naf2xmi.py: No such file or directory

I know what happens. Galaxy creates a directory "working" in the container and runs from there the code that was generated for calling your component.

So, xmi2naf.py is here / and can't be found. You have to make your executables (xmi2naf.py, ixa-pipe-tok-exec.jar, ...) visible/runnable from everywhere. See more info here https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

galanisd commented 6 years ago

... 2 solutions

We are pretty close

gkirtzou commented 6 years ago

@ragerri As far as the metadata of your component is concerned, I would like to propose a few changes, in order to have meaningful metadata, for better visibility and usability of your component. There are not obligatory changes, but recommented.

In the description of your component, you say "It provides tokenizer, POS tagger, lemmatizer, NER tagger, Chunking and Document Classification. ". It would be nice to add this information also to the outputResourceInfo.annotationTypes. I think the following types of annotations are generated by your component, correct?

Also, it would be nice to add the language element in the outputResourceInfo, since you provide this information also to the inputContentResourceInfo.

pennyl67 commented 6 years ago

@ragerri Hi Rodrigo A couple of additional recommendations for the metadata - and a question: how did you generate it? Straight as an XML file or through the editor? (this will help us keep track of some administrative issues)

ragerri commented 6 years ago

Hello Dimitrios,

I have them the changes regarding the absolute paths.

https://test.openminted.eu/landingPage/component/ff94e664-8555-4f04-bb03-1be6d225c9e1

Thanks for your help,

Rodrigo

On Mon, Apr 16, 2018 at 7:26 PM, Dimitrios Galanis <notifications@github.com

wrote:

... 2 solutions

  • Add them all to /usr/bin/ OR
  • Call them in en-ixa-pipes.sh using absolute paths as you do with en-ixa-pipes.sh. en-ixa-pipes.sh is called /en-ixa-pipes.sh ...

We are pretty close

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ragerri commented 6 years ago

Dear Katerina and Penny,

Indeed it would be nice to add:

  1. outputResourceInfo.annotationTypes (6 types you mentioned).
  2. outputResourceInfo: language element
  3. resourceCreationInfo and resourceCreator
  4. Extra Information material on the IXA pipes (resourceDocumentionInfo)

The problem is that I have never managed to register a component through the editor. I have tried today again in order to fill in those elements but I always get the same error regarding the contactType: I get to add the contactPoint, but I cannot choose or see the contactType (in my case, landingPage), so the editor gives me this error. As I cannot save or see a preview of the editor, I cannot copy those fields to the XML I manually upload to register the component.

I can try and manually add those elements. I will do that when the component passes the OMTD Galaxy tests.

Thanks,

Rodrigo

On Tue, Apr 17, 2018 at 11:46 AM, Penny Labropoulou < notifications@github.com> wrote:

@ragerri https://github.com/ragerri Hi Rodrigo A couple of additional recommendations for the metadata - and a question: how did you generate it? Straight as an XML file or through the editor? (this will help us keep track of some administrative issues)

  • for the function, please use http://w3id.org/meta-share/ omtd-share/Annotator as it describes better what the component does - it's not an operational issue, but a discoverability one
  • could you add resourceCreationInfo with resourceCreator? It's not mandatory but it will help the citation process
  • if you have any extra information material (e.g. publications, user manual etc.) on the IXA pipes, you can use the resourceDocumentationInfo for that reason Thanks, Penny

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pennyl67 commented 6 years ago

For the metadata elements, don't worry; once you finish all the tests, and everything is ok, send me the record and I'll add them for you. For the editor, the problem is due to the fact that it automatically considers that the person adding the metadata is also the contact person; I'll report to the implementors - thanks for noticing!

galanisd commented 6 years ago

Succeeded...Please have a look

The workflow was omtdImporter -> IXA The first step just gets the data from the OMTD Storage.

Good news :-)

I assume that if we create a workflow omtdImporter -> PDFReader -> IXA and provide a corpus of PDFs it will also work.

ragerri commented 6 years ago

Hello,

Excellent. I assume that I can go on uploading the rest of my components to following this structure, right?

Best,

Rodrigo

On Tue, Apr 17, 2018 at 4:34 PM, Dimitrios Galanis <notifications@github.com

wrote:

Succeeded...Please have a look

The workflow was omtdImporter -> IXA The first step just gets the data from the OMTD Storage.

Good news :-)

I assume that if we create a workflow omtdImporter -> PDFReader -> IXA and provide a corpus of PDFs it will also work.

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galanisd commented 6 years ago

I created an OMTD app/workflow. omtdImporter -> PDF2XMI (PDFReader) -> IXA It is private https://test.openminted.eu/landingPage/application/4bd8e0ee-7953-43ae-b917-4466b253fe39

I fed it with a corpus Results here. https://test.openminted.eu/landingPage/corpus/a479260f-7bd3-4931-835f-4fc8c1e13cda and here a50fa880-8f47-4bd2-898d-014c8d99fb2d.zip

I see some ixa annotations but I was expecting more.

Any ideas?

In case you want to test PDFReader output is here (previous step) PdfReader_output.zip

I assume that if you don't see any issues relevant to the above you can start uploading and the rest IXA components. Keep in mind that each time you register a component a wrapper is generated for Galaxy. When you delete a component the respective wrapper is not deleted. I have opened an issue for this. https://github.com/openminted/omtd-registry/issues/22

This issue might cause problems. I was deleting the old wrappers manually before testing your component.

ragerri commented 6 years ago

Hello Dimitrios,

No, the output was not right, because there were not any annotations. It turns out there was an issue when reading the XMI format which we have solved.

I attach the results of the docker output which now looks fine. Perhaps you can give it a try now with the new version of the component (0.1.3) in the same workflow? I will then proceed uploading the rest of the components.

Thanks!

R

corpus_out.tar.gz

galanisd commented 6 years ago

Edited workflow to use version 0.1.3. Retested with the same input. Output is here https://test.openminted.eu/landingPage/corpus/7861a770-f4fc-48d0-be61-47dfe2df1fc8 and it seems ok. Please have a look.

And one screenshot. ixa

Many thanks!

Dimitris

galanisd commented 6 years ago

Probably you can't download the output. here you are... a3f3abbe-cf1c-4d35-be16-672a45004d9c.zip

Forgot to say IXA took about 30 minutes for processing the 3 files. Is this OK?

ragerri commented 6 years ago

Hello,

The output is exactly the same as mine. So, it works as it should. Regarding processing time, it is not OK to be 30 minutes processing these files :)

I have just run the process in my PC (normal core i5 intel 8GB RAM PC)

time docker run -v /home/ragerri/corpus_in:/corpus_in -v /home/ragerri/corpus_out:/corpus_out -i ragerri/en-ixa-pipes-omtd:0.1.3 en-ixa-pipes.sh --input corpus_in --output corpus_out

real 3m41.934s user 0m0.092s sys 0m0.024s

Best,

R

On Wed, Apr 18, 2018 at 4:19 PM, Dimitrios Galanis <notifications@github.com

wrote:

Probably you can't download the output. here you are... a3f3abbe-cf1c-4d35-be16-672a45004d9c.zip https://github.com/openminted/Open-Call-Discussions/files/1924429/a3f3abbe-cf1c-4d35-be16-672a45004d9c.zip

Forgot to say IXA took about 30 minutes for processing the 3 files. Is this OK?

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galanisd commented 6 years ago

Sorry ... it was ~20 minutes...Still much slower than yours. ~4 min vs ~20.

image

This a test cluster that we are using ....and I think that each container gets 2-3 GB maximum. We will see what happens in the production. @antleb @greenwoodma

saxtouri commented 6 years ago

I confirm that each container is restricted to just 2G or RAM and 1 core of CPU.

ragerri commented 6 years ago

Hello,

IXA pipes uses multi-threading and creating XMI for tokens, pos tags, named entities and chunks requires (some) RAM. Thus, the processing time could be justified by the restrictions for each container.

Thanks,

R

On Wed, Apr 18, 2018 at 5:09 PM, Stavros Sachtouris < notifications@github.com> wrote:

I confirm that each container is restricted to just 2G or RAM and 1 core of CPU.

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ragerri commented 6 years ago

Hello,

I have been adding the rest of my components. Just two of them remain. Over the weekend I will upload them.

Cheers,

Rodrigo

On Wed, Apr 18, 2018 at 5:32 PM, Rodrigo Agerri agerri.rodrigo@gmail.com wrote:

Hello,

IXA pipes uses multi-threading and creating XMI for tokens, pos tags, named entities and chunks requires (some) RAM. Thus, the processing time could be justified by the restrictions for each container.

Thanks,

R

On Wed, Apr 18, 2018 at 5:09 PM, Stavros Sachtouris < notifications@github.com> wrote:

I confirm that each container is restricted to just 2G or RAM and 1 core of CPU.

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galanisd commented 6 years ago

I see en, de, es, eu, gl, it, nl

pennyl67 commented 6 years ago

@ragerri When you finish uploading and testing, could you also upload here the metadata files for a final check? Thanks

ragerri commented 6 years ago

Hello,

There are 8 components: de, en, es, eu, fr, gl, it, nl. I attach the descriptors here as requested.

Cheers,

Rodrigo ixa-pipes-omtd-descriptors.tar.gz

galanisd commented 6 years ago

Thanks!

pennyl67 commented 6 years ago

Hi @ragerri For the metadata records, they're ok. I would only recommend that

ragerri commented 6 years ago

Hello Penny,

Sure, I would like to follow your recommendation and add the resourceCreator element. Could you give me an example so I can just fill it in with my own info?

Thanks,

R

On Tue, Apr 24, 2018 at 10:57 AM, Penny Labropoulou < notifications@github.com> wrote:

Hi @ragerri https://github.com/ragerri For the metadata records, they're ok. I would only recommend that

  • you turn "public" to "false" when you upload them - just so that you can check them; remember that if metadata records are set to public you cannot modify them
  • the only recommended piece of information that you might still want to add is the "resourceCreator" - important for citation purposes. Again, these are only recommendations. Apart from that, I think you're ok now also with the testing - @galanisd https://github.com/galanisd am I correct? So, we will soon inform you where to upload the metadata for the final delivery.

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pennyl67 commented 6 years ago

I've added in one of your descriptors the resourceCreationInfo module; if you have an XML editor, you can select the value person/group/organization in the and then you will be asked to fill in the rest of the appropriate elements. On the other hand, you can just give me the details (e.g. IXA group, person name or organization name or whatever) and I'll fill it in for you. nl-ixa-pipes-omtd-descriptorNew.zip

ragerri commented 6 years ago

Hello again,

I have uploaded another 4 components (the last ones) to test.openminted

en-ixa-pipe-opinion.sh es-ixa-pipe-opinion.sh fr-ixa-pipe-opinion.sh nl-ixa-pipe-opinion.sh

For example, this is the landing page of en-ixa-pipe-opinion.sh

https://test.openminted.eu/landingPage/component/5f9a4850-af3a-486d-8821-60f20fff2198

I have also updated every share descriptor with the resource creation info. In this link you can find all of them. The new ones:

https://github.com/ragerri/ixa-pipes-omtd/tree/master/absa2016

The previous ones:

https://github.com/ragerri/ixa-pipes-omtd

I think the one thing remaining is uploading the components wherever you tell me.

Best regards,

Rodrigo

On Tue, Apr 24, 2018 at 11:28 AM, Penny Labropoulou < notifications@github.com> wrote:

I've added in one of your descriptors the resourceCreationInfo module; if you have an XML editor, you can select the value person/group/organization in the and then you will be asked to fill in the rest of the appropriate elements. On the other hand, you can just give me the details (e.g. IXA group, person name or organization name or whatever) and I'll fill it in for you. nl-ixa-pipes-omtd-descriptorNew.zip https://github.com/openminted/Open-Call-Discussions/files/1942085/nl-ixa-pipes-omtd-descriptorNew.zip

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pennyl67 commented 6 years ago

@ragerri thanks; just to be sure, we now have 12 components from you, right? We'll get right back with the final uploading process

ragerri commented 6 years ago

Yes, 12 components.

Cheers

R

On Thu, 26 Apr 2018, 10:45 Penny Labropoulou, notifications@github.com wrote:

@ragerri https://github.com/ragerri thanks; just to be sure, we now have 12 components from you, right? We'll get right back with the final uploading process

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galanisd commented 6 years ago

For each component you have created a separate image?

ragerri commented 6 years ago

Yes

On Thu, Apr 26, 2018 at 11:17 AM, Dimitrios Galanis < notifications@github.com> wrote:

For each component you have created a separate image?

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pennyl67 commented 6 years ago

@ragerri You can proceed with the final uploading at services.openminted.eu. If you encounter any problems, please let us know. Thanks!