Branch: refs/heads/master
Home: https://github.com/PathwayCommons/factoid
Commit: ed87aea7a330ba461f4e902316f8d89f3b5794b8
https://github.com/PathwayCommons/factoid/commit/ed87aea7a330ba461f4e902316f8d89f3b5794b8
Author: Jeffrey <[email protected]>
Date: 2020-10-05 (Mon, 05 Oct 2020)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
Merge pull request #859 from PathwayCommons/v0.11.0
0.11.0
Commit: 4b70bad414ba3f9c9d7cf1bb3bdc536e6d1ec984
https://github.com/PathwayCommons/factoid/commit/4b70bad414ba3f9c9d7cf1bb3bdc536e6d1ec984
Author: Max Franz <[email protected]>
Date: 2020-10-08 (Thu, 08 Oct 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Take into account `lastEditedDate` in the document image cache
Refs. : Document post-mortem: Missing metadata and misc problems #851
Commit: e370d3392bf09eeb14357418e2b52bf9fe60d282
https://github.com/PathwayCommons/factoid/commit/e370d3392bf09eeb14357418e2b52bf9fe60d282
Author: Max Franz <[email protected]>
Date: 2020-10-08 (Thu, 08 Oct 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Remove logs
Commit: 605163b93797984bbae27f7b20c114c9aff14b92
https://github.com/PathwayCommons/factoid/commit/605163b93797984bbae27f7b20c114c9aff14b92
Author: Max Franz <[email protected]>
Date: 2020-10-08 (Thu, 08 Oct 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
-----------
More aggressive Indra retries
- Increase the number of retries.
- Add a random delta so that different queries don't tend to come in at the
same time.
Refs. : Document post-mortem: Missing metadata and misc problems #851
Commit: 2cdb267547d8b70061ea24b6a777826ec30194de
https://github.com/PathwayCommons/factoid/commit/2cdb267547d8b70061ea24b6a777826ec30194de
Author: Max Franz <[email protected]>
Date: 2020-10-08 (Thu, 08 Oct 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #864 from PathwayCommons/clear-img-cache-851
Take into account `lastEditedDate` in the document image cache
Commit: 4def92b647b003cc1fdecaa2ffeb7442e820a01b
https://github.com/PathwayCommons/factoid/commit/4def92b647b003cc1fdecaa2ffeb7442e820a01b
Author: Max Franz <[email protected]>
Date: 2020-10-08 (Thu, 08 Oct 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/model/document/document.js
M src/model/element/entity.js
M src/model/organism.js
Log Message:
-----------
More salient organism in entity grounding popover
- Make the organism name salient (at the top) in the grounding popover.
- Add `ent.organism()` shortcut function to get the `Organism` an `Entity` is
grounded to (may be null for chemical).
- Add `doc.commonOrganism()` to get the most common `Organism` in a `Document`
-- may be null in the case of a tie.
- Add `doc.irregularOrganismEntities()` to get an array of entities that are
grounded to an organism other than the common one.
Refs. :
- Grounding: Entity organism preference / mixed organisms for genes #861
- Block users from submitting empty documents #860
Commit: 47c3f163325086e71ddd1f75ea8c1c809ad11308
https://github.com/PathwayCommons/factoid/commit/47c3f163325086e71ddd1f75ea8c1c809ad11308
Author: Jeffrey <[email protected]>
Date: 2020-10-08 (Thu, 08 Oct 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/model/document/document.js
M src/model/element/entity.js
M src/model/organism.js
Log Message:
-----------
Merge pull request #866 from PathwayCommons/organism-validation
More salient organism in entity grounding popover
Commit: 636a1b628d5d0e5178fbeee630d3ccd39bf88e98
https://github.com/PathwayCommons/factoid/commit/636a1b628d5d0e5178fbeee630d3ccd39bf88e98
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-08 (Thu, 08 Oct 2020)
Changed paths:
M src/client/components/tasks.js
M src/model/element/entity.js
M src/styles/tasks.css
Log Message:
-----------
- Warn if organisms are different
- Create task list component
Commit: c5dc3e0e66b25d6842500690b113f5b8e1889102
https://github.com/PathwayCommons/factoid/commit/c5dc3e0e66b25d6842500690b113f5b8e1889102
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-08 (Thu, 08 Oct 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
-----------
Make the message for organisms more generic
Commit: 9d7bfe4a1b1437a55497595b0d0e9150a14f9a45
https://github.com/PathwayCommons/factoid/commit/9d7bfe4a1b1437a55497595b0d0e9150a14f9a45
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
-----------
Irregular organism message and list text
Commit: ff88cfa44ad873528dffd50dd52580ab1b079db7
https://github.com/PathwayCommons/factoid/commit/ff88cfa44ad873528dffd50dd52580ab1b079db7
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/editor/submit.js
M src/client/components/tasks.js
Log Message:
-----------
- Add warning for no entity in submit
- Add components for closing tooltip on click
Commit: 6f188549f20ca283f9fc0f198081059f353f56a8
https://github.com/PathwayCommons/factoid/commit/6f188549f20ca283f9fc0f198081059f353f56a8
Author: Max Franz <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/model/document/document.js
Log Message:
-----------
Allow for excluding entities in doc organism counts
Commit: b0431a20c3ace13ddeed366ce6942fddf9234198
https://github.com/PathwayCommons/factoid/commit/b0431a20c3ace13ddeed366ce6942fddf9234198
Author: Max Franz <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/model/element/element.js
Log Message:
-----------
Allow for entity comparison via `ele.same(otherEle)`
Commit: 79c9ca34b8ed0943f19437421994299f4fb60e49
https://github.com/PathwayCommons/factoid/commit/79c9ca34b8ed0943f19437421994299f4fb60e49
Author: Max Franz <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Exclude popover entity from being included in organism count
E.g. while typing 'smad3':
(1) You probably type 'smad' quickly. That's one query. The node is now
grounded to smad9 (mouse).
(2) You now add '3'. The grounding is now for smad3 mouse instead of human,
because (1) added a bias to mouse.
Commit: 4eee4b6b8b28e030a92867899b78d21895cc9c99
https://github.com/PathwayCommons/factoid/commit/4eee4b6b8b28e030a92867899b78d21895cc9c99
Author: Max Franz <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Use grounding IDs instead of indices for dropdowns
- Use `ns:id` as ID.
- Use `value` instead of `defaultValue`. React doesn't use `defaultValue`
properly.
Commit: 6588858e7d9edab23601718c368c764b6e546d30
https://github.com/PathwayCommons/factoid/commit/6588858e7d9edab23601718c368c764b6e546d30
Author: Max Franz <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
-----------
Merge pull request #865 from PathwayCommons/indra-more-retries-851
More aggressive Indra retries
Commit: 0102a3f99974c62401ecbae6df4267dd1d250bba
https://github.com/PathwayCommons/factoid/commit/0102a3f99974c62401ecbae6df4267dd1d250bba
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
-----------
Swap out 'Submit' with 'Show me how' button
Commit: 9c2039e8646499d6e85637144f2bd0dc386202c6
https://github.com/PathwayCommons/factoid/commit/9c2039e8646499d6e85637144f2bd0dc386202c6
Author: Jeffrey <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/editor/submit.js
M src/client/components/tasks.js
M src/model/element/entity.js
M src/styles/tasks.css
Log Message:
-----------
Merge pull request #868 from
PathwayCommons/iss860_empty-submit_iss861_irregular-org
Iss860 empty submit iss861 irregular org
Commit: 7ae22ec9e6625d69a5ce32561873673e1bab77c8
https://github.com/PathwayCommons/factoid/commit/7ae22ec9e6625d69a5ce32561873673e1bab77c8
Author: Max Franz <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/model/document/document.js
M src/model/element/element.js
Log Message:
-----------
Merge pull request #869 from PathwayCommons/org-dropdown-misc
Organism dropdown misc
Commit: e95cc4284ed4935682770988138ff7ae734b8158
https://github.com/PathwayCommons/factoid/commit/e95cc4284ed4935682770988138ff7ae734b8158
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/document-management-components.js
Log Message:
-----------
Remove disabling of email buttons
Commit: 132469357f9270c245d14de2250e3ab9528299ce
https://github.com/PathwayCommons/factoid/commit/132469357f9270c245d14de2250e3ab9528299ce
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/document-management.js
M src/styles/document-management.css
Log Message:
-----------
Add spinner on load
Commit: b5b7d8c10d6dfd5ec1990f2d3b7d18c3f84f289d
https://github.com/PathwayCommons/factoid/commit/b5b7d8c10d6dfd5ec1990f2d3b7d18c3f84f289d
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/styles/document-management.css
Log Message:
-----------
Remove the extremely large width of the page.
Commit: 8de2c0a5e0620dee959c7e3bca3734df641ab965
https://github.com/PathwayCommons/factoid/commit/8de2c0a5e0620dee959c7e3bca3734df641ab965
Author: Jeffrey <[email protected]>
Date: 2020-10-09 (Fri, 09 Oct 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/client/components/document-management.js
M src/styles/document-management.css
Log Message:
-----------
Merge pull request #870 from PathwayCommons/iss852_eliminate-disable-email
Admin: Email disabling, spinner and large page width
Commit: 74ceb106f67faec335b601d2e5b487a7630c9c51
https://github.com/PathwayCommons/factoid/commit/74ceb106f67faec335b601d2e5b487a7630c9c51
Author: Max Franz <[email protected]>
Date: 2020-10-13 (Tue, 13 Oct 2020)
Changed paths:
M package-lock.json
M package.json
M src/client/index.js
M src/client/polyfills.js
Log Message:
-----------
Use smooth scroll polyfill for the carousel on Safari
Commit: 0388c7e2e7cc9f4cc1b8eadc912ac6912c05cf52
https://github.com/PathwayCommons/factoid/commit/0388c7e2e7cc9f4cc1b8eadc912ac6912c05cf52
Author: Max Franz <[email protected]>
Date: 2020-10-13 (Tue, 13 Oct 2020)
Changed paths:
M src/styles/carousel.css
Log Message:
-----------
Allow long interaction strings to be readable in the carousel
Commit: 52568e9b0df73a1b663994f8a95e164acd26e653
https://github.com/PathwayCommons/factoid/commit/52568e9b0df73a1b663994f8a95e164acd26e653
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-13 (Tue, 13 Oct 2020)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
0.12.0
Commit: 6751b8551227b3ce15f2824bce069922a767f947
https://github.com/PathwayCommons/factoid/commit/6751b8551227b3ce15f2824bce069922a767f947
Author: Max Franz <[email protected]>
Date: 2020-10-13 (Tue, 13 Oct 2020)
Changed paths:
M package-lock.json
M package.json
M src/client/index.js
M src/client/polyfills.js
M src/styles/carousel.css
Log Message:
-----------
Merge pull request #871 from PathwayCommons/carousel-misc-tweaks
Carousel misc tweaks
Commit: c7c45b52beed2cc7eef2b074997ea1bff19fcf02
https://github.com/PathwayCommons/factoid/commit/c7c45b52beed2cc7eef2b074997ea1bff19fcf02
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-13 (Tue, 13 Oct 2020)
Changed paths:
M package-lock.json
M package.json
M src/client/index.js
M src/client/polyfills.js
M src/styles/carousel.css
Log Message:
-----------
Merge branch 'unstable' into v0.12.0
Commit: 4d85fedc4ade225ffe1d9dc110fe3560ec4d30fd
https://github.com/PathwayCommons/factoid/commit/4d85fedc4ade225ffe1d9dc110fe3560ec4d30fd
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-13 (Tue, 13 Oct 2020)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
0.12.1
Commit: 8fdabfd4699a8fbfcba8bc4855605da299148b88
https://github.com/PathwayCommons/factoid/commit/8fdabfd4699a8fbfcba8bc4855605da299148b88
Author: Jeffrey <[email protected]>
Date: 2020-10-13 (Tue, 13 Oct 2020)
Changed paths:
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/submit.js
M src/client/components/element-info/entity-info.js
M src/client/components/tasks.js
M src/client/index.js
M src/client/polyfills.js
M src/model/document/document.js
M src/model/element/element.js
M src/model/element/entity.js
M src/model/organism.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
M src/styles/carousel.css
M src/styles/document-management.css
M src/styles/tasks.css
Log Message:
-----------
Merge pull request #872 from PathwayCommons/v0.12.0
V0.12.0
Compare:
https://github.com/PathwayCommons/factoid/compare/eef3d919966f...8fdabfd4699a
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