Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Unable to access PMC BioC service #4556

Closed
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
Assignees
@reckart
Labels
🐛 Bug Something isn't working Module: PubMed/PMC Requires upstream changes
Milestone
31.2

Comments

@reckart
Copy link
Member

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 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
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
@reckart reckart added this to Kanban Aug 7, 2024
@reckart reckart moved this to 🍹 Done in Kanban Aug 7, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@reckart reckart

Labels
🐛 Bug Something isn't working Module: PubMed/PMC Requires upstream changes
Projects
Kanban
Archived in project
Milestone
31.2
Development

No branches or pull requests
1 participant
@reckart