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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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building commit 22fd2d6b9cf122023aba7d4384cf23ceff6d5940 fails #1707

Closed childers closed 7 years ago

childers commented 7 years ago

STDERR from terminal:

 $ ./apollo deploy
javac 1.8.0_112 found
javac installed
JDK 1.8 found: javac 1.8.0_112

FAILURE: Build failed with an exception.

* Where:
Build file '/apollo_master/build.gradle' line: 80

* What went wrong:
A problem occurred evaluating root project 'nathanApolloMaster'.
> startup failed:
  script15004844661701540049598.groovy: 176: expecting ']', found 'tmp_dir' @ line 176, column 7.
           tmp_dir: "/opt/apollo/tmp" //optional param, uses system tmp dir by default
           ^

  1 error

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 5.106 secs
***************************************
NOTE: Please set the memory for your servlet container (tomcat, jetty, etc.) or Apollo may not start correctly: http://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#suggested-tomcat-memory-settings
***************************************

Running with --stacktrace gave the same output. I was able to build and test successfully yesterday.

nathandunn commented 7 years ago

This is saying that there is an error in your apollo-config.groovy as the line its failing on is here:

revisedConfig = new ConfigSlurper().parse(new File("apollo-config.groovy").toURI().toURL()) Let me know if that is not correct.

On Jul 19, 2017, at 10:38 AM, childers notifications@github.com wrote:

Search mailing list http://gmod.827538.n3.nabble.com/Apollo-f815553.html or email list apollo@lists.lbl.gov if a general setup question.

Provide what you were doing and what you expected to see. Screenshots, directory, config files are a plus if relevant. Trying to build mater failed very fast. I expected to see it succeed. It looks like there is still soem temporary code specific to the @nathandunn https://github.com/nathandunn local system.

STDERR from terminal:

$ ./apollo deploy javac 1.8.0_112 found javac installed JDK 1.8 found: javac 1.8.0_112

FAILURE: Build failed with an exception.

  • Where: Build file '/app/data/cchilders_dev/apollo_master/build.gradle' line: 80

  • What went wrong: A problem occurred evaluating root project 'nathanApolloMaster'.

    startup failed: script15004844661701540049598.groovy: 176: expecting ']', found 'tmp_dir' @ line 176, column 7. tmp_dir: "/opt/apollo/tmp" //optional param, uses system tmp dir by default ^

    1 error

  • Try: Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 5.106 secs

NOTE: Please set the memory for your servlet container (tomcat, jetty, etc.) or Apollo may not start correctly: http://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#suggested-tomcat-memory-settings

Running with --stacktrace gave the same output. I was able to build and test successfully yesterday.

Provide the javascript console log output generated from the action. N/A Provide the server log output generated from the action (typically catalina.out). N/A — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GMOD/Apollo/issues/1707, or mute the thread https://github.com/notifications/unsubscribe-auth/AAt2qoc7ap-y_adejtT2uhbjHYlkGBBgks5sPj8ZgaJpZM4OdD4G.

childers commented 7 years ago

I did just add a new apollo section to my apollo-config.groovy. Pasted the new section below for your perusal. I do see the line now, but since it was flagged as the default settings I didn't think to change or comment it out.

apollo {
  default_minimum_intron_size = 1
  history_size = 0
  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"
  track_name_comparator = "/config/track_name_comparator.js"
  use_cds_for_new_transcripts = true
  user_pure_memory_store = true
  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"
  is_partial_translation_allowed = false // unused so far
  get_translation_code = 1
  only_owners_delete = false
  sequence_search_tools = [
    blat_nuc: [
      search_exe: "/usr/local/bin/blat",
      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
      name: "Blat nucleotide",
      params: ""
    ],
    blat_prot: [
      search_exe: "/usr/local/bin/blat",
      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
      name: "Blat protein",
      params: ""
//might want to comment the following line in your example text...
      tmp_dir: "/opt/apollo/tmp" //optional param, uses system tmp dir by default
    ]
  ]

  splice_donor_sites = [ "GT" ]
  splice_acceptor_sites = [ "AG"]
  gff3.source= "." bootstrap = false

  info_editor = {
    feature_types = "default"
    attributes = true
    dbxrefs = true
    pubmed_ids = true
    go_ids = true
    comments = true
  }
}
nathandunn commented 7 years ago

You’re missing a comma after:

params: ""

I personally like it when they don’t require commas, but such is life.

On Jul 19, 2017, at 10:52 AM, childers notifications@github.com wrote:

I did just add a new apollo section to my apollo-config.groovy. Pasted the new section below for your perusal. I do see the line now, but since it was flagged as the default settings I didn't think to change or comment it out.

apollo { default_minimum_intron_size = 1 history_size = 0 overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper" track_name_comparator = "/config/track_name_comparator.js" use_cds_for_new_transcripts = true user_pure_memory_store = true translation_table = "/config/translation_tables/ncbi_1_translation_table.txt" is_partial_translation_allowed = false // unused so far get_translation_code = 1 only_owners_delete = false sequence_search_tools = [ blat_nuc: [ search_exe: "/usr/local/bin/blat", search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide", name: "Blat nucleotide", params: "" ], blat_prot: [ search_exe: "/usr/local/bin/blat", search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide", name: "Blat protein", params: "" //might want to comment the following line in your example text... tmp_dir: "/opt/apollo/tmp" //optional param, uses system tmp dir by default ] ]

splice_donor_sites = [ "GT" ] splice_acceptor_sites = [ "AG"] gff3.source= "." bootstrap = false

info_editor = { feature_types = "default" attributes = true dbxrefs = true pubmed_ids = true go_ids = true comments = true } } — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GMOD/Apollo/issues/1707#issuecomment-316465749, or mute the thread https://github.com/notifications/unsubscribe-auth/AAt2qvPEdfO-o_HlF3CmixV0_NlOi4-Fks5sPkJcgaJpZM4OdD4G.

childers commented 7 years ago

Thanks! These changes still didn't affect the results of ./apollo deploy, but I did make a suggested update to the example in Configure.md Do all lines in the lists bracketed by '[]' need to end with a comma?

nathandunn commented 7 years ago

When specified that way, yes. The [ ] method is what groovy uses to identify the maps. In the other types (like info_editor) it is different.

nathandunn commented 7 years ago

What error are you getting now and what does your config look like?

childers commented 7 years ago

I can send you the full apollo-config.groovy offline, but this is the only section I changed (or added) when it stopped building.

apollo {
  default_minimum_intron_size = 1
  history_size = 0
  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"
  track_name_comparator = "/config/track_name_comparator.js"
  use_cds_for_new_transcripts = true
  user_pure_memory_store = true
  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"
  is_partial_translation_allowed = false // unused so far
  get_translation_code = 1
  only_owners_delete = false
  sequence_search_tools = [
    blat_nuc: [
      search_exe: "/usr/local/bin/blat",
      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
      name: "Blat nucleotide",
      params: "",
    ],
    blat_prot: [
      search_exe: "/usr/local/bin/blat",
      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
      name: "Blat protein",
      params: "",
//      tmp_dir: "/opt/apollo/tmp" //optional param, uses system tmp dir by default
    ]
  ]    

  splice_donor_sites = [ "GT" ]
  splice_acceptor_sites = [ "AG"]
  gff3.source= "." bootstrap = false

  info_editor = {
    feature_types = "default"
    attributes = true
    dbxrefs = true
    pubmed_ids = true
    go_ids = true
    comments = true
  }
}
childers commented 7 years ago

The error looks the same. Is there a way to report the actual line that it is having problems with? --debug, --info and --stacktrace all give the same output.

$ ./apollo deploy --info 
javac 1.8.0_112 found
javac installed
JDK 1.8 found: javac 1.8.0_112

FAILURE: Build failed with an exception.

* Where:
Build file '/apollo_master/build.gradle' line: 80

* What went wrong:
A problem occurred evaluating root project 'nathanApolloMaster'.
> No signature of method: groovy.util.ConfigSlurper$_parse_closure5..() is applicable for argument types: (java.lang.Boolean) values: [false]
  Possible solutions: is(java.lang.Object), is(java.lang.Object), any(), any(), any(groovy.lang.Closure), use([Ljava.lang.Object;)

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 5.037 secs
***************************************
NOTE: Please set the memory for your servlet container (tomcat, jetty, etc.) or Apollo may not start correctly: http://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#suggested-tomcat-memory-settings
***************************************
nathandunn commented 7 years ago

You only end with a comma if you have another line, but you don't, you don't need to end with a comma. So for both blat cases you should end without the comma after the params. You only need the comma if you comment out tmp_dir

I'm also not sure if it works with the comment in there, but I suspect it does or I wouldn't have had that in the initial configuration.

nathandunn commented 7 years ago

so:

 blat_nuc: [
      search_exe: "/usr/local/bin/blat",
      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
      name: "Blat nucleotide",
      params: ""
    ],
    blat_prot: [
      search_exe: "/usr/local/bin/blat",
      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
      name: "Blat protein",
      params: ""
    ]
childers commented 7 years ago

Ok, then feel free to ignore my comment on the Configure.md changes. I'll get back to you momentarily.... ... I removed the commented line and the commas on the params[] lines and it failed again.

apollo {
  default_minimum_intron_size = 1
  history_size = 0
  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"
  track_name_comparator = "/config/track_name_comparator.js"
  use_cds_for_new_transcripts = true
  user_pure_memory_store = true
  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"
  is_partial_translation_allowed = false // unused so far
  get_translation_code = 1
  only_owners_delete = false
  sequence_search_tools = [
    blat_nuc: [
      search_exe: "/usr/local/bin/blat",
      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
      name: "Blat nucleotide",
      params: ""
    ],
    blat_prot: [
      search_exe: "/usr/local/bin/blat",
      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
      name: "Blat protein",
      params: ""
    ]
  ]

  splice_donor_sites = [ "GT" ]
  splice_acceptor_sites = [ "AG"]
  gff3.source= "." bootstrap = false

  info_editor = {
    feature_types = "default"
    attributes = true
    dbxrefs = true
    pubmed_ids = true
    go_ids = true
    comments = true
  }
}
childers commented 7 years ago

If I leave a part out, does it fall back to the built in defaults? If so I can start removing pieces until it starts working.

nathandunn commented 7 years ago

@childers That is exactly right. You only use apollo-config.groovy to override the defaults in Config.groovy

childers commented 7 years ago

Commenting this line out causes ./apollo deploy to work

  gff3.source= "." bootstrap = false
childers commented 7 years ago

Looks like that should be split into two lines after comparing to Config.groovy: Lines 312, 313: gff3.source= "." bootstrap = false

childers commented 7 years ago

patch for the updated verbiage here: https://github.com/GMOD/Apollo/compare/master...childers:patch-2

nathandunn commented 7 years ago

Awesome .. can this be closed?

childers commented 7 years ago

Thanks for hashing through the configuration example.

nathandunn commented 7 years ago

NP. Thanks for improving the doc.