Branch: refs/heads/master
Home: https://github.com/PathwayCommons/factoid
Commit: 349eda716ca707a4fb97a210ac27ebd507bb9619
https://github.com/PathwayCommons/factoid/commit/349eda716ca707a4fb97a210ac27ebd507bb9619
Author: Jeffrey <[email protected]>
Date: 2024-07-26 (Fri, 26 Jul 2024)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
Merge pull request #1290 from PathwayCommons/v0.31.0
v0.31.0
Commit: 9213bf6b30104280a4c9e2303abaa072c349d512
https://github.com/PathwayCommons/factoid/commit/9213bf6b30104280a4c9e2303abaa072c349d512
Author: fileoy <[email protected]>
Date: 2024-07-29 (Mon, 29 Jul 2024)
Changed paths:
M src/model/hint.js
A test/pubtator/10.1016_j.molcel.2019.03.023.json
A test/pubtator/10.1016_j.molcel.2024.01.007.json
A test/pubtator/10.1038_s41556-021-00642-9.json
A test/pubtator/10.1126_scisignal.abf3535.json
A test/pubtator/10.15252_embj.2023113616.json
A test/pubtator/pubtator.js
Log Message:
-----------
first commit
Commit: e9e05e450bbc3cd620b60921b3821d19b02a3b76
https://github.com/PathwayCommons/factoid/commit/e9e05e450bbc3cd620b60921b3821d19b02a3b76
Author: Faisal Alkulaib <[email protected]>
Date: 2024-07-31 (Wed, 31 Jul 2024)
Changed paths:
M src/model/hint.js
A test/pubtator/10.1016_j.molcel.2019.03.023.json
A test/pubtator/10.1016_j.molcel.2024.01.007.json
A test/pubtator/10.1038_s41556-021-00642-9.json
A test/pubtator/10.1126_scisignal.abf3535.json
A test/pubtator/10.15252_embj.2023113616.json
A test/pubtator/pubtator.js
Log Message:
-----------
Merge pull request #1292 from PathwayCommons/iss1148_organism-hints-tests
Testing organism hints
Commit: 80ddd831b7cb731a3baa99df549fa566e0b47484
https://github.com/PathwayCommons/factoid/commit/80ddd831b7cb731a3baa99df549fa566e0b47484
Author: fileoy <[email protected]>
Date: 2024-07-31 (Wed, 31 Jul 2024)
Changed paths:
A test/pubtator/map.js
M test/pubtator/pubtator.js
Log Message:
-----------
Testing organism hints mapper for BioC documents.
The mapper return an array of arryays,
- where the first array is the hints extracted from the title,
- and the second array is the hints extracted from the abstract.
each hint is a normailzed id of the organism.
Commit: 567f0264d23f0b4dfed88b4a6e24f2746507ab60
https://github.com/PathwayCommons/factoid/commit/567f0264d23f0b4dfed88b4a6e24f2746507ab60
Author: fileoy <[email protected]>
Date: 2024-08-04 (Sun, 04 Aug 2024)
Changed paths:
M src/model/hint.js
A src/server/routes/api/document/hint/pubtator.js
A src/util/registry.js
R test/pubtator/map.js
M test/pubtator/pubtator.js
Log Message:
-----------
Tested the map function in the pubtator.js file.
It detects organism hints ONLY. It does not detect other hints YET.
Commit: d733b4b4ad739f648a3c6ea0016af55c042e2392
https://github.com/PathwayCommons/factoid/commit/d733b4b4ad739f648a3c6ea0016af55c042e2392
Author: fileoy <[email protected]>
Date: 2024-08-07 (Wed, 07 Aug 2024)
Changed paths:
M src/model/hint.js
M src/server/routes/api/document/hint/pubtator.js
M test/pubtator/10.1016_j.molcel.2019.03.023.json
R test/pubtator/10.1016_j.molcel.2024.01.007.json
M test/pubtator/10.1038_s41556-021-00642-9.json
M test/pubtator/10.1126_scisignal.abf3535.json
M test/pubtator/10.15252_embj.2023113616.json
M test/pubtator/pubtator.js
A test/pubtator/pubtator_8.json
Log Message:
-----------
// Content:
- Some tweaks to the hint model
- Added a new test case for hints mapper
- added a new JSON file with many-to-many organism's hints
Commit: a491ddf33b556fcd1e8a6a582535cfe0533391ae
https://github.com/PathwayCommons/factoid/commit/a491ddf33b556fcd1e8a6a582535cfe0533391ae
Author: fileoy <[email protected]>
Date: 2024-08-08 (Thu, 08 Aug 2024)
Changed paths:
M test/pubtator/pubtator.js
Log Message:
-----------
.
Commit: d0c02d4399114d89b4d949a241f4d5701b894d01
https://github.com/PathwayCommons/factoid/commit/d0c02d4399114d89b4d949a241f4d5701b894d01
Author: fileoy <[email protected]>
Date: 2024-08-08 (Thu, 08 Aug 2024)
Changed paths:
M test/pubtator/pubtator.js
Log Message:
-----------
typo
Commit: dbd1ca0b5468ff03a77defe523d8cb6bedd1b145
https://github.com/PathwayCommons/factoid/commit/dbd1ca0b5468ff03a77defe523d8cb6bedd1b145
Author: Jeffrey <[email protected]>
Date: 2024-08-08 (Thu, 08 Aug 2024)
Changed paths:
M src/model/hint.js
A src/server/routes/api/document/hint/pubtator.js
A src/util/registry.js
M test/pubtator/10.1016_j.molcel.2019.03.023.json
R test/pubtator/10.1016_j.molcel.2024.01.007.json
M test/pubtator/10.1038_s41556-021-00642-9.json
M test/pubtator/10.1126_scisignal.abf3535.json
M test/pubtator/10.15252_embj.2023113616.json
M test/pubtator/pubtator.js
A test/pubtator/pubtator_8.json
Log Message:
-----------
Merge pull request #1293 from PathwayCommons/iss1148_testing-hints-mapper
Testing organism hints mapper for BioC documents.
Commit: 4c77a8bc2c783c6f74dcb13f89382ad1870fa4e2
https://github.com/PathwayCommons/factoid/commit/4c77a8bc2c783c6f74dcb13f89382ad1870fa4e2
Author: fileoy <[email protected]>
Date: 2024-08-08 (Thu, 08 Aug 2024)
Changed paths:
M src/model/hint.js
M src/server/routes/api/document/hint/pubtator.js
M src/util/registry.js
A test/pubtator/10.1016_j.molcel.2016.11.034.json
A test/pubtator/10.1016_j.molcel.2019.04.005.json
A test/pubtator/10.1016_j.molcel.2024.01.007.json
M test/pubtator/pubtator.js
M test/pubtator/pubtator_8.json
Log Message:
-----------
// Contents:
- Now it accepts all hint types from PubTator rather than just organisms. e.g.
genes, cell lines, diseases, chemicals
- Added tests for the new hint types.
- Updated the hint model to accept all hint types.
Commit: 47880d9ab103b86af78b994afa34fd979a7cab8c
https://github.com/PathwayCommons/factoid/commit/47880d9ab103b86af78b994afa34fd979a7cab8c
Author: fileoy <[email protected]>
Date: 2024-08-08 (Thu, 08 Aug 2024)
Changed paths:
M test/pubtator/pubtator.js
Log Message:
-----------
typo
Commit: c33831e3541db8d47cae9e5fbe44c17850dfa872
https://github.com/PathwayCommons/factoid/commit/c33831e3541db8d47cae9e5fbe44c17850dfa872
Author: fileoy <[email protected]>
Date: 2024-08-08 (Thu, 08 Aug 2024)
Changed paths:
M src/server/routes/api/document/hint/pubtator.js
Log Message:
-----------
fixed logic error
Commit: 0db77393c2139f8e322917313454ccb724b3c723
https://github.com/PathwayCommons/factoid/commit/0db77393c2139f8e322917313454ccb724b3c723
Author: fileoy <[email protected]>
Date: 2024-08-09 (Fri, 09 Aug 2024)
Changed paths:
M src/model/hint.js
M test/pubtator/pubtator.js
Log Message:
-----------
// Content:
- hint model constructor modified to use setters to initialize properties and
enforce validation
- pubtator test updated to use new getter methods to access hint properties
rather than direct access to properties
Commit: 38e475973773c8ad1691bbd95f88dec017c36501
https://github.com/PathwayCommons/factoid/commit/38e475973773c8ad1691bbd95f88dec017c36501
Author: Faisal Alkulaib <[email protected]>
Date: 2024-08-09 (Fri, 09 Aug 2024)
Changed paths:
M src/model/hint.js
M src/server/routes/api/document/hint/pubtator.js
M src/util/registry.js
A test/pubtator/10.1016_j.molcel.2016.11.034.json
A test/pubtator/10.1016_j.molcel.2019.04.005.json
A test/pubtator/10.1016_j.molcel.2024.01.007.json
M test/pubtator/pubtator.js
M test/pubtator/pubtator_8.json
Log Message:
-----------
Merge pull request #1294 from PathwayCommons/iss1148_all-hint-types
Expanding hints scope
Commit: e4ebd49610f38794f6137fa6be0af97516de6ca8
https://github.com/PathwayCommons/factoid/commit/e4ebd49610f38794f6137fa6be0af97516de6ca8
Author: fileoy <[email protected]>
Date: 2024-08-12 (Mon, 12 Aug 2024)
Changed paths:
M README.md
M src/config.js
M src/server/routes/api/document/hint/pubtator.js
M test/pubtator/pubtator.js
Log Message:
-----------
// Contents:
- PubTator API path is now configurable
- get a BioCDocument from the PubTator
- A simple wrapper to retrieve Hints from PubTator
Commit: c4fc849824d96f7a4c705bc01eacd4ef50d12fb2
https://github.com/PathwayCommons/factoid/commit/c4fc849824d96f7a4c705bc01eacd4ef50d12fb2
Author: Jeffrey Wong <[email protected]>
Date: 2024-08-14 (Wed, 14 Aug 2024)
Changed paths:
M test/pubtator/pubtator.js
Log Message:
-----------
Test the rejected get case.
Commit: 5c2cdcc460457973a55e7621b7d17e00004aa830
https://github.com/PathwayCommons/factoid/commit/5c2cdcc460457973a55e7621b7d17e00004aa830
Author: Jeffrey <[email protected]>
Date: 2024-08-14 (Wed, 14 Aug 2024)
Changed paths:
M README.md
M src/config.js
M src/server/routes/api/document/hint/pubtator.js
M test/pubtator/pubtator.js
Log Message:
-----------
Merge pull request #1296 from PathwayCommons/iss1148_fetch-hints
Fetch hints
Commit: b4bcafd411618c3091d90d7334a20c425ee82edb
https://github.com/PathwayCommons/factoid/commit/b4bcafd411618c3091d90d7334a20c425ee82edb
Author: Jeffrey Wong <[email protected]>
Date: 2024-10-30 (Wed, 30 Oct 2024)
Changed paths:
A src/util/article.js
A test/util/article.js
Log Message:
-----------
Initial test cases - plain alphabetical and punctuation.
Commit: 2c5de2a4574f2f4f9f7b3ceb41a5ea9d38b55727
https://github.com/PathwayCommons/factoid/commit/2c5de2a4574f2f4f9f7b3ceb41a5ea9d38b55727
Author: Jeffrey Wong <[email protected]>
Date: 2024-10-30 (Wed, 30 Oct 2024)
Changed paths:
M package-lock.json
M package.json
M src/util/article.js
M test/util/article.js
Log Message:
-----------
Strip HTML formatting tags and take into account dashes
Commit: 757c02b1ab6e2273f183c7adea138a0ed3006f39
https://github.com/PathwayCommons/factoid/commit/757c02b1ab6e2273f183c7adea138a0ed3006f39
Author: Jeffrey Wong <[email protected]>
Date: 2024-10-31 (Thu, 31 Oct 2024)
Changed paths:
M src/util/article.js
M test/util/article.js
Log Message:
-----------
debur characters as Medline supports this.
Commit: 696aee932123fe9e79957f80760534e9a9dee5bd
https://github.com/PathwayCommons/factoid/commit/696aee932123fe9e79957f80760534e9a9dee5bd
Author: Jeffrey Wong <[email protected]>
Date: 2024-10-31 (Thu, 31 Oct 2024)
Changed paths:
M test/util/article.js
Log Message:
-----------
Negative controls, cases where pubmed or crossref are flaky (web search
differs from web service)
Commit: 7c40d9b09248c75e1dd3f67b3b7d481ca3666bfd
https://github.com/PathwayCommons/factoid/commit/7c40d9b09248c75e1dd3f67b3b7d481ca3666bfd
Author: Jeffrey Wong <[email protected]>
Date: 2024-10-31 (Thu, 31 Oct 2024)
Changed paths:
M src/server/routes/api/document/crossref/works.js
M src/server/routes/api/document/pubmed/index.js
Log Message:
-----------
Replace existing 'match' functions for title.
Commit: 51d261f4a51daee28e922d14bd5dfe42a101bf5c
https://github.com/PathwayCommons/factoid/commit/51d261f4a51daee28e922d14bd5dfe42a101bf5c
Author: Jeffrey <[email protected]>
Date: 2024-10-31 (Thu, 31 Oct 2024)
Changed paths:
M package-lock.json
M package.json
M src/server/routes/api/document/crossref/works.js
M src/server/routes/api/document/pubmed/index.js
A src/util/article.js
A test/util/article.js
Log Message:
-----------
Merge pull request #1303 from PathwayCommons/iss1297_title-match
Module for testing title similarity
Commit: 7d94a0088474a9e943348a3e98b3e0988c422c75
https://github.com/PathwayCommons/factoid/commit/7d94a0088474a9e943348a3e98b3e0988c422c75
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-01 (Fri, 01 Nov 2024)
Changed paths:
M src/client/components/document-management.js
Log Message:
-----------
Allow ids in url params
Commit: 0c0d526236caaedf8eb2ddc192da8e770f38321d
https://github.com/PathwayCommons/factoid/commit/0c0d526236caaedf8eb2ddc192da8e770f38321d
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-01 (Fri, 01 Nov 2024)
Changed paths:
M src/client/components/document-management.js
Log Message:
-----------
Enable filtering by Document ids; switch between this filter and general
range finder.
Commit: 5a5b82298aa1c9f05d74b20219b8396bf882bfb7
https://github.com/PathwayCommons/factoid/commit/5a5b82298aa1c9f05d74b20219b8396bf882bfb7
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-01 (Fri, 01 Nov 2024)
Changed paths:
M src/client/components/document-management.js
Log Message:
-----------
Debounce the getDocs after status change.
Commit: 6bfe770c5e031c17a186e7c2e34c3343a70d0788
https://github.com/PathwayCommons/factoid/commit/6bfe770c5e031c17a186e7c2e34c3343a70d0788
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-01 (Fri, 01 Nov 2024)
Changed paths:
M src/client/components/document-management.js
Log Message:
-----------
Getting and setting query params.
Commit: dab39ed5ca98bcfa0174748b691adc67eef33d95
https://github.com/PathwayCommons/factoid/commit/dab39ed5ca98bcfa0174748b691adc67eef33d95
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-06 (Wed, 06 Nov 2024)
Changed paths:
M README.md
M src/config.js
Log Message:
-----------
Add a config variable for cron scheduling a Document cache
Commit: 2b38c1a8cf6f72be83b1f68fc0917d4cba44a04a
https://github.com/PathwayCommons/factoid/commit/2b38c1a8cf6f72be83b1f68fc0917d4cba44a04a
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-06 (Wed, 06 Nov 2024)
Changed paths:
A src/server/routes/api/document/cache.js
Log Message:
-----------
Warp the Document cache implementation to have update and schedule cron jobs
Commit: 01c373e81a9aa9cea6aefb3bc4881cc3f8031b27
https://github.com/PathwayCommons/factoid/commit/01c373e81a9aa9cea6aefb3bc4881cc3f8031b27
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-06 (Wed, 06 Nov 2024)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Use the Document cache to retrieve items safely on request.
Commit: 6e886e944f22ba5c77e02265028c01d483c2f249
https://github.com/PathwayCommons/factoid/commit/6e886e944f22ba5c77e02265028c01d483c2f249
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-06 (Wed, 06 Nov 2024)
Changed paths:
M src/config.js
Log Message:
-----------
Cron scheduled at midnight, daily.
Commit: 6dd825d434e364723cf2d379806f437544786096
https://github.com/PathwayCommons/factoid/commit/6dd825d434e364723cf2d379806f437544786096
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-07 (Thu, 07 Nov 2024)
Changed paths:
M src/server/routes/api/document/cache.js
Log Message:
-----------
Cron update should refresh all docs
Commit: 638d1269d67dde9e8234528522520a45ba6e1a30
https://github.com/PathwayCommons/factoid/commit/638d1269d67dde9e8234528522520a45ba6e1a30
Author: Jeffrey <[email protected]>
Date: 2024-11-07 (Thu, 07 Nov 2024)
Changed paths:
M README.md
M src/config.js
A src/server/routes/api/document/cache.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #1305 from PathwayCommons/iss1304_search-cache
Updatable Document cache
Commit: 25166d850c1a19b6a49daed6eed701afed542091
https://github.com/PathwayCommons/factoid/commit/25166d850c1a19b6a49daed6eed701afed542091
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-07 (Thu, 07 Nov 2024)
Changed paths:
M README.md
M src/config.js
Log Message:
-----------
Document the requirement for the BIOPAX_CONVERTER_URL in production
environment
Commit: 96c6b5ecb91acdb151467f9cf4b0d2292b8c0c6d
https://github.com/PathwayCommons/factoid/commit/96c6b5ecb91acdb151467f9cf4b0d2292b8c0c6d
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-07 (Thu, 07 Nov 2024)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Throw errors when the BIOPAX_CONVERTER_URL is missing and needed (production)
Commit: eda211ed7ea872a53c4737d1e58d9f6b21ce8fb6
https://github.com/PathwayCommons/factoid/commit/eda211ed7ea872a53c4737d1e58d9f6b21ce8fb6
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-07 (Thu, 07 Nov 2024)
Changed paths:
M src/client/components/document-management.js
M src/styles/document-management.css
Log Message:
-----------
Implement UD Query form
Commit: 94e8746229436542a662fe8ef040ab7b3d61fec4
https://github.com/PathwayCommons/factoid/commit/94e8746229436542a662fe8ef040ab7b3d61fec4
Author: Jeffrey <[email protected]>
Date: 2024-11-08 (Fri, 08 Nov 2024)
Changed paths:
M README.md
M src/config.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #1307 from PathwayCommons/iss1306_require-biopax-converter
Update the biopax converter URL
Commit: 81a17d8165d648c09e36c33847a68a54d76e450f
https://github.com/PathwayCommons/factoid/commit/81a17d8165d648c09e36c33847a68a54d76e450f
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-08 (Fri, 08 Nov 2024)
Changed paths:
M src/server/index.js
Log Message:
-----------
Disable GraphDB initialization (for now)
Commit: 88facceea4cade6a0b42172b8f48c9ae27d9ddf3
https://github.com/PathwayCommons/factoid/commit/88facceea4cade6a0b42172b8f48c9ae27d9ddf3
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-08 (Fri, 08 Nov 2024)
Changed paths:
M src/client/components/document-management.js
Log Message:
-----------
Functional ID search box
Commit: af0a84d3009ee407b51fe72f247b7041ea08b7b6
https://github.com/PathwayCommons/factoid/commit/af0a84d3009ee407b51fe72f247b7041ea08b7b6
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-08 (Fri, 08 Nov 2024)
Changed paths:
M src/client/components/document-management.js
Log Message:
-----------
Do nothing when the ID input is empty.
Commit: 0efcb5d2690c0184a11ce8e8c92eb4482236f073
https://github.com/PathwayCommons/factoid/commit/0efcb5d2690c0184a11ce8e8c92eb4482236f073
Author: Jeffrey <[email protected]>
Date: 2024-11-08 (Fri, 08 Nov 2024)
Changed paths:
M src/client/components/document-management.js
M src/server/index.js
M src/styles/document-management.css
Log Message:
-----------
Merge pull request #1308 from PathwayCommons/iss1240_admin-get-by-id
Admin retrieve Document by ID
Commit: 83ebe46f7baf405278167875913fe122281167f7
https://github.com/PathwayCommons/factoid/commit/83ebe46f7baf405278167875913fe122281167f7
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-08 (Fri, 08 Nov 2024)
Changed paths:
M src/client/components/document-management.js
Log Message:
-----------
Respect the api key on load.
Commit: 180ba2add599d88614ddcd3050277a2ef376c133
https://github.com/PathwayCommons/factoid/commit/180ba2add599d88614ddcd3050277a2ef376c133
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-09 (Sat, 09 Nov 2024)
Changed paths:
M src/client/components/document-management.js
M src/styles/document-management.css
Log Message:
-----------
Cleanup component names and organisation.
Commit: b34018d6596f035ca9ed9be4ff277dc3762ad5e6
https://github.com/PathwayCommons/factoid/commit/b34018d6596f035ca9ed9be4ff277dc3762ad5e6
Author: Jeffrey <[email protected]>
Date: 2024-11-09 (Sat, 09 Nov 2024)
Changed paths:
M src/client/components/document-management.js
M src/styles/document-management.css
Log Message:
-----------
Merge pull request #1309 from PathwayCommons/iss1240_api-key-missing
Load admin with apiKey
Commit: f6dd74392787b771dbbc325e44192887c1e0488f
https://github.com/PathwayCommons/factoid/commit/f6dd74392787b771dbbc325e44192887c1e0488f
Author: Jeffrey Wong <[email protected]>
Date: 2024-11-09 (Sat, 09 Nov 2024)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
0.32.0
Commit: d11c3daadfcc5eb8b6ffc836f79ca6278c72fc35
https://github.com/PathwayCommons/factoid/commit/d11c3daadfcc5eb8b6ffc836f79ca6278c72fc35
Author: Jeffrey <[email protected]>
Date: 2024-11-09 (Sat, 09 Nov 2024)
Changed paths:
M README.md
M package-lock.json
M package.json
M src/client/components/document-management.js
M src/config.js
M src/model/hint.js
M src/server/index.js
A src/server/routes/api/document/cache.js
M src/server/routes/api/document/crossref/works.js
A src/server/routes/api/document/hint/pubtator.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/index.js
M src/styles/document-management.css
A src/util/article.js
A src/util/registry.js
A test/pubtator/10.1016_j.molcel.2016.11.034.json
A test/pubtator/10.1016_j.molcel.2019.03.023.json
A test/pubtator/10.1016_j.molcel.2019.04.005.json
A test/pubtator/10.1016_j.molcel.2024.01.007.json
A test/pubtator/10.1038_s41556-021-00642-9.json
A test/pubtator/10.1126_scisignal.abf3535.json
A test/pubtator/10.15252_embj.2023113616.json
A test/pubtator/pubtator.js
A test/pubtator/pubtator_8.json
A test/util/article.js
Log Message:
-----------
Merge pull request #1311 from PathwayCommons/v0.32
v0.32
Compare:
https://github.com/PathwayCommons/factoid/compare/24e233df9c04...d11c3daadfcc
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