Script to get bibliography for (all) dandisets (prototype) #1449
Conversation
sandbox/dandi.bib
Outdated
|
|
||
|
|
||
| # DANDISET 000029 | ||
| <!DOCTYPE html> |
There was a problem hiding this comment.
Ho ho -- we might be identifying problems for dandisets where we have releases and DOI minting has failed! someone might need to look into that!
There was a problem hiding this comment.
filed
Meanwhile will adjust script to skip those
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1449 +/- ##
==========================================
+ Coverage 88.47% 88.65% +0.18%
==========================================
Files 77 78 +1
Lines 10518 10589 +71
==========================================
+ Hits 9306 9388 +82
+ Misses 1212 1201 -11
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
| url = {https://dandiarchive.org/dandiset/000404/0.230605.2024}, | ||
| author = {Athalye, Vivek R and Khanna, Preeya and Gowda, Suraj and Orsborn, Amy L and Costa, Rui M and Carmena, Jose M}, | ||
| keywords = {neural population dynamics, motor cortex, motor control, brain-machine interface, neuroprosthetics, optimal feedback control, motor commands, movement representations, dynamical systems}, | ||
| title = {Monkey 2D cursor BMI}, |
There was a problem hiding this comment.
apparently data.crosscite.org is not doing that great of a job here -- for BibTeX it ideally should have made it into
| title = {Monkey 2D cursor BMI}, | |
| title = {Monkey {2D} cursor {BMI}}, |
to prevent LaTeX lower casing them... now we just need to figure out where is that code to file a complaint :-/
There was a problem hiding this comment.
the easiest of cause IIRC is just to double {} it ie
| title = {Monkey 2D cursor BMI}, | |
| title = {{Monkey 2D cursor BMI}}, |
and in principle we could do that ourselves here after someone confirms that my concern here is correct
attn @TheChymera as who might know and @bendichter as who might care ;-)
| # for dandiset in [{'identifier': '000027', 'most_recent_published_version': | ||
| # {'version': '0.210831.2033'}}]: |
Check notice
Code scanning / CodeQL
Commented-out code Note
|
|
||
| # OUTPUT BibTeX | ||
| try: | ||
| out = open(args.bibtex, "w") if args.bibtex else sys.stdout |
Check warning
Code scanning / CodeQL
File is not always closed Warning
| datacite_records = [] | ||
| for m in metadata_records: | ||
| try: | ||
| datacite_record = to_datacite(m) |
Check failure
Code scanning / CodeQL
Potentially uninitialized local variable Error
| try: | ||
| datacite_record = to_datacite(m) | ||
| try: | ||
| validate_datacite(datacite_record) |
Check failure
Code scanning / CodeQL
Potentially uninitialized local variable Error
| datacite_record = to_datacite(m) | ||
| try: | ||
| validate_datacite(datacite_record) | ||
| except JSONValidationError as exc: |
Check failure
Code scanning / CodeQL
Potentially uninitialized local variable Error
| "schema_path": list(exc.schema_path), | ||
| } | ||
| datacite_errors[m["identifier"]].append(error_rec) | ||
| except ValidationError as exc: |
Check failure
Code scanning / CodeQL
Potentially uninitialized local variable Error
a follow up to @bendichter 's
I think this is a viable prototype with some TODOs (provided in the script) for us to collate/update an ultimate DANDI bibliography (as bibtex). WDYT?
Also includes the
dandi.bibwhich script produced.Related: