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Unable to access PMC BioC service #4556

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reckart opened this issue Feb 24, 2024 · 0 comments
Closed

Unable to access PMC BioC service #4556

reckart opened this issue Feb 24, 2024 · 0 comments
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@reckart
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🐛Bug Something isn't working Module: PubMed/PMC Requires upstream changes
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Milestone
31.2

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@reckart
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reckart commented Feb 24, 2024

Describe the bug
When trying to access the PMC BioC service to download texts, we get a 500 server error.

To Reproduce
Steps to reproduce the behavior:

  1. Try accessing http://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_xml/PMC7096989/unicode

Expected behavior
Should work

Please complete the following information:

  • Version and build ID: 31.1
@reckart reckart added this to the 31.2 milestone Feb 24, 2024
@reckart reckart added this to 🔖 To do in Kanban via automation Feb 24, 2024
@reckart reckart self-assigned this Feb 24, 2024
reckart added a commit that referenced this issue Feb 24, 2024
@reckart
#4556 - Unable to access PMC BioC service
72ee5a7 
- Disable tests that try to obtain BioC from PMC since the service seems to be broken
reckart added a commit that referenced this issue Feb 24, 2024
@reckart
Merge branch 'release/31.x'
1a90912 
* release/31.x:
  #4556 - Unable to access PMC BioC service
reckart added a commit that referenced this issue Feb 24, 2024
@reckart
Merge branch 'main' into feature/4554-Allow-displaying-comments-from-…
528107a 
…annotators-on-hover-when-curating-using-curation-sidebar-on-the-annotation-page

* main:
  #4556 - Unable to access PMC BioC service
reckart added a commit that referenced this issue Feb 25, 2024
@reckart
Merge branch 'main' into refactoring/Upgrade-to-Spring-Boot-3
7b03898 
* main: (95 commits)
  #4556 - Unable to access PMC BioC service
  #4554 - Allow displaying comments from annotators on hover when curating using curation sidebar on the annotation page
  #4552 - No details shown when hovering over annotations in lower part of the curation page
  #4550 - Clean up code
  #4550 - Clean up code
  #4547 - Cannot create long-distance relation in PDF editor
  #4545 - Upgrade dependencies
  #4545 - Upgrade dependencies
  #4543 - UI for creating new concept or properties has broken layout
  #4541 - Upgrade dependencies
  #4538 - Lazy details and selecting annotations my break after opening a read-only document and not performing actions for a short time
  #4537 - Ability to group annotations by layer
  #4533 - BioC exported from INCEpTION cannot be imported again due to missing mandatory metadata
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-31.1
  #4530 - Keyboard shortcuts for feature values may not work in certain editors
  #4528 - Display key bindings in radio group string feature editor
  #4525 - Support recommendations for non-string primitive features
  #4523 - Factor endpoint-specific FTS code out into adapter classes
  #4523 - Factor endpoint-specific FTS code out into adapter classes
  ...

% Conflicts:
%	inception/inception-dependencies/pom.xml
%	inception/inception-imls-weblicht/pom.xml
%	inception/inception-kb/src/main/java/de/tudarmstadt/ukp/inception/kb/KnowledgeBaseServiceImpl.java
%	inception/inception-project-export/src/test/resources/log4j2-test.xml
%	inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/PredictionTask.java
%	inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/SelectionTask.java
%	inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/TrainingTask.java
%	inception/inception-ui-curation/pom.xml
%	inception/inception-ui-dashboard-activity/pom.xml
%	inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/initializers/NamedEntityIdentifierFeatureInitializer.java
%	inception/inception-ui-scheduling/pom.xml
%	inception/inception-ui-scheduling/src/main/java/de/tudarmstadt/ukp/inception/ui/scheduling/TaskMonitorPanel.java
%	pom.xml
reckart added a commit that referenced this issue Mar 2, 2024
@reckart
#4556 - Unable to access PMC BioC service
4631370 
- Re-enable tests
reckart added a commit that referenced this issue Mar 4, 2024
@reckart
- #4556 - Unable to access PMC BioC service
215083f 
- Fix PubAnnotation document access
- Re-enable tests
reckart added a commit that referenced this issue Mar 4, 2024
@reckart
Merge pull request #4575 from inception-project/bugfix/4556-Unable-to…
e0f2141 
…-access-PMC-BioC-service

#4556 - Unable to access PMC BioC service
@reckart reckart closed this as completed Mar 4, 2024
Kanban automation moved this from 🔖 To do to 🍹 Done Mar 4, 2024
reckart added a commit that referenced this issue Mar 4, 2024
@reckart
Merge branch 'release/31.x'
315a92d 
* release/31.x:
  - #4556 - Unable to access PMC BioC service
  #4587 - Annotations are misaligned when PDF pages vary in dimensions
  #4556 - Unable to access PMC BioC service
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@reckart reckart

Labels
🐛Bug Something isn't working Module: PubMed/PMC Requires upstream changes
Projects
Kanban
  
🍹 Done
Milestone
31.2
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@reckart