Branch: refs/heads/master
Home: https://github.com/PathwayCommons/factoid
Commit: 87435ffd60b75819fd4ca350087d4b5b379fd7cb
https://github.com/PathwayCommons/factoid/commit/87435ffd60b75819fd4ca350087d4b5b379fd7cb
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-16 (Thu, 16 Jan 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
Log Message:
-----------
Set the user agent in fetch to NCBI.
Commit: 8a7115a5c734264926ca01f3105b42c8564a5591
https://github.com/PathwayCommons/factoid/commit/8a7115a5c734264926ca01f3105b42c8564a5591
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-16 (Thu, 16 Jan 2020)
Changed paths:
M src/server/routes/api/document/pubmed/searchPubmed.js
Log Message:
-----------
User agent added to search pubmed function.
Commit: 0c1f2db9db27b277149a995315190516e8638bb9
https://github.com/PathwayCommons/factoid/commit/0c1f2db9db27b277149a995315190516e8638bb9
Author: Jeffrey <[email protected]>
Date: 2020-01-17 (Fri, 17 Jan 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/searchPubmed.js
Log Message:
-----------
Merge pull request #612 from PathwayCommons/iss610_user-agent-node-fetch-ncbi
Set the user agent in fetch to NCBI.
Commit: 54dfd6f1f8580c8b8d0657ee3ccac74436fa3cc4
https://github.com/PathwayCommons/factoid/commit/54dfd6f1f8580c8b8d0657ee3ccac74436fa3cc4
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-20 (Mon, 20 Jan 2020)
Changed paths:
M src/config.js
M src/server/index.js
M src/server/routes/index.js
A src/views/404.ejs
R src/views/404.html
Log Message:
-----------
Added a 404 page response if trying to access a document that doesn't exist.
Commit: 77d332fb5996f96de6ddaefce1b79143301b7dfd
https://github.com/PathwayCommons/factoid/commit/77d332fb5996f96de6ddaefce1b79143301b7dfd
Author: Max Franz <[email protected]>
Date: 2020-01-20 (Mon, 20 Jan 2020)
Changed paths:
M src/config.js
M src/server/index.js
M src/server/routes/index.js
A src/views/404.ejs
R src/views/404.html
Log Message:
-----------
Merge pull request #615 from PathwayCommons/iss614_handle-bad-document-path
Help page for missing/removed documents
Commit: d44beadc725fb756965bb0b576a7fa93db1bc7ec
https://github.com/PathwayCommons/factoid/commit/d44beadc725fb756965bb0b576a7fa93db1bc7ec
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-21 (Tue, 21 Jan 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
M test/pubmed/fetchPubmed.js
Log Message:
-----------
Properly format abstract, include labels ('OBJECTIVE', 'METHODS') if they
exist.
Commit: 88b29213bc357fb9dd4a50e42f497068a7c1136a
https://github.com/PathwayCommons/factoid/commit/88b29213bc357fb9dd4a50e42f497068a7c1136a
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-21 (Tue, 21 Jan 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
M test/pubmed/fetchPubmed.js
Log Message:
-----------
Fetch any UI attributes for Chemicals.
Commit: 641b344eaea9de1a31181fcb65b4efd2c7c1d4bc
https://github.com/PathwayCommons/factoid/commit/641b344eaea9de1a31181fcb65b4efd2c7c1d4bc
Author: Jeffrey <[email protected]>
Date: 2020-01-21 (Tue, 21 Jan 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
M test/pubmed/fetchPubmed.js
Log Message:
-----------
Merge pull request #618 from PathwayCommons/iss617_fetchPubmed-enhancements
Fetch Pubmed: bugs/enhancements
Commit: 9921e4b378dd71994dfe717096c50de96b5fb2f0
https://github.com/PathwayCommons/factoid/commit/9921e4b378dd71994dfe717096c50de96b5fb2f0
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-24 (Fri, 24 Jan 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
Log Message:
-----------
Allow search for all unrecogized ids
Commit: 0f6fa9fbc6dd785b21deabbf7f3ddec93347da7a
https://github.com/PathwayCommons/factoid/commit/0f6fa9fbc6dd785b21deabbf7f3ddec93347da7a
Author: Jeffrey <[email protected]>
Date: 2020-01-24 (Fri, 24 Jan 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
Log Message:
-----------
Merge pull request #621 from PathwayCommons/flexible-pubmed-search
Leverage PubMed to search for paper IDs
Commit: a9a1a115f023e58e64d2a66d1c42d2116b9c6a89
https://github.com/PathwayCommons/factoid/commit/a9a1a115f023e58e64d2a66d1c42d2116b9c6a89
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-27 (Mon, 27 Jan 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/searchPubmed.js
Log Message:
-----------
- Added HTTP error handling on pubmed efetch modules
- Added apiKey check on journal context; else must be 'signup'
- Stubbed out send notification module following doc creation and fill
Commit: e10cf5cc1bdc5ef52aef1ddaef349305ecb53826
https://github.com/PathwayCommons/factoid/commit/e10cf5cc1bdc5ef52aef1ddaef349305ecb53826
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-27 (Mon, 27 Jan 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/util/email.js
Log Message:
-----------
- implemented automatic sending of email invitations on request
- documenting email util api functions
Commit: c054c12555dee91e1e299da7194a479e9d319ae8
https://github.com/PathwayCommons/factoid/commit/c054c12555dee91e1e299da7194a479e9d319ae8
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-27 (Mon, 27 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/model/document/document.js
Log Message:
-----------
- Add a 'verified' metadata to document model.
- Indicate in admin that email is verified
Commit: 621898957543ef9f6a32091575e80e6e999211a8
https://github.com/PathwayCommons/factoid/commit/621898957543ef9f6a32091575e80e6e999211a8
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-27 (Mon, 27 Jan 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
- Immeidately respond with 'ok' when request is received
Commit: 82df81946181b1af887abb5d9f655514cf8d9c88
https://github.com/PathwayCommons/factoid/commit/82df81946181b1af887abb5d9f655514cf8d9c88
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-27 (Mon, 27 Jan 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Put catch statement in create route.
Commit: 33fc0b5db2a9d40dab0a9ff34fc7e151d60bdfec
https://github.com/PathwayCommons/factoid/commit/33fc0b5db2a9d40dab0a9ff34fc7e151d60bdfec
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-28 (Tue, 28 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/server/routes/api/document/index.js
M src/util/email.js
Log Message:
-----------
Remove useless send email util function. Fix bug in /api/doucment/email route.
Commit: bb4c257a4c12995b7f389cdde4aa274c4fb7eebf
https://github.com/PathwayCommons/factoid/commit/bb4c257a4c12995b7f389cdde4aa274c4fb7eebf
Author: Max Franz <[email protected]>
Date: 2020-01-28 (Tue, 28 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/model/document/document.js
Log Message:
-----------
Merge pull request #624 from PathwayCommons/iss623_doc-verified
Add a 'verified' metadata to document model.
Commit: 453684f73aaae28f87373018186a5fcf0a1c9f8e
https://github.com/PathwayCommons/factoid/commit/453684f73aaae28f87373018186a5fcf0a1c9f8e
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-28 (Tue, 28 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/server/routes/api/document/index.js
Log Message:
-----------
- Include useful message on email failure
- Log in admin
Commit: 47a9183c9a4f5b8558ffa29dcf18275ae8188112
https://github.com/PathwayCommons/factoid/commit/47a9183c9a4f5b8558ffa29dcf18275ae8188112
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-28 (Tue, 28 Jan 2020)
Changed paths:
M src/util/email.js
M src/util/pubmed.js
Log Message:
-----------
Remove 'undefined' if any part of the citation does not exist.
Commit: a67f4f6c3138b6b080a098df4119f333fad87ed6
https://github.com/PathwayCommons/factoid/commit/a67f4f6c3138b6b080a098df4119f333fad87ed6
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-28 (Tue, 28 Jan 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/index.js
M src/util/email.js
Log Message:
-----------
Adding automated response to invitation with issue.
Commit: b9cbed275a02acfe4a85c62a99598bc07298c375
https://github.com/PathwayCommons/factoid/commit/b9cbed275a02acfe4a85c62a99598bc07298c375
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-28 (Tue, 28 Jan 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Fixed bug where valid journal requests were not being sent
Commit: c9b226bc3fd36bfc571b4f4f503079534f942552
https://github.com/PathwayCommons/factoid/commit/c9b226bc3fd36bfc571b4f4f503079534f942552
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-29 (Wed, 29 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/index.js
Log Message:
-----------
More well defined control of conditions to be met in order for automated
email for invitation or error email will be sent.
Commit: c650c3a4f1bce143f20964a3c54458bd66e31bf6
https://github.com/PathwayCommons/factoid/commit/c650c3a4f1bce143f20964a3c54458bd66e31bf6
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-29 (Wed, 29 Jan 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Doc create api endpoint must have catch following all statements.
Commit: b76003af5294609d46fafeb184895491aa76fd18
https://github.com/PathwayCommons/factoid/commit/b76003af5294609d46fafeb184895491aa76fd18
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-29 (Wed, 29 Jan 2020)
Changed paths:
M README.md
Log Message:
-----------
Update README with new config variables for request error/issue.
Commit: 918f2070d1266378dfdd3144aaf0bab6490be08d
https://github.com/PathwayCommons/factoid/commit/918f2070d1266378dfdd3144aaf0bab6490be08d
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-29 (Wed, 29 Jan 2020)
Changed paths:
M src/util/email.js
Log Message:
-----------
Remove the provided data from data sent to email templates.
Commit: 577a0d940ed1084cbeb33e3f42c005d93d39a2f9
https://github.com/PathwayCommons/factoid/commit/577a0d940ed1084cbeb33e3f42c005d93d39a2f9
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-29 (Wed, 29 Jan 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Automatically set approved state when no issues exist in create doc route.
Commit: 35a57c74731d634f7d27520b9c529bd789fde7e8
https://github.com/PathwayCommons/factoid/commit/35a57c74731d634f7d27520b9c529bd789fde7e8
Author: Jeffrey <[email protected]>
Date: 2020-01-30 (Thu, 30 Jan 2020)
Changed paths:
M README.md
M src/client/components/document-management-components.js
M src/config.js
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:
-----------
Merge pull request #625 from
PathwayCommons/iss620_automate-correspondence-invite
Automation: Invitations
Commit: 48b396b31b0f5497286f905a17f730efa76cca94
https://github.com/PathwayCommons/factoid/commit/48b396b31b0f5497286f905a17f730efa76cca94
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-30 (Thu, 30 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Automate verification of email address (exact match in pubmed) on create
route.
Commit: 5a36ebe39f59c5eb4ce7bf854109c91c7edf6d1c
https://github.com/PathwayCommons/factoid/commit/5a36ebe39f59c5eb4ce7bf854109c91c7edf6d1c
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-30 (Thu, 30 Jan 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Automate verification of email address (exact match in pubmed) on create
route.
Commit: 94eff7f6e5cc443249c132af4642fbeba63fe470
https://github.com/PathwayCommons/factoid/commit/94eff7f6e5cc443249c132af4642fbeba63fe470
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-30 (Thu, 30 Jan 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Automatically verify emails when the context is journal
Commit: 13f18ad3303e77ab6033a1413f8e362231bdd93f
https://github.com/PathwayCommons/factoid/commit/13f18ad3303e77ab6033a1413f8e362231bdd93f
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-31 (Fri, 31 Jan 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Now, try verify only adds but never removes verified flag.
Commit: e5f1d7f9b9e40f0122c05632e66454674bec2036
https://github.com/PathwayCommons/factoid/commit/e5f1d7f9b9e40f0122c05632e66454674bec2036
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-31 (Fri, 31 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
Log Message:
-----------
Add admin toggle to set 'verified'
Commit: ad706ff421bc15a28e85b7bb361c025f70278244
https://github.com/PathwayCommons/factoid/commit/ad706ff421bc15a28e85b7bb361c025f70278244
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-31 (Fri, 31 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
Log Message:
-----------
Bug in setting verified from admin.
Commit: 2e85504009fd54f12559abcfca4c3d96edaeef5e
https://github.com/PathwayCommons/factoid/commit/2e85504009fd54f12559abcfca4c3d96edaeef5e
Author: Jeffrey Wong <[email protected]>
Date: 2020-01-31 (Fri, 31 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/styles/document-management.css
Log Message:
-----------
- Add a text editable style option
- change radioset attribute to checked - yeah no idea but it works!
Commit: 7ce1b3ea5c694962a76e3ad534cf1eb82415d8c3
https://github.com/PathwayCommons/factoid/commit/7ce1b3ea5c694962a76e3ad534cf1eb82415d8c3
Author: Jeffrey <[email protected]>
Date: 2020-01-31 (Fri, 31 Jan 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/server/routes/api/document/index.js
M src/styles/document-management.css
Log Message:
-----------
Merge pull request #626 from PathwayCommons/iss620_verify-by-email
Admin automation: Check if provided email should be considered 'verified'
Commit: 3defff46c851c2f5382f5673e3e8db53c7d323d9
https://github.com/PathwayCommons/factoid/commit/3defff46c851c2f5382f5673e3e8db53c7d323d9
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-05 (Wed, 05 Feb 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/server/routes/api/document/index.js
Log Message:
-----------
In the admin, use PATCH method with named route params when modifying
resource partially
Commit: 0672389ed7b6aa461d2bc8b4d75b749fa6e1b31a
https://github.com/PathwayCommons/factoid/commit/0672389ed7b6aa461d2bc8b4d75b749fa6e1b31a
Author: Jeffrey <[email protected]>
Date: 2020-02-05 (Wed, 05 Feb 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #629 from PathwayCommons/admin-refactor-doc-patch
Admin: Refactoring doc modification, routes
Commit: c04512fad2dc4001f527b41f923f04d0eb685e7e
https://github.com/PathwayCommons/factoid/commit/c04512fad2dc4001f527b41f923f04d0eb685e7e
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-05 (Wed, 05 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
A src/client/components/tasks.js
M src/styles/editor/editor.css
M src/styles/index.css
A src/styles/tasks.css
Log Message:
-----------
Added back previous code for Submit in editor
Commit: 344dee11de8cc796aae69fc7ee595a036b37747c
https://github.com/PathwayCommons/factoid/commit/344dee11de8cc796aae69fc7ee595a036b37747c
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-06 (Thu, 06 Feb 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
-----------
Event for submit action is under doc 'status'.
Commit: 9555fb81cc1a2f4c47f10eca433a55570cb9b1a4
https://github.com/PathwayCommons/factoid/commit/9555fb81cc1a2f4c47f10eca433a55570cb9b1a4
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-06 (Thu, 06 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
Log Message:
-----------
Listen to status updates in the admin and on the editor and update UI
accordingly.
Commit: 8e998ccbf881db1d4fa773bef214461fd4257bd0
https://github.com/PathwayCommons/factoid/commit/8e998ccbf881db1d4fa773bef214461fd4257bd0
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-07 (Fri, 07 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/model/document/document.js
Log Message:
-----------
Ensure that the document submit button is in a consistent state with the
status.
Commit: 78a8dc512a894fba640218b52d8d2ffd93cd5f8c
https://github.com/PathwayCommons/factoid/commit/78a8dc512a894fba640218b52d8d2ffd93cd5f8c
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-10 (Mon, 10 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
M src/styles/help.css
M src/styles/image/welcome-aboard-3.svg
A src/styles/image/welcome-aboard-4.svg
Log Message:
-----------
- Added complex, submit panels
- Updated copy for overview and captions
Commit: b9357c9c450233c8bdf1f0c9d0cb216242032316
https://github.com/PathwayCommons/factoid/commit/b9357c9c450233c8bdf1f0c9d0cb216242032316
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
Minor modifications to copy.
Commit: e301d978fe6f0aa0c38ee0c87d042e57dec0e589
https://github.com/PathwayCommons/factoid/commit/e301d978fe6f0aa0c38ee0c87d042e57dec0e589
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
-----------
Drop interactions from task validation list
Commit: d1019a59e6d26862a9feee9e2fe58ad5ddf41a4c
https://github.com/PathwayCommons/factoid/commit/d1019a59e6d26862a9feee9e2fe58ad5ddf41a4c
Author: Jeffrey <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
A src/client/components/tasks.js
M src/model/document/document.js
M src/styles/editor/editor.css
M src/styles/index.css
A src/styles/tasks.css
Log Message:
-----------
Merge pull request #630 from PathwayCommons/iss627_add-back-submit
Add back submit
Commit: 59161a56bb2fe2f9a9bf38206b51fd9ba360a662
https://github.com/PathwayCommons/factoid/commit/59161a56bb2fe2f9a9bf38206b51fd9ba360a662
Author: Jeffrey <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
M src/styles/help.css
M src/styles/image/welcome-aboard-3.svg
A src/styles/image/welcome-aboard-4.svg
Log Message:
-----------
Merge pull request #631 from PathwayCommons/iss628_onboarding-submit-complex
Welcome modal update: submit, complex
Commit: 9a213aa471b16d9bc8938d713932b725bc4ebd9d
https://github.com/PathwayCommons/factoid/commit/9a213aa471b16d9bc8938d713932b725bc4ebd9d
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/util/pubmed.js
Log Message:
-----------
Drop unnecessary period in journal title reference
Commit: bb3cc1f7fe1c03c13a367689ca0102a2dea238b6
https://github.com/PathwayCommons/factoid/commit/bb3cc1f7fe1c03c13a367689ca0102a2dea238b6
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/client/components/editor/index.js
M src/server/routes/api/document/index.js
M src/util/pubmed.js
Log Message:
-----------
Add the entire author list under the citation attribute 'authors'
Commit: 375c234fc93ad857181820b265d1d6dbadfc87d5
https://github.com/PathwayCommons/factoid/commit/375c234fc93ad857181820b265d1d6dbadfc87d5
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/util/pubmed.js
Log Message:
-----------
Expose getAuthorName in pubmed util.
Commit: ca9512cd201d29b55b4462a2592564e583259ca6
https://github.com/PathwayCommons/factoid/commit/ca9512cd201d29b55b4462a2592564e583259ca6
Author: Jeffrey <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/client/components/editor/index.js
M src/server/routes/api/document/index.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #632 from PathwayCommons/iss622_pubmed-utils-author
Minor tweaks to pubmed data munging utils
Commit: f4a2490f22c4668429a0cfb523f293515498891a
https://github.com/PathwayCommons/factoid/commit/f4a2490f22c4668429a0cfb523f293515498891a
Author: Max Franz <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
GET /api/document : remove API key requirement & order by date
It is necessary for the home page exploration list to get the list of recent
documents without the API key, because the home page is public. In order to
simplify things, the API key restriction has been removed: The API key is not
necessary in order to list the documents. All documents are considered public
information.
Further, the list of documents in the explore view should be ordered by most
recent to least recent. This ordering is applied by default by this route now.
Commit: 321ea3f309dc489d92f35218cf5d709c46d14392
https://github.com/PathwayCommons/factoid/commit/321ea3f309dc489d92f35218cf5d709c46d14392
Author: Max Franz <[email protected]>
Date: 2020-02-11 (Tue, 11 Feb 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #633 from PathwayCommons/get-docs-route-changes
GET /api/document : remove API key requirement & order by date
Commit: 2ee6eddf64acc51a8cbc9a2175d937d2569640f1
https://github.com/PathwayCommons/factoid/commit/2ee6eddf64acc51a8cbc9a2175d937d2569640f1
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-13 (Thu, 13 Feb 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/util/pubmed.js
Log Message:
-----------
Generally improving robustness of PubMed data processing:
- Include defaults for (possibly empty) citation data returned from PubMed data
utility
- Admin check for empty citation 'contacts' field
Commit: 139bab6ce756dfaa092971aa355da16411d9a333
https://github.com/PathwayCommons/factoid/commit/139bab6ce756dfaa092971aa355da16411d9a333
Author: Jeffrey <[email protected]>
Date: 2020-02-13 (Thu, 13 Feb 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #634 from PathwayCommons/refactor-citation-module
Increasing robustness to missing PubMed data
Commit: 48e3ab64737d607526ef344ebf08dcc32cf49691
https://github.com/PathwayCommons/factoid/commit/48e3ab64737d607526ef344ebf08dcc32cf49691
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-14 (Fri, 14 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/styles/editor/editor.css
M src/styles/tasks.css
Log Message:
-----------
- Make submitted button salient green
- TaskView for 'done' has check icon and simple, direct message.
Commit: 06dcff0600f41f9bdaf55d083c99427978823e2d
https://github.com/PathwayCommons/factoid/commit/06dcff0600f41f9bdaf55d083c99427978823e2d
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-14 (Fri, 14 Feb 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
-----------
Remove periods from text.
Commit: 5c62aeb9df447edb701f5d1ff5f42d0ce18ba09f
https://github.com/PathwayCommons/factoid/commit/5c62aeb9df447edb701f5d1ff5f42d0ce18ba09f
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-14 (Fri, 14 Feb 2020)
Changed paths:
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
Log Message:
-----------
- added document PATCH API endpoit for updating status
- publish request checks for non-empty doc
- automated follow-up email
Commit: 31a98576f234a8babd2ca725dac45f4a89c7c28e
https://github.com/PathwayCommons/factoid/commit/31a98576f234a8babd2ca725dac45f4a89c7c28e
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-14 (Fri, 14 Feb 2020)
Changed paths:
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Removed apiKey check
Commit: bf8044033600bdd1228e5b06b2c99b34b70aa7af
https://github.com/PathwayCommons/factoid/commit/bf8044033600bdd1228e5b06b2c99b34b70aa7af
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-14 (Fri, 14 Feb 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Add publish criteria that no entity can be incomplete
Commit: 9555e2e5735f7159fce519b45241c83066618bba
https://github.com/PathwayCommons/factoid/commit/9555e2e5735f7159fce519b45241c83066618bba
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-18 (Tue, 18 Feb 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
- Perform PATCH operations in sequence.
- Put doc JSON in response
Commit: 4c1ada73770759a2ab046fbf3ae1153ad6d30475
https://github.com/PathwayCommons/factoid/commit/4c1ada73770759a2ab046fbf3ae1153ad6d30475
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-18 (Tue, 18 Feb 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
-----------
Use named variable for setting status value in Tasks.js
Commit: 1b1824f81d6686736b96868dcfd054467f0b39de
https://github.com/PathwayCommons/factoid/commit/1b1824f81d6686736b96868dcfd054467f0b39de
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-18 (Tue, 18 Feb 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
-----------
Remove comments in tasks.js
Commit: 0b67b447d40038925dbee101308e4a26d650a06d
https://github.com/PathwayCommons/factoid/commit/0b67b447d40038925dbee101308e4a26d650a06d
Author: Max Franz <[email protected]>
Date: 2020-02-18 (Tue, 18 Feb 2020)
Changed paths:
M src/client/components/document-management.js
M src/client/components/editor/index.js
M src/client/components/home.js
M src/config.js
M src/server/routes/api/document/index.js
M src/styles/animations.css
M src/styles/editor/editor.css
M src/styles/home.css
M src/styles/image/banner.jpg
M src/styles/image/home-figure-1.jpg
A src/styles/image/logo-horizontal-name-only-white.svg
A src/styles/image/uni-logos-bw.png
Log Message:
-----------
Homepage redesign re. exploration & CTA
The homepage has been redesigned to allow for simple exploration of the
published documents. Above the fold, all documents in the published state are
listed in the homepage's new horizontal scroller UI. The scroller allows for
navigation of the list of available documents using a familiar interface.
In addition, the overall design of the homepage has been simplified. It now
contains only two full-page views. Below the fold, the project's aim and the
prospective contributor's task are concisely defined. The call to action is at
the end: With two simple pieces of information, the prospect's email and his
article's title, the prospect can become a user.
Other design details:
- The banner images have been improved, applying darkening and gaussian blur to
areas.
- There are new Contact, Github, and Twitter links.
- The page title is set depending on the view. The prospect in the organic
growth cycle would have two open tabs when he becomes a user. This
disambiguates them.
- Home: `Biofactoid`
- Editor or explore: `Article title : Biofactoid`
- Admin: `Admin : Biofactoid`
- A sliding gradient animation is shown on a scroller document that is loading.
Other technical details:
- The document list route is amended to show only public information without
the API key. With the API key, secret information is returned.
- Requests for document snapshot thumbnails are cached in memory in an LRU
cache. At most `DOCUMENT_IMAGE_CACHE_SIZE` images are cached. These images
are cached as base 64 buffers.
- The scroller lists all documents when the app is run in debug mode.
Commit: f43cb17c885bf109dea6a41eecd9862a2505a866
https://github.com/PathwayCommons/factoid/commit/f43cb17c885bf109dea6a41eecd9862a2505a866
Author: Max Franz <[email protected]>
Date: 2020-02-20 (Thu, 20 Feb 2020)
Changed paths:
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #639 from PathwayCommons/iss627_email-on-publish
Submit: Publish & Email follow-up notification
Commit: 3c8c2d692774cdddeae435daf78fede8c0d1c5f4
https://github.com/PathwayCommons/factoid/commit/3c8c2d692774cdddeae435daf78fede8c0d1c5f4
Author: Max Franz <[email protected]>
Date: 2020-02-20 (Thu, 20 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/styles/editor/editor.css
M src/styles/tasks.css
Log Message:
-----------
Merge pull request #637 from PathwayCommons/iss627_submit-dialog
Submit button and tooltip / message
Commit: 2eb6b90a6fae342ac099791859b3a941b8994968
https://github.com/PathwayCommons/factoid/commit/2eb6b90a6fae342ac099791859b3a941b8994968
Author: Jeffrey <[email protected]>
Date: 2020-02-20 (Thu, 20 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
M src/styles/editor/editor.css
M src/styles/tasks.css
Log Message:
-----------
Merge branch 'unstable' into homepage-explore-etc
Commit: fa931a01319bce7b3b67fc71459384af7f938e1f
https://github.com/PathwayCommons/factoid/commit/fa931a01319bce7b3b67fc71459384af7f938e1f
Author: Max Franz <[email protected]>
Date: 2020-02-21 (Fri, 21 Feb 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Org case
Commit: d3a2d37609b58e85c3e5e27ce0d487dfdf06f603
https://github.com/PathwayCommons/factoid/commit/d3a2d37609b58e85c3e5e27ce0d487dfdf06f603
Author: Max Franz <[email protected]>
Date: 2020-02-21 (Fri, 21 Feb 2020)
Changed paths:
M src/client/components/document-management.js
M src/client/components/editor/index.js
M src/client/components/home.js
M src/config.js
M src/server/routes/api/document/index.js
M src/styles/animations.css
M src/styles/editor/editor.css
M src/styles/home.css
M src/styles/image/banner.jpg
M src/styles/image/home-figure-1.jpg
A src/styles/image/logo-horizontal-name-only-white.svg
A src/styles/image/uni-logos-bw.png
Log Message:
-----------
Merge pull request #641 from PathwayCommons/homepage-explore-etc
Homepage redesign re. exploration & CTA
Commit: 9dcc800d1b6ced36f66a4e91f4feee83e4962c24
https://github.com/PathwayCommons/factoid/commit/9dcc800d1b6ced36f66a4e91f4feee83e4962c24
Author: Max Franz <[email protected]>
Date: 2020-02-24 (Mon, 24 Feb 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
Log Message:
-----------
These changes resolve the alignment issue on NODE_ENV=production builds.
Ref : Footer logos on homepage are misaligned on production build #642
Commit: 221e1626a8d4d4dd1d29451a0c746167391e766b
https://github.com/PathwayCommons/factoid/commit/221e1626a8d4d4dd1d29451a0c746167391e766b
Author: Jeffrey Wong <[email protected]>
Date: 2020-02-25 (Tue, 25 Feb 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
- fall back in journal context to stubbing out article data with title
Commit: d456044c970d8b56041c38567b43aa810fc0ab37
https://github.com/PathwayCommons/factoid/commit/d456044c970d8b56041c38567b43aa810fc0ab37
Author: Max Franz <[email protected]>
Date: 2020-02-25 (Tue, 25 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/home.js
M src/server/routes/api/document/index.js
M src/styles/base.css
M src/styles/editor/editor.css
Log Message:
-----------
Link out to DOI in the editor title & relax pubmed rules for signup
Commit: 52cd368af753f3254a13f89709f618c6f7fc568e
https://github.com/PathwayCommons/factoid/commit/52cd368af753f3254a13f89709f618c6f7fc568e
Author: Max Franz <[email protected]>
Date: 2020-02-25 (Tue, 25 Feb 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Change "pathway" to "article" in recent docs ui
Commit: 505c207de7755a7dce9f71df2a37f6288208694e
https://github.com/PathwayCommons/factoid/commit/505c207de7755a7dce9f71df2a37f6288208694e
Author: Max Franz <[email protected]>
Date: 2020-02-25 (Tue, 25 Feb 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Only show published docs in the scroller -- even in debug mode
Commit: 9243d097c32df50a622634c7e22ef7cfd33f86ea
https://github.com/PathwayCommons/factoid/commit/9243d097c32df50a622634c7e22ef7cfd33f86ea
Author: Max Franz <[email protected]>
Date: 2020-02-25 (Tue, 25 Feb 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/home.js
M src/server/routes/api/document/index.js
M src/styles/base.css
M src/styles/editor/editor.css
Log Message:
-----------
Merge pull request #643 from PathwayCommons/journal-request-nopubmed
Journal request nopubmed
Commit: 868bc81496bbbe29f909553868fe39bcbb0cf0f4
https://github.com/PathwayCommons/factoid/commit/868bc81496bbbe29f909553868fe39bcbb0cf0f4
Author: Max Franz <[email protected]>
Date: 2020-02-25 (Tue, 25 Feb 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
lint
Commit: 5b001c07688994868c12085d0bbea521837fbb5b
https://github.com/PathwayCommons/factoid/commit/5b001c07688994868c12085d0bbea521837fbb5b
Author: Max Franz <[email protected]>
Date: 2020-02-25 (Tue, 25 Feb 2020)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
0.7.0
Commit: 8d1ed98c5eb1eb1182c09258ee635cf516c491a2
https://github.com/PathwayCommons/factoid/commit/8d1ed98c5eb1eb1182c09258ee635cf516c491a2
Author: Jeffrey <[email protected]>
Date: 2020-02-25 (Tue, 25 Feb 2020)
Changed paths:
M README.md
M package-lock.json
M package.json
M src/client/components/document-management-components.js
M src/client/components/document-management.js
M src/client/components/editor/index.js
M src/client/components/home.js
A src/client/components/tasks.js
M src/config.js
M src/model/document/document.js
M src/server/index.js
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/server/routes/index.js
M src/styles/animations.css
M src/styles/base.css
M src/styles/document-management.css
M src/styles/editor/editor.css
M src/styles/help.css
M src/styles/home.css
M src/styles/image/banner.jpg
M src/styles/image/home-figure-1.jpg
A src/styles/image/logo-horizontal-name-only-white.svg
A src/styles/image/uni-logos-bw.png
M src/styles/image/welcome-aboard-3.svg
A src/styles/image/welcome-aboard-4.svg
M src/styles/index.css
A src/styles/tasks.css
M src/util/email.js
M src/util/pubmed.js
A src/views/404.ejs
R src/views/404.html
M test/pubmed/fetchPubmed.js
Log Message:
-----------
Merge pull request #644 from PathwayCommons/v0.7.0-release
V0.7.0 release
Compare:
https://github.com/PathwayCommons/factoid/compare/a82288b0c42b...8d1ed98c5eb1
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