Closed Borda closed 2 years ago
This was caused by the switch to the new converter. I have reverted the change until we are sure that things work as expected.
Thank you for the report and apologies for the inconvenience.
just for the record, the revert was done in 2ea66a08ee0ff4bc4baa1cb442d81fde35faf447
Hi,
I think I might be hitting the same issue. I get a Build Draft PDF fail. The full output is: Run openjournals/openjournals-draft-action@master with: journal: joss paper-path: paper.md /usr/bin/docker run --name openjournalsinaralatest_af3d73 --label 29a95e --workdir /github/workspace --rm -e INPUT_JOURNAL -e INPUT_PAPER-PATH -e GIT_SHA -e JOURNAL -e HOME -e GITHUB_JOB -e GITHUB_REF -e GITHUB_SHA -e GITHUB_REPOSITORY -e GITHUB_REPOSITORY_OWNER -e GITHUB_RUN_ID -e GITHUB_RUN_NUMBER -e GITHUB_RETENTION_DAYS -e GITHUB_RUN_ATTEMPT -e GITHUB_ACTOR -e GITHUB_WORKFLOW -e GITHUB_HEAD_REF -e GITHUB_BASE_REF -e GITHUB_EVENT_NAME -e GITHUB_SERVER_URL -e GITHUB_API_URL -e GITHUB_GRAPHQL_URL -e GITHUB_REF_NAME -e GITHUB_REF_PROTECTED -e GITHUB_REF_TYPE -e GITHUB_WORKSPACE -e GITHUB_ACTION -e GITHUB_EVENT_PATH -e GITHUB_ACTION_REPOSITORY -e GITHUB_ACTION_REF -e GITHUB_PATH -e GITHUB_ENV -e GITHUB_STEP_SUMMARY -e RUNNER_OS -e RUNNER_ARCH -e RUNNER_NAME -e RUNNER_TOOL_CACHE -e RUNNER_TEMP -e RUNNER_WORKSPACE -e ACTIONS_RUNTIME_URL -e ACTIONS_RUNTIME_TOKEN -e ACTIONS_CACHE_URL -e GITHUB_ACTIONS=true -e CI=true -v "/var/run/docker.sock":"/var/run/docker.sock" -v "/home/runner/work/_temp/_github_home":"/github/home" -v "/home/runner/work/_temp/_github_workflow":"/github/workflow" -v "/home/runner/work/_temp/_runner_file_commands":"/github/file_commands" -v "/home/runner/work/ccg-v3d/ccg-v3d":"/github/workspace" openjournals/inara:latest "-o pdf" "paper.md" [INFO] Running filter /usr/local/share/openjournals/data/filters/inline-cited-references.lua [INFO] Loaded paper.bib from paper.bib [INFO] Completed filter /usr/local/share/openjournals/data/filters/inline-cited-references.lua in 8 ms [INFO] Loaded apa.csl from /usr/local/share/openjournals/apa.csl [INFO] Running filter /usr/local/share/openjournals/data/filters/add-images.lua [INFO] Loaded joss/aas-logo.png from /usr/local/share/openjournals/joss/aas-logo.png [INFO] Loaded joss/logo.png from /usr/local/share/openjournals/joss/logo.png [INFO] Completed filter /usr/local/share/openjournals/data/filters/add-images.lua in 4 ms [INFO] Running filter /usr/local/share/openjournals/data/filters/normalize-metadata.lua Error running filter /usr/local/share/openjournals/data/filters/normalize-metadata.lua: ...al/share/openjournals/data/filters/normalize/authors.lua:68: attempt to index a nil value (field 'name') stack traceback: ...l/share/openjournals/data/filters/normalize-metadata.lua:56: in function 'Meta'
Do you have any advice?
Thanks,
Andy
@agdturner The issue is in the affiliations
field. Please remove the dash before index
, i.e., replace
affiliations:
- name: CCG, School of Geography, University of Leeds
- index: 1
with
affiliations:
- name: CCG, School of Geography, University of Leeds
index: 1
Thanks @tarleb, but I made the change and things seem to have got a bit further, but I still get a Build Draft PDF fail with the output appearing as follows: Run openjournals/openjournals-draft-action@master /usr/bin/docker run --name openjournalsinaralatest_f54a97 --label 29a95e --workdir /github/workspace --rm -e INPUT_JOURNAL -e INPUT_PAPER-PATH -e GIT_SHA -e JOURNAL -e HOME -e GITHUB_JOB -e GITHUB_REF -e GITHUB_SHA -e GITHUB_REPOSITORY -e GITHUB_REPOSITORY_OWNER -e GITHUB_RUN_ID -e GITHUB_RUN_NUMBER -e GITHUB_RETENTION_DAYS -e GITHUB_RUN_ATTEMPT -e GITHUB_ACTOR -e GITHUB_WORKFLOW -e GITHUB_HEAD_REF -e GITHUB_BASE_REF -e GITHUB_EVENT_NAME -e GITHUB_SERVER_URL -e GITHUB_API_URL -e GITHUB_GRAPHQL_URL -e GITHUB_REF_NAME -e GITHUB_REF_PROTECTED -e GITHUB_REF_TYPE -e GITHUB_WORKSPACE -e GITHUB_ACTION -e GITHUB_EVENT_PATH -e GITHUB_ACTION_REPOSITORY -e GITHUB_ACTION_REF -e GITHUB_PATH -e GITHUB_ENV -e GITHUB_STEP_SUMMARY -e RUNNER_OS -e RUNNER_ARCH -e RUNNER_NAME -e RUNNER_TOOL_CACHE -e RUNNER_TEMP -e RUNNER_WORKSPACE -e ACTIONS_RUNTIME_URL -e ACTIONS_RUNTIME_TOKEN -e ACTIONS_CACHE_URL -e GITHUB_ACTIONS=true -e CI=true -v "/var/run/docker.sock":"/var/run/docker.sock" -v "/home/runner/work/_temp/_github_home":"/github/home" -v "/home/runner/work/_temp/_github_workflow":"/github/workflow" -v "/home/runner/work/_temp/_runner_file_commands":"/github/file_commands" -v "/home/runner/work/ccg-v3d/ccg-v3d":"/github/workspace" openjournals/inara:latest "-o pdf" "paper.md" [INFO] Running filter /usr/local/share/openjournals/data/filters/inline-cited-references.lua [INFO] Loaded paper.bib from paper.bib [INFO] Completed filter /usr/local/share/openjournals/data/filters/inline-cited-references.lua in 10 ms [INFO] Loaded apa.csl from /usr/local/share/openjournals/apa.csl [INFO] Running filter /usr/local/share/openjournals/data/filters/add-images.lua [INFO] Loaded joss/aas-logo.png from /usr/local/share/openjournals/joss/aas-logo.png [INFO] Loaded joss/logo.png from /usr/local/share/openjournals/joss/logo.png [INFO] Completed filter /usr/local/share/openjournals/data/filters/add-images.lua in 5 ms [INFO] Running filter /usr/local/share/openjournals/data/filters/normalize-metadata.lua Error running filter /usr/local/share/openjournals/data/filters/normalize-metadata.lua: ...al/share/openjournals/data/filters/normalize/authors.lua:68: attempt to index a nil value (field 'name') stack traceback: ...l/share/openjournals/data/filters/normalize-metadata.lua:56: in function 'Meta'
Is there something else I must do?
That's weird, and I'm not sure I understand: The builds at https://github.com/agdturner/ccg-v3d/actions appear to succeed now. Where and how do you run the action?
I think I am running the action on GitHub infrastructure by selecting the workflow draft-pdf.yml and pressing Re-run all jobs. It is the Build draft PDF part that seems fails...
OK, I see. This re-runs the job with the specific commit that was testes, not with the latest commit. There were no changes to the GitHub Action, so the job will continue to fail for that commit. Jobs running on the latest paper version succeed as expected: https://github.com/agdturner/ccg-v3d/actions/runs/1980248251
Thank you for your help @tarleb. It seems it wasn't working they way I thought it would, but I am assuming all is fine. (I had expected the paper.pdf to appear in the repository, but it seems it gets deleted as part of the workflow which is no worries). All the best from Leeds in the UK :)
The compiled PDF can be downloaded as an artifact from the workflow, e.g. here. I believe it would be possible to modify the workflow such that the PDF would be added to the repo; you'd need to amend the workflow steps
with something along the lines of
- name: add paper.pdf
run: git add paper.pdf
- name: commit changes
run: git commit -m 'Update paper.pdf'
- name: push changes to repo
run: git push origin
I didn't try it though, there may be unexpected things getting in the way. E.g., this could lead to an endless loop where the paper is recompiled repeatedly.
Hello, I believe that #5 was implemented in 4a10348f3a5ed042fb12cd18c3d18ea246532848 and just after our paper builds start to fail, also checked with our master that using the listed action does not compile... Is this expected to happen?
discovered while updating our JOSS draft in https://github.com/PyTorchLightning/metrics/pull/819