Branch: refs/heads/unstable
Home: https://github.com/PathwayCommons/factoid
Commit: 9e2351134fc7fa17d51dc9564a930f4a0799f945
https://github.com/PathwayCommons/factoid/commit/9e2351134fc7fa17d51dc9564a930f4a0799f945
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-07 (Wed, 07 Nov 2018)
Changed paths:
A src/model/element/interaction-type/binding.js
M src/model/element/interaction-type/biopax-type.js
A src/model/element/interaction-type/demethylation.js
A src/model/element/interaction-type/dephosphorylation.js
A src/model/element/interaction-type/deubiquination.js
M src/model/element/interaction-type/enum.js
R src/model/element/interaction-type/expression.js
R src/model/element/interaction-type/general.js
M src/model/element/interaction-type/interaction-type.js
A src/model/element/interaction-type/interaction.js
M src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
M src/model/element/interaction-type/phosphorylation.js
R src/model/element/interaction-type/protein-chemical.js
A src/model/element/interaction-type/transcription-translation.js
M src/model/element/interaction-type/ubiquination.js
Log Message:
-----------
Initial changes to the model re. 'Factoid binary interactions' specification
- Change General type to Interaction. It still has the enum string
'interaction', but its display value has changed to 'Other' and its class name
is more like Biopax.
- Remove the ProteinChemical type.
- Add Binding type.
- Add De- variants of Phosphorylation, Methylation, and Ubiquination.
- Change Expression type to TranscriptionTranslation.
- Update the isAllowedForInteraction rules. These rules are not yet as strict
as in the spec, because it may otherwise over-restrict the allowed types in the
UI. We may have to re-evaluate how these rules get applied on the UI level.
- There are TODO BIOPAX comments for places in the code that definitely need to
be updated for the Biopax template convertor.
- Good news: The network editor still works -- well enough for testing exports
anyway.
Commit: 471234ce4c0bd7665095f8037652ca6481bee99f
https://github.com/PathwayCommons/factoid/commit/471234ce4c0bd7665095f8037652ca6481bee99f
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-07 (Wed, 07 Nov 2018)
Changed paths:
M test/interaction.js
Log Message:
-----------
Fix changed EXPRESSION reference
Commit: 5d9ffb096cee6deb75765cdd7d87ae99880fe384
https://github.com/PathwayCommons/factoid/commit/5d9ffb096cee6deb75765cdd7d87ae99880fe384
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M src/model/element/interaction-type/demethylation.js
Log Message:
-----------
Rename internal Demethylation class name
Commit: 13d94464acbb5790466d23c421efbfb902a3b50f
https://github.com/PathwayCommons/factoid/commit/13d94464acbb5790466d23c421efbfb902a3b50f
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
R src/model/element/interaction-type/deubiquination.js
A src/model/element/interaction-type/deubiquitination.js
M src/model/element/interaction-type/enum.js
R src/model/element/interaction-type/ubiquination.js
A src/model/element/interaction-type/ubiquitination.js
Log Message:
-----------
Ubiquitination typo
Commit: a88eff08a23f66fae6ef6e28fecb528240e7c105
https://github.com/PathwayCommons/factoid/commit/a88eff08a23f66fae6ef6e28fecb528240e7c105
Author: IgorRodchenkov <rod...@gmail.com>
Date: 2018-11-11 (Sun, 11 Nov 2018)
Changed paths:
M .gitignore
M package-lock.json
M src/client/components/editor/cy/edgehandles.js
M src/client/components/element-info/interaction-info.js
M src/client/components/form-editor/index.js
M src/model/document/document.js
M src/model/element/entity-type.js
M src/model/element/entity.js
M src/model/element/interaction-type/binding.js
M src/model/element/interaction-type/biopax-type.js
M src/model/element/interaction-type/demethylation.js
M src/model/element/interaction-type/dephosphorylation.js
M src/model/element/interaction-type/deubiquitination.js
M src/model/element/interaction-type/enum.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction-type/interaction.js
M src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
M src/model/element/interaction-type/phosphorylation.js
M src/model/element/interaction-type/transcription-translation.js
M src/model/element/interaction-type/ubiquitination.js
M src/server/routes/api/document/reach.js
Log Message:
-----------
Implemented what refs #382 and fixed a couple of prev. refactoring bugs
(e.g., got rid of old "chemicalprotein" type)
You cannot export to BioPAX until factoid-converters is updated too
(but you can see the intermediate JSON output in the log; see TODOs..)
Commit: 11278d0f0b7b2f4ced3d8dccc345890a2c0ccf7c
https://github.com/PathwayCommons/factoid/commit/11278d0f0b7b2f4ced3d8dccc345890a2c0ccf7c
Author: IgorRodchenkov <rod...@gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M package-lock.json
M src/client/components/editor/cy/edgehandles.js
M src/model/document/document.js
M src/model/element/interaction-type/modification.js
Log Message:
-----------
Refs #382 and PR #384 (to fix lint errors); also changed modification type
name to "Modification/activity change "
Commit: 20d270350ea3e35e06fdf233e67f02e1c79dfb54
https://github.com/PathwayCommons/factoid/commit/20d270350ea3e35e06fdf233e67f02e1c79dfb54
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M src/client/components/element-info/interaction-info.js
Log Message:
-----------
Remove unneeded code
Commit: 0f6d6ce052dbf0568865815b2917da178817f0ea
https://github.com/PathwayCommons/factoid/commit/0f6d6ce052dbf0568865815b2917da178817f0ea
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M src/client/components/element-info/interaction-info.js
Log Message:
-----------
Fix linting
Commit: 2bcf6c9ff15e0ebf8ca5a12c019b1ce673baf030
https://github.com/PathwayCommons/factoid/commit/2bcf6c9ff15e0ebf8ca5a12c019b1ce673baf030
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M src/model/document/document.js
Log Message:
-----------
Remove log
Commit: 4e3da330bbb8db2156ecd286dc9dd3217599237c
https://github.com/PathwayCommons/factoid/commit/4e3da330bbb8db2156ecd286dc9dd3217599237c
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M src/model/element/interaction-type/binding.js
M src/model/element/interaction-type/enum.js
Log Message:
-----------
Misc comments
Commit: 909002de326bed8bbfff8488f8b4fdc25935169f
https://github.com/PathwayCommons/factoid/commit/909002de326bed8bbfff8488f8b4fdc25935169f
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M src/model/element/interaction-type/modification.js
Log Message:
-----------
Use old name for PTM
Commit: c80e0eebe802baebdc34c6e8e9fe388a580eac06
https://github.com/PathwayCommons/factoid/commit/c80e0eebe802baebdc34c6e8e9fe388a580eac06
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M src/model/element/interaction-type/interaction.js
Log Message:
-----------
Just use superclass toString
Commit: be5886ac95456464af039c919736ee1d0f339f6b
https://github.com/PathwayCommons/factoid/commit/be5886ac95456464af039c919736ee1d0f339f6b
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M .gitignore
M package-lock.json
M src/client/components/editor/cy/edgehandles.js
M src/client/components/element-info/interaction-info.js
M src/client/components/form-editor/index.js
M src/model/element/entity-type.js
M src/model/element/entity.js
M src/model/element/interaction-type/binding.js
M src/model/element/interaction-type/biopax-type.js
M src/model/element/interaction-type/demethylation.js
M src/model/element/interaction-type/dephosphorylation.js
M src/model/element/interaction-type/deubiquitination.js
M src/model/element/interaction-type/enum.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction-type/interaction.js
M src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
M src/model/element/interaction-type/phosphorylation.js
M src/model/element/interaction-type/transcription-translation.js
M src/model/element/interaction-type/ubiquitination.js
M src/server/routes/api/document/reach.js
Log Message:
-----------
Merge IgorRodchenkov-model-bin-intns into model-bin-intns
Commit: e7e63ef8e6f51e72535a927d6ca0a4a85fcb05f2
https://github.com/PathwayCommons/factoid/commit/e7e63ef8e6f51e72535a927d6ca0a4a85fcb05f2
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M .gitignore
M package-lock.json
M src/client/components/editor/cy/edgehandles.js
M src/client/components/element-info/interaction-info.js
M src/client/components/form-editor/index.js
M src/model/element/entity-type.js
M src/model/element/entity.js
A src/model/element/interaction-type/binding.js
M src/model/element/interaction-type/biopax-type.js
A src/model/element/interaction-type/demethylation.js
A src/model/element/interaction-type/dephosphorylation.js
A src/model/element/interaction-type/deubiquitination.js
M src/model/element/interaction-type/enum.js
R src/model/element/interaction-type/expression.js
R src/model/element/interaction-type/general.js
M src/model/element/interaction-type/interaction-type.js
A src/model/element/interaction-type/interaction.js
M src/model/element/interaction-type/modification.js
R src/model/element/interaction-type/protein-chemical.js
A src/model/element/interaction-type/transcription-translation.js
R src/model/element/interaction-type/ubiquination.js
A src/model/element/interaction-type/ubiquitination.js
M src/server/routes/api/document/reach.js
M test/interaction.js
Log Message:
-----------
Merge pull request #381 from PathwayCommons/model-bin-intns
Initial changes to the model re. 'Factoid binary interactions' specification
Compare:
https://github.com/PathwayCommons/factoid/compare/d80dd3abf03c...e7e63ef8e6f5
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https://developer.github.com/changes/2018-04-25-github-services-deprecation/
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