Branch: refs/heads/form-templates
Home: https://github.com/PathwayCommons/factoid
Commit: 55fd78553f8ab344b40835471f83b27a33a37437
https://github.com/PathwayCommons/factoid/commit/55fd78553f8ab344b40835471f83b27a33a37437
Author: Max Franz <[email protected]>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
M src/server/routes/api/document/reach.js
Log Message:
-----------
Change reach to use the upload file route
Commit: f195f078189be3b914feddb5470a7e2ba1b0df0b
https://github.com/PathwayCommons/factoid/commit/f195f078189be3b914feddb5470a7e2ba1b0df0b
Author: Max Franz <[email protected]>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M src/model/document/document.js
M src/util/obj.js
M test/document.js
Log Message:
-----------
Add a count for organism mentions
- An explicit mention counts as 1.
- Each entity associated with the organism counts as 1.
- This gives a total for the number of implicit and explicit organism mentions.
- Add tests.
- There is no caching, so you probably shouldn't call `doc.organismCount()`
over and over.
Commit: e5a6be9de1469bb398c00477be7822617f0c708c
https://github.com/PathwayCommons/factoid/commit/e5a6be9de1469bb398c00477be7822617f0c708c
Author: Max Franz <[email protected]>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M src/util/memoize.js
Log Message:
-----------
Allow `util.memoize()` to specify the key function args more naturally
Commit: bd52ef6f748b83fd66c46c559dae243aee209cc6
https://github.com/PathwayCommons/factoid/commit/bd52ef6f748b83fd66c46c559dae243aee209cc6
Author: Max Franz <[email protected]>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M src/server/routes/api/element-association/aggregate.js
Log Message:
-----------
Decorate the entities returned by the aggregate search service with distance
Commit: 12196ad74a29845cbd9126947ca733f7731750c1
https://github.com/PathwayCommons/factoid/commit/12196ad74a29845cbd9126947ca733f7731750c1
Author: Max Franz <[email protected]>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Do not filter by organism in the entity association UI
Commit: 326f3aa0ac58f7d1bea920a57469224e9c35d280
https://github.com/PathwayCommons/factoid/commit/326f3aa0ac58f7d1bea920a57469224e9c35d280
Author: Max Franz <[email protected]>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M src/util/memoize.js
Log Message:
-----------
Use a map by default for memoize
Commit: f6a4cfc930f937ed83eb713c5f8127da1430a310
https://github.com/PathwayCommons/factoid/commit/f6a4cfc930f937ed83eb713c5f8127da1430a310
Author: Max Franz <[email protected]>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/model/document/document.js
M src/server/routes/api/element-association/aggregate.js
M src/server/routes/api/element-association/index.js
Log Message:
-----------
Search takes into account organism counts
Commit: 5c705bc4dbbcbcfae31c097a0f6a759dc21e6160
https://github.com/PathwayCommons/factoid/commit/5c705bc4dbbcbcfae31c097a0f6a759dc21e6160
Author: Max Franz <[email protected]>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M src/config.js
Log Message:
-----------
Use `'http://reach.baderlab.org/api/textBody'` by default for `REACH_URL`
Ref : Expose the Reach Docker service as reach.baderlab.org #233
Commit: 5ad5506f6755cd6bcd4cd9d4156c8a9a5c330c2f
https://github.com/PathwayCommons/factoid/commit/5ad5506f6755cd6bcd4cd9d4156c8a9a5c330c2f
Author: Max Franz <[email protected]>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M src/config.js
Log Message:
-----------
Do not let empty strings (e.g. `export REACH_URL=''`) override defaults
Commit: be6492f165c2c446f30cfe8cf4da0beeca521e68
https://github.com/PathwayCommons/factoid/commit/be6492f165c2c446f30cfe8cf4da0beeca521e68
Author: Max Franz <[email protected]>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M src/model/organism.js
M src/server/routes/api/element-association/aggregate.js
Log Message:
-----------
Add a default organism ordering for unseeded, empty documents
Commit: f0f4a7bd5077702de158b6b39a380ab9f76e8837
https://github.com/PathwayCommons/factoid/commit/f0f4a7bd5077702de158b6b39a380ab9f76e8837
Author: Max Franz <[email protected]>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/model/document/document.js
M src/model/organism.js
M src/server/routes/api/element-association/aggregate.js
M src/server/routes/api/element-association/index.js
M src/util/memoize.js
M src/util/obj.js
M test/document.js
Log Message:
-----------
Automate organism input #169
Commit: d7c465a213d37f4b9f0bd39587ed32dbd2f41b5c
https://github.com/PathwayCommons/factoid/commit/d7c465a213d37f4b9f0bd39587ed32dbd2f41b5c
Author: Max Franz <[email protected]>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Even the selected modification may be clicked to go to the next stage.
This is useful in the case where a user cancels modification when he goes back.
Commit: 526745883ea74c194d413c2da450d597c5cac874
https://github.com/PathwayCommons/factoid/commit/526745883ea74c194d413c2da450d597c5cac874
Author: Max Franz <[email protected]>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M src/server/routes/api/document/reach.js
Log Message:
-----------
Use the uploadFile endpoint for REACH docker instance. #231
Merge reach-upload into unstable
Commit: 1b7cb381723ed706336040581a1f2ac5e3e6f201
https://github.com/PathwayCommons/factoid/commit/1b7cb381723ed706336040581a1f2ac5e3e6f201
Author: Max Franz <[email protected]>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M src/config.js
Log Message:
-----------
Change default reach ref on baderlab.org to use uploadFIle
Commit: 7811a1c1382cdb6fc5a9b661d18748e2f7e9353e
https://github.com/PathwayCommons/factoid/commit/7811a1c1382cdb6fc5a9b661d18748e2f7e9353e
Author: Max Franz <[email protected]>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/styles/notification.css
Log Message:
-----------
Tweaks to the notifications #238
- Make the notifications have shorter text.
- Increase the font size of the notifications.
- Resolve a minor alignment issue for inline notifications on large screens.
Commit: 22affccd71eec0242336659c5e22777cc112d369
https://github.com/PathwayCommons/factoid/commit/22affccd71eec0242336659c5e22777cc112d369
Author: fdurupinar <[email protected]>
Date: 2018-04-03 (Tue, 03 Apr 2018)
Changed paths:
A .idea/codeStyles/Project.xml
A .idea/codeStyles/codeStyleConfig.xml
A .idea/inspectionProfiles/Project_Default.xml
A .idea/vcs.xml
Log Message:
-----------
title names
Commit: 7927cdbd783922603bbf2774f730e7cac5cbd5bd
https://github.com/PathwayCommons/factoid/commit/7927cdbd783922603bbf2774f730e7cac5cbd5bd
Author: fdurupinar <[email protected]>
Date: 2018-04-04 (Wed, 04 Apr 2018)
Changed paths:
R .idea/codeStyles/codeStyleConfig.xml
M src/client/components/element-info/entity-info.js
A src/client/components/form-editor/activation-inhibition-form.js
A src/client/components/form-editor/biochemical-reaction-form.js
A src/client/components/form-editor/complex-interaction-form.js
A src/client/components/form-editor/entity-form.js
A src/client/components/form-editor/expression-regulation-form.js
M src/client/components/form-editor/index.js
A src/client/components/form-editor/interaction-form.js
A src/client/components/form-editor/location-change-form.js
A src/client/components/form-editor/physical-interaction-form.js
A src/client/components/form-editor/protein-modification-form.js
M src/config.js
M src/model/document/document.js
M src/model/organism.js
M src/server/routes/api/document/reach.js
M src/server/routes/api/element-association/aggregate.js
M src/server/routes/api/element-association/index.js
M src/styles/notification.css
M src/util/memoize.js
M src/util/obj.js
M test/document.js
Log Message:
-----------
restructured
Compare:
https://github.com/PathwayCommons/factoid/compare/96207844fa8b...7927cdbd7839
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