Branch: refs/heads/iss635_readonly-doc
Home: https://github.com/PathwayCommons/factoid
Commit: f744379c14df98ad5dbdfd2aa1e9b538a08dfd41
https://github.com/PathwayCommons/factoid/commit/f744379c14df98ad5dbdfd2aa1e9b538a08dfd41
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-28 (Fri, 28 Feb 2020)
Changed paths:
M src/client/components/document-management.js
M src/server/routes/api/document/index.js
Log Message:
-----------
- add a document api route 'api-key-verify'
- admin checks the apiKey in order to load 'secret'-enabled docs into component
Commit: 92e2e813234aecdc251d072b46e69aed9c1fb1f9
https://github.com/PathwayCommons/factoid/commit/92e2e813234aecdc251d072b46e69aed9c1fb1f9
Author: Jeffrey <[email protected]>
Date: 2020-02-28 (Fri, 28 Feb 2020)
Changed paths:
M src/client/components/document-management.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #654 from PathwayCommons/iss651_password-protect-admin
Document route check for apiKey, used by admin
Commit: 20e36fdfd7c60eaa70643e3c5d9132f455cffa4a
https://github.com/PathwayCommons/factoid/commit/20e36fdfd7c60eaa70643e3c5d9132f455cffa4a
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-03 (Tue, 03 Mar 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/util/pubmed.js
Log Message:
-----------
- Update the PubDate to reflect possible values, i.e. seasons, MedlineDate
- fetchPubmed returns a Journal article representation in a way that is
faithful to the XML DTD
- Update the citation field to read from this updated Journal representation
Commit: 5ed65b5da534aeea22942aad67e98d015d9e2820
https://github.com/PathwayCommons/factoid/commit/5ed65b5da534aeea22942aad67e98d015d9e2820
Author: Jeffrey <[email protected]>
Date: 2020-03-03 (Tue, 03 Mar 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #657 from PathwayCommons/iss656_refactor-pubmed-pubdate
Refactoring: Fetching data from PubMed
Commit: fa276eca8d8dfa312c23c608f7e500a63cb48f37
https://github.com/PathwayCommons/factoid/commit/fa276eca8d8dfa312c23c608f7e500a63cb48f37
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-03 (Tue, 03 Mar 2020)
Changed paths:
M test/pubmed/fetchPubmed.js
Log Message:
-----------
Updated tests to reflect changes in Journal schema.
Commit: 0e8e3d54ebecfc8405687e5b8b2fd75b636e2133
https://github.com/PathwayCommons/factoid/commit/0e8e3d54ebecfc8405687e5b8b2fd75b636e2133
Author: Jeffrey <[email protected]>
Date: 2020-03-03 (Tue, 03 Mar 2020)
Changed paths:
M test/pubmed/fetchPubmed.js
Log Message:
-----------
Merge pull request #658 from PathwayCommons/pubmed-tests
Updated tests to reflect changes in Journal schema.
Commit: 125f927e397deb043fea1599dbd81043fe42fbc2
https://github.com/PathwayCommons/factoid/commit/125f927e397deb043fea1599dbd81043fe42fbc2
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-03 (Tue, 03 Mar 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/searchPubmed.js
A src/util/fetch.js
M src/util/index.js
Log Message:
-----------
Adding a HTTPStatusError that is called by checkHTTPStatus util function
Commit: 36b36f6f3d60e9fc7bb8a94ff9b8e5df4b27cac3
https://github.com/PathwayCommons/factoid/commit/36b36f6f3d60e9fc7bb8a94ff9b8e5df4b27cac3
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/index.js
M src/server/routes/api/document/pubmed/searchPubmed.js
M src/util/email.js
M src/util/pubmed.js
Log Message:
-----------
- Improved documentation, particularly of different types of errors
- move ArticleIDError and a new createPubmedArticle factory to pubmed utils
- email utility to check email addresses, before attempting to send
- abstracted a fetch http status check and HTTPStatusError for tracking server
errors
- Set email and paperId errors inside issue so that they can be tracked, but
send email invitation when valid email exists, regardless of the paperId
Commit: fe16cafa4d7196a9401fd7f02be0c0cb3581d5b2
https://github.com/PathwayCommons/factoid/commit/fe16cafa4d7196a9401fd7f02be0c0cb3581d5b2
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
M src/util/pubmed.js
Log Message:
-----------
Add the id to the ArticleIDError class.
Commit: cf9124fc8f3a07e971ce1a5c561b05d75dbbc8fa
https://github.com/PathwayCommons/factoid/commit/cf9124fc8f3a07e971ce1a5c561b05d75dbbc8fa
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
paperId issue should have 'error' attribute.
Commit: 73481dedc286856f63ed30f4a07fa1713d2eda2b
https://github.com/PathwayCommons/factoid/commit/73481dedc286856f63ed30f4a07fa1713d2eda2b
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/index.js
M src/util/fetch.js
M src/util/pubmed.js
Log Message:
-----------
- More informative Error message for admin
- Bug in pubmed citation code for dates
- check for missing paperId and email
Commit: ef3dea5c3fcbd1a3d4717d4633ec0052c08f9cbc
https://github.com/PathwayCommons/factoid/commit/ef3dea5c3fcbd1a3d4717d4633ec0052c08f9cbc
Author: Jeffrey <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/index.js
M src/server/routes/api/document/pubmed/searchPubmed.js
M src/util/email.js
A src/util/fetch.js
M src/util/index.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #660 from
PathwayCommons/iss655_document-creation-error-handling
Admin: Documentation, explicit errors for bad/missing doc data
Commit: 0e607689fd7296e54af9a10a609ecf7960bfed29
https://github.com/PathwayCommons/factoid/commit/0e607689fd7296e54af9a10a609ecf7960bfed29
Author: Jeffrey <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/index.js
M src/server/routes/api/document/pubmed/searchPubmed.js
M src/util/email.js
R src/util/fetch.js
M src/util/index.js
M src/util/pubmed.js
Log Message:
-----------
Revert "Admin: Documentation, explicit errors for bad/missing doc data "
Commit: 857fc25e6fedf2297fbd769046ef45b57c5d2fd9
https://github.com/PathwayCommons/factoid/commit/857fc25e6fedf2297fbd769046ef45b57c5d2fd9
Author: Jeffrey <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/index.js
M src/server/routes/api/document/pubmed/searchPubmed.js
M src/util/email.js
R src/util/fetch.js
M src/util/index.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #661 from
PathwayCommons/revert-660-iss655_document-creation-error-handling
Revert "Admin: Documentation, explicit errors for bad/missing doc data "
Commit: 60c0384f89fe92ab8b2222feeb1b01dc8204b643
https://github.com/PathwayCommons/factoid/commit/60c0384f89fe92ab8b2222feeb1b01dc8204b643
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/util/email.js
A src/util/fetch.js
M src/util/index.js
M src/util/pubmed.js
Log Message:
-----------
- Utility for checking fetch status
- Error types for email and article ids
Commit: b5121b5e2af5f6774e74d71db90e235988b233a6
https://github.com/PathwayCommons/factoid/commit/b5121b5e2af5f6774e74d71db90e235988b233a6
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
Log Message:
-----------
- fetchPubmed uses HTTP status fetch utility
- check efetch result from server
Commit: f7acc3b609c1aac02288f4b2b0e66b4648f0543b
https://github.com/PathwayCommons/factoid/commit/f7acc3b609c1aac02288f4b2b0e66b4648f0543b
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/pubmed/searchPubmed.js
Log Message:
-----------
- searchPubmed uses fetch http status check utility
- check the esearch response for errors
Commit: b8c5dd61a47974e3b24f2463bd61616588b2fa2c
https://github.com/PathwayCommons/factoid/commit/b8c5dd61a47974e3b24f2463bd61616588b2fa2c
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
Log Message:
-----------
- Improved documentation for pubmed module api functions
- Use the pubmed article ID error utility
Commit: 3acf865aed316787dd5e22eb07d9defd8d18c21b
https://github.com/PathwayCommons/factoid/commit/3acf865aed316787dd5e22eb07d9defd8d18c21b
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
- Validate and extract email addresses from raw input
- Set error on doc issue for email and paperId
- Send invitation is no email issue
- Set email address array on correspondence attribute of doc
Commit: 19e226503f8e11ad79dd1400bc5e7b810439e674
https://github.com/PathwayCommons/factoid/commit/19e226503f8e11ad79dd1400bc5e7b810439e674
Author: Jeffrey Wong <[email protected]>
Date: 2020-03-04 (Wed, 04 Mar 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
Log Message:
-----------
Bug in PubMed JournalIssue PubDate parsing.
Commit: 1bad9e6afe42df30c2c5d8fee10c856fd42f4e34
https://github.com/PathwayCommons/factoid/commit/1bad9e6afe42df30c2c5d8fee10c856fd42f4e34
Author: Jeffrey <[email protected]>
Date: 2020-03-05 (Thu, 05 Mar 2020)
Changed paths:
M src/client/components/document-management.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #654 from PathwayCommons/iss651_password-protect-admin
Document route check for apiKey, used by admin
Commit: 6d5381e94134553273ed78a977d63d594a200241
https://github.com/PathwayCommons/factoid/commit/6d5381e94134553273ed78a977d63d594a200241
Author: Jeffrey <[email protected]>
Date: 2020-03-05 (Thu, 05 Mar 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #657 from PathwayCommons/iss656_refactor-pubmed-pubdate
Refactoring: Fetching data from PubMed
Commit: 91176e8d1b5678df561d7b847af0da66a52c5074
https://github.com/PathwayCommons/factoid/commit/91176e8d1b5678df561d7b847af0da66a52c5074
Author: Jeffrey <[email protected]>
Date: 2020-03-05 (Thu, 05 Mar 2020)
Changed paths:
M test/pubmed/fetchPubmed.js
Log Message:
-----------
Merge pull request #658 from PathwayCommons/pubmed-tests
Updated tests to reflect changes in Journal schema.
Commit: 8893b0b3183c1b3161d9af95aea45d3d5cf40867
https://github.com/PathwayCommons/factoid/commit/8893b0b3183c1b3161d9af95aea45d3d5cf40867
Author: Jeffrey <[email protected]>
Date: 2020-03-05 (Thu, 05 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/index.js
M src/server/routes/api/document/pubmed/searchPubmed.js
M src/util/email.js
A src/util/fetch.js
M src/util/index.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #660 from
PathwayCommons/iss655_document-creation-error-handling
Admin: Documentation, explicit errors for bad/missing doc data
Commit: 223e9dc11c62069791cd7c9cf06e2611eea07b84
https://github.com/PathwayCommons/factoid/commit/223e9dc11c62069791cd7c9cf06e2611eea07b84
Author: Jeffrey <[email protected]>
Date: 2020-03-05 (Thu, 05 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/index.js
M src/server/routes/api/document/pubmed/searchPubmed.js
M src/util/email.js
R src/util/fetch.js
M src/util/index.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #661 from
PathwayCommons/revert-660-iss655_document-creation-error-handling
Revert "Admin: Documentation, explicit errors for bad/missing doc data "
Commit: a8340ef5a85cf3e153eea7bec22f36aa523d69c3
https://github.com/PathwayCommons/factoid/commit/a8340ef5a85cf3e153eea7bec22f36aa523d69c3
Author: Jeffrey <[email protected]>
Date: 2020-03-05 (Thu, 05 Mar 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/index.js
M src/server/routes/api/document/pubmed/searchPubmed.js
M src/util/email.js
A src/util/fetch.js
M src/util/index.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #662 from PathwayCommons/iss655_admin-error-tracking
Admin: Error tracking on doc creation, improved documentation
Compare:
https://github.com/PathwayCommons/factoid/compare/739cf454dfd9...a8340ef5a85c
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