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solgenomics / breedbase_dockerfile

The Dockerfiles for breeDBase
MIT License
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lynx result: HTTP request sent; waiting for response. #24

Closed billzt closed 3 years ago

billzt commented 3 years ago

I followed all the steps using docker composer, but Lynx shows:

HTTP request sent; waiting for response.

No changes in /var/log/sgn/error.log (many warnings but seems to have already existed)

Attempting to create directory /home/production/cxgn/local-lib
start_server (pid:216) starting now...
starting new worker 219
WWW::Form::UrlEncoded::XS 0.25 is require. fallback to PP version at /home/production/cxgn/local-lib/lib/perl5/x86_64-linux-gnu-thread-multi/WWW/Form/UrlEncoded.pm line 17.
Any::Moose is deprecated. Please use Moo instead at /home/production/cxgn/local-lib/lib/perl5/Config/JFDI.pm line 11.
"my" variable $exists masks earlier declaration in same scope at lib/CXGN/Stock.pm line 595.
Smartmatch is experimental at lib/SGN/Controller/Bulk.pm line 220.
"my" variable $q2 masks earlier declaration in same scope at lib/CXGN/Cross.pm line 923.
"my" variable $h2 masks earlier declaration in same scope at lib/CXGN/Cross.pm line 924.
Useless use of a constant ("searchResultsDbId") in void context at lib/CXGN/BrAPI/v1/Studies.pm line 116.
"my" variable @data_files masks earlier declaration in same scope at lib/CXGN/BrAPI/v1/ObservationTables.pm line 69.
"my" variable $page masks earlier declaration in same scope at lib/CXGN/BrAPI/v1/Images.pm line 114.
"my" variable $total_count masks earlier declaration in same scope at lib/CXGN/BrAPI/v1/Images.pm line 185.
"my" variable $total_count masks earlier declaration in same scope at lib/CXGN/BrAPI/v1/Images.pm line 395.
"my" variable $total_count masks earlier declaration in same scope at lib/CXGN/BrAPI/v2/Germplasm.pm line 449.
"my" variable $total_count masks earlier declaration in same scope at lib/CXGN/BrAPI/v2/Images.pm line 242.
Useless use of private variable in void context at lib/CXGN/BrAPI/v2/Observations.pm line 43.
Useless use of private variable in void context at lib/CXGN/BrAPI/v2/Observations.pm line 144.
"my" variable $include_timestamp masks earlier declaration in same scope at lib/CXGN/BrAPI/v2/Observations.pm line 369.
"my" variable @data_files masks earlier declaration in same scope at lib/CXGN/BrAPI/v2/ObservationTables.pm line 66.
"my" variable @data_files masks earlier declaration in same scope at lib/CXGN/BrAPI/v2/ObservationTables.pm line 149.
"my" variable $folder masks earlier declaration in same scope at lib/CXGN/BrAPI/v2/Trials.pm line 269.
"my" variable $folder_id masks earlier declaration in same scope at lib/CXGN/BrAPI/v2/Trials.pm line 274.
"my" variable $breeding_program_id masks earlier declaration in same scope at lib/CXGN/BrAPI/v2/Trials.pm line 276.
"my" variable @server_permission masks earlier declaration in same scope at lib/SGN/Controller/AJAX/BrAPI.pm line 202.
Smartmatch is experimental at lib/SGN/Controller/AJAX/Cross.pm line 542.
Smartmatch is experimental at lib/SGN/Controller/AJAX/Cross.pm line 548.
Smartmatch is experimental at lib/SGN/Controller/AJAX/Cross.pm line 554.
Smartmatch is experimental at lib/SGN/Controller/AJAX/Cross.pm line 560.
Smartmatch is experimental at lib/SGN/Controller/AJAX/Cross.pm line 566.
Smartmatch is experimental at lib/SGN/Controller/AJAX/Cross.pm line 572.
"my" variable $total_count masks earlier declaration in same scope at lib/SGN/Controller/AJAX/Image.pm line 431.
Unrecognized escape \k passed through at lib/solGS/AnalysisReport.pm line 484.
False [] range "+-\d" in regex; marked by <-- HERE in m/[\d+-\d <-- HERE +]/ at lib/SGN/Controller/solGS/Utils.pm line 121.
"my" variable $protocol_url masks earlier declaration in same scope at lib/SGN/Controller/solGS/solGS.pm line 826.
"my" variable $identifier masks earlier declaration in same scope at lib/SGN/Controller/solGS/solGS.pm line 837.
"my" variable $gebvs_file masks earlier declaration in same scope at lib/SGN/Controller/solGS/solGS.pm line 839.
Useless use of private array in void context at lib/SGN/Controller/solGS/solGS.pm line 1311.
Unrecognized escape \s passed through at lib/SGN/Controller/solGS/solGS.pm line 2409.
Possible attempt to separate words with commas at lib/SGN/Controller/solGS/Anova.pm line 171.
"my" variable $cache_data masks earlier declaration in same scope at lib/SGN/Controller/solGS/Files.pm line 267.
"my" variable $cache_data masks earlier declaration in same scope at lib/SGN/Controller/solGS/Files.pm line 298.
"my" variable $people_schema masks earlier declaration in same scope at lib/SGN/Controller/AJAX/Solgwas.pm line 64.
"my" variable $schema masks earlier declaration in same scope at lib/SGN/Controller/AJAX/Solgwas.pm line 65.
"my" variable $figure2file masks earlier declaration in same scope at lib/SGN/Controller/AJAX/Solgwas.pm line 269.
Odd number of elements in anonymous hash at /home/production/cxgn/local-lib/lib/perl5/Catalyst/Component.pm line 132.
Smartmatch is experimental at lib/SGN/Controller/solGS/Download.pm line 179.
require SGN::Controller::MetabolomicsHost was successful but the package is not defined. at /home/production/cxgn/local-lib/lib/perl5/Catalyst/Utils.pm line 315.
"my" variable $people_schema masks earlier declaration in same scope at lib/SGN/Controller/AJAX/Heritability.pm line 47.
"my" variable $schema masks earlier declaration in same scope at lib/SGN/Controller/AJAX/Heritability.pm line 48.
"my" variable $figure_path masks earlier declaration in same scope at lib/SGN/Controller/AJAX/Heritability.pm line 182.
Overwriting existing sub 'CXGN::Trial::FieldMap::after' with sub 'after' exported by List::MoreUtils at lib/CXGN/Trial/FieldMap.pm line 11.
Overwriting existing sub 'CXGN::Trial::FieldMap::before' with sub 'before' exported by List::MoreUtils at lib/CXGN/Trial/FieldMap.pm line 11.
Overwriting existing sub 'CXGN::Phenotypes::TrialPhenotype::after' with sub 'after' exported by List::MoreUtils at lib/CXGN/Phenotypes/TrialPhenotype.pm line 33.
Overwriting existing sub 'CXGN::Phenotypes::TrialPhenotype::before' with sub 'before' exported by List::MoreUtils at lib/CXGN/Phenotypes/TrialPhenotype.pm line 33.
Overwriting existing sub 'SGN::Controller::AJAX::TrialMetadata::any' with sub 'any' exported by List::MoreUtils at lib/SGN/Controller/AJAX/TrialMetadata.pm line 24.
Overwriting existing sub 'SGN::Controller::AJAX::TrialMetadata::after' with sub 'after' exported by List::MoreUtils at lib/SGN/Controller/AJAX/TrialMetadata.pm line 24.
Prototype mismatch: sub SGN::Controller::AJAX::TrialMetadata::qsort (&\@) vs none at lib/SGN/Controller/AJAX/TrialMetadata.pm line 32.
Prototype mismatch: sub SGN::Controller::AJAX::TrialMetadata::bsearch (&@) vs none at lib/SGN/Controller/AJAX/TrialMetadata.pm line 32.
Smartmatch is experimental at lib/SGN/Controller/solGS/CachedResult.pm line 250.
Useless use of sort in scalar context at lib/SGN/Controller/solGS/CachedResult.pm line 251.
Useless use of sort in scalar context at lib/SGN/Controller/solGS/CachedResult.pm line 251.
Smartmatch is experimental at lib/SGN/Controller/AJAX/BreedingProgram.pm line 664.
"my" variable $common_traits masks earlier declaration in same scope at lib/SGN/Controller/solGS/combinedTrials.pm line 1334.
"my" variable $q4 masks earlier declaration in same scope at lib/SGN/Controller/AJAX/DroneImagery/DroneImagery.pm line 11571.
"my" variable $h4 masks earlier declaration in same scope at lib/SGN/Controller/AJAX/DroneImagery/DroneImagery.pm line 11585.
require SGN::Controller::BreedersToolbox::TrialComparison was successful but the package is not defined. at /home/production/cxgn/local-lib/lib/perl5/Catalyst/Utils.pm line 315.
require SGN::Controller::AJAX::BreedersToolbox::GraphicalFilteringAJAX was successful but the package is not defined. at /home/production/cxgn/local-lib/lib/perl5/Catalyst/Utils.pm line 315.
CURRENT USER IDS: 0, 0
TEMP_SUBDIR: /home/production/cxgn/sgn/static/documents/tempfiles
TEMP_BASE: /home/production/tmp/breedbase-site
symlinking tempfiles_base '/home/production/tmp/breedbase-site' -> legacy location '/home/production/cxgn/sgn/static/documents/tempfiles'
Successfully created dir /home/production/tmp/breedbase-site.
CHOWNING WITH 33, 33
CHOWNING WITH 33, 33
rm: cannot remove 'build/': No such file or directory
npm WARN deprecated @babel/polyfill@7.12.1: 🚨 This package has been deprecated in favor of separate inclusion of a polyfill and regenerator-runtime (when needed). See the @babel/polyfill docs (ht
npm WARN deprecated uglify-es@3.3.9: support for ECMAScript is superseded by `uglify-js` as of v3.13.0
npm WARN deprecated request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3
npm WARN deprecated request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
npm WARN deprecated core-js@2.6.12: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-j
npm WARN deprecated har-validator@5.1.5: this library is no longer supported
npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node v14+. Upgrade to chokidar 3 with 15x less dependencies.
npm WARN deprecated fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
npm WARN deprecated resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
npm WARN deprecated urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
(END)
billzt commented 3 years ago

After a long time (~1 hour), the web could be open:

Caught exception in SGN::Controller::Root->auto "DBI connect('dbname=XXX;host=breedbase_db;port=5432','XXX',...) failed: could not translate host name "breedbase_db" to address: Temporary failure in name resolution at /home/production/cxgn/local-lib/lib/perl5/DBIx/Connector.pm line 32."
billzt commented 3 years ago

After manually turn on the database and set dbname, it has been fixed.