Branch: refs/heads/alpha
Home: https://github.com/PathwayCommons/factoid
Commit: f1f109367045d96f1a2b41a0ee7419b219e2d04c
https://github.com/PathwayCommons/factoid/commit/f1f109367045d96f1a2b41a0ee7419b219e2d04c
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-07-14 (Fri, 14 Jul 2017)
Changed paths:
M package.json
Log Message:
-----------
`forever stopall` for `npm stop` to avoid forever non-zero exit codes
Commit: 537c2082be40f22d34bc14a658f6ec4ef02d8a66
https://github.com/PathwayCommons/factoid/commit/537c2082be40f22d34bc14a658f6ec4ef02d8a66
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M .travis.yml
M README.md
M Vagrantfile
M package.json
M src/client/components/editor/buttons.js
M src/client/components/editor/cy/automove.js
M src/client/components/editor/cy/cxtmenu.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/edgehandles.js
M src/client/components/editor/cy/index.js
M src/client/components/editor/cy/layout.js
M src/client/components/editor/cy/make-cy-eles.js
M src/client/components/editor/cy/qtip.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/editor/index.js
M src/client/components/element-info.js
M src/client/components/entity-info.js
M src/client/components/interaction-info.js
M src/model/document/document.js
M src/model/element-set.js
M src/model/element/entity.js
M src/model/element/interaction.js
M src/model/syncher.js
M src/styles/base.css
M src/styles/editor/editor.css
M src/styles/editor/element-info.css
M src/styles/editor/entity-info.css
M src/styles/editor/interaction-info.css
M src/styles/vars.css
M src/util/dom.js
M src/util/is.js
M src/util/promise.js
Log Message:
-----------
Merge branch 'unstable'
Commit: a760377d69047c00495b2d391aeaeff4f477426b
https://github.com/PathwayCommons/factoid/commit/a760377d69047c00495b2d391aeaeff4f477426b
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M package.json
A src/client/components/document-filler.js
A src/client/components/document-linkout.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/index.js
M src/client/components/editor/cy/layout.js
R src/client/components/editor/cy/make-cy-eles.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/editor/index.js
R src/client/components/editor/linkout.js
M src/client/components/editor/menu.js
M src/client/components/entity-info.js
A src/client/components/home.js
M src/client/components/interaction-info.js
R src/client/cytoscape-extensions.js
M src/client/index.js
M src/client/logger.js
M src/client/router.js
M src/model/document/document.js
M src/model/element-set.js
M src/model/element/element.js
M src/model/element/entity.js
M src/model/element/factory.js
M src/model/element/interaction.js
M src/model/organism.js
M src/server/index.js
M src/server/routes/api/document/index.js
A src/server/routes/api/document/reach.js
M src/styles/base.css
A src/styles/document-filler.css
A src/styles/document-linkout.css
M src/styles/editor/editor.css
A src/styles/home.css
M src/styles/index.css
A src/util/cy.js
M src/util/index.js
M src/util/is.js
M src/views/style-demo.html
Log Message:
-----------
Merge unstable into master
Commit: 6cf86f0ce767b5334c49ef9fc259768325a42c4b
https://github.com/PathwayCommons/factoid/commit/6cf86f0ce767b5334c49ef9fc259768325a42c4b
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M package.json
M src/client/components/document-filler.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/reach.js
Log Message:
-----------
Merge unstable into master
Commit: da0b609a3e49a1dbe26e2dcc0d8573346e3d8cf0
https://github.com/PathwayCommons/factoid/commit/da0b609a3e49a1dbe26e2dcc0d8573346e3d8cf0
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-12 (Tue, 12 Sep 2017)
Changed paths:
M src/server/routes/api/document/reach.js
Log Message:
-----------
Grounds in the map must be null checked because we now allow ungrounded
entities #145
Commit: 9e6cd247b5df2301004c6329bdc288280565f9c0
https://github.com/PathwayCommons/factoid/commit/9e6cd247b5df2301004c6329bdc288280565f9c0
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-16 (Mon, 16 Oct 2017)
Changed paths:
M .babelrc
R .cssnano.json
R .cssnext.json
M .eslintrc.json
R .uglify.json
M README.md
A browser-sync.config.js
R gulpfile.js
M package.json
A postcss.config.js
A public/deps.css
A src/client/components/animate.js
M src/client/components/document-linkout.js
M src/client/components/editor/buttons.js
M src/client/components/editor/cy/defs.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/edgehandles.js
M src/client/components/editor/cy/index.js
M src/client/components/editor/cy/layout.js
M src/client/components/editor/cy/stylesheet.js
A src/client/components/editor/cy/tippy.js
M src/client/components/editor/index.js
M src/client/components/entity-info.js
A src/client/components/highlighter.js
M src/client/components/interaction-info.js
A src/client/components/participant-info.js
M src/client/components/popover.js
M src/client/components/tooltip.js
M src/client/debug.js
M src/client/defs.js
M src/model/element/entity.js
M src/server/routes/api/document/reach.js
M src/server/routes/api/element-association/uniprot.js
M src/styles/base.css
A src/styles/deps.css
M src/styles/editor/editor.css
M src/styles/editor/element-info.css
M src/styles/editor/entity-info.css
M src/styles/editor/index.css
M src/styles/editor/interaction-info.css
A src/styles/editor/participant-info.css
A src/styles/highlighter.css
A src/styles/image/ic_keyboard_tab_24px.svg
M src/styles/index.css
M src/styles/popover.css
R src/styles/qtip.css
M src/styles/tippy.css
M src/styles/tooltip.css
M src/styles/vars.css
A src/styles/vendor/fonts/inconsolata-ascii/inconsolata-webfont.woff
A src/styles/vendor/fonts/inconsolata-ascii/inconsolata-webfont.woff2
A src/styles/vendor/fonts/open-sans-latin-greek/generator_config.txt
A src/styles/vendor/fonts/open-sans-latin-greek/opensans-bold-webfont.woff
A src/styles/vendor/fonts/open-sans-latin-greek/opensans-bold-webfont.woff2
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-bolditalic-webfont.woff
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-bolditalic-webfont.woff2
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-extrabold-webfont.woff
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-extrabold-webfont.woff2
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-extrabolditalic-webfont.woff
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-extrabolditalic-webfont.woff2
A src/styles/vendor/fonts/open-sans-latin-greek/opensans-italic-webfont.woff
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-italic-webfont.woff2
A src/styles/vendor/fonts/open-sans-latin-greek/opensans-light-webfont.woff
A src/styles/vendor/fonts/open-sans-latin-greek/opensans-light-webfont.woff2
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-lightitalic-webfont.woff
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-lightitalic-webfont.woff2
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-regular-webfont.woff
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-regular-webfont.woff2
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-semibold-webfont.woff
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-semibold-webfont.woff2
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-semibolditalic-webfont.woff
A
src/styles/vendor/fonts/open-sans-latin-greek/opensans-semibolditalic-webfont.woff2
A src/styles/vendor/inconsolata-ascii.css
A src/styles/vendor/open-sans-latin-greek.css
M src/util/cy.js
M src/util/dom.js
M src/views/404.html
M src/views/error.html
M src/views/index.html
M src/views/style-demo.html
M test/document.js
A webpack.config.js
Log Message:
-----------
User testing round 1 tweaks complete: Merge unstable into master
Commit: 4f1d5e153a948564617c8fbd96b31750d2f9db56
https://github.com/PathwayCommons/factoid/commit/4f1d5e153a948564617c8fbd96b31750d2f9db56
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-18 (Wed, 18 Oct 2017)
Changed paths:
M src/config.js
M src/server/routes/api/document/reach.js
M src/server/routes/api/element-association/uniprot.js
Log Message:
-----------
Merge unstable into master
Commit: ac9fef96b0cda6bbb02b6d9481e3760898241db0
https://github.com/PathwayCommons/factoid/commit/ac9fef96b0cda6bbb02b6d9481e3760898241db0
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M .babelrc
M .nvmrc
M README.md
M browser-sync.config.js
A jenkins.sh
A package-lock.json
M package.json
A src/client/components/conditional-tooltip.js
M src/client/components/dirty-component.js
M src/client/components/editor/cy/defs.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/index.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/defs.js
M src/client/components/editor/index.js
M src/client/components/element-info.js
M src/client/components/entity-info.js
M src/client/components/interaction-info.js
A src/client/components/notification/base.js
A src/client/components/notification/corner.js
A src/client/components/notification/index.js
A src/client/components/notification/inline.js
A src/client/components/notification/list.js
A src/client/components/notification/notification.js
A src/client/components/notification/panel.js
A src/client/components/notification/popover.js
M src/client/components/popover.js
M src/config.js
M src/model/document/document.js
M src/model/element-set.js
M src/model/element/element.js
M src/model/element/entity.js
M src/model/element/factory.js
R src/model/element/protein.js
M src/model/organism.js
M src/model/syncher.js
M src/server/routes/api/document/index.js
M src/server/routes/api/element-association/index.js
M src/server/routes/api/element-association/uniprot.js
M src/server/routes/api/index.js
M src/styles/base.css
M src/styles/editor/element-info.css
M src/styles/editor/entity-info.css
M src/styles/index.css
A src/styles/notification.css
M src/styles/tippy.css
M src/styles/vars.css
M src/util/cy.js
M src/util/index.js
A src/util/memoize.js
M src/util/obj.js
M test/document.js
M test/syncher.js
M test/util/socket-io.js
Log Message:
-----------
UI iteration complete, ready for user testing
Changes overview:
- Includes general UI improvements
- Includes staged entity grounding UI
- Includes notification system
Commit: 1cb14a87ff24907d9833902e9193cfca9d3999ab
https://github.com/PathwayCommons/factoid/commit/1cb14a87ff24907d9833902e9193cfca9d3999ab
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-11-29 (Wed, 29 Nov 2017)
Changed paths:
M src/styles/base.css
Log Message:
-----------
Fix joined input buttons, e.g. on textmining test page.
Commit: 04308810a88985c7a83bcda54ff0ac434a4f8fda
https://github.com/PathwayCommons/factoid/commit/04308810a88985c7a83bcda54ff0ac434a4f8fda
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-11-29 (Wed, 29 Nov 2017)
Changed paths:
M src/server/routes/api/document/reach.js
Log Message:
-----------
Ensure that all associated entities coming from textmining are considered
completed, though this may not be true if services like Reach do not include
information like entity state.
Commit: 427d7cc20c9670a6cf9b76881e12374f65ca1163
https://github.com/PathwayCommons/factoid/commit/427d7cc20c9670a6cf9b76881e12374f65ca1163
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-11-30 (Thu, 30 Nov 2017)
Changed paths:
M src/client/components/editor/cy/tippy.js
Log Message:
-----------
Avoid error when deleting an entity that has its entity popover shown.
Commit: cf506d4f0a98a899922f220fb450855079879daf
https://github.com/PathwayCommons/factoid/commit/cf506d4f0a98a899922f220fb450855079879daf
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-01-26 (Fri, 26 Jan 2018)
Changed paths:
M package-lock.json
M package.json
M src/client/components/editor/buttons.js
M src/client/components/editor/cy/automove.js
M src/client/components/editor/cy/cxtmenu.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/edgehandles.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/index.js
A src/client/components/editor/undo-remove.js
M src/client/components/entity-info.js
M src/client/components/highlighter.js
M src/client/components/notification/corner.js
M src/client/components/notification/popover.js
M src/client/components/popover.js
M src/client/components/tooltip.js
M src/client/defs.js
M src/config.js
M src/model/document/document.js
M src/model/element-set.js
M src/model/element/element.js
M src/model/element/entity.js
M src/model/element/factory.js
M src/model/element/interaction.js
M src/model/organism.js
M src/model/syncher.js
M src/server/routes/api/document/reach.js
A src/server/routes/api/element-association/aggregate.js
A src/server/routes/api/element-association/chebi.js
M src/server/routes/api/element-association/index.js
A src/server/routes/api/element-association/pubchem.js
A src/server/routes/api/element-association/search-string-conversion.js
M src/server/routes/api/element-association/uniprot.js
M src/styles/editor/element-info.css
M src/styles/editor/entity-info.css
M src/styles/editor/index.css
A src/styles/editor/undo-remove.css
M src/styles/notification.css
M src/styles/tippy.css
M src/styles/tooltip.css
M src/util/memoize.js
M src/util/obj.js
Log Message:
-----------
Iteration complete
Merge unstable into master
Commit: b7058749b891c37f46cb94044eef7c3fb4d70f82
https://github.com/PathwayCommons/factoid/commit/b7058749b891c37f46cb94044eef7c3fb4d70f82
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-02-06 (Tue, 06 Feb 2018)
Changed paths:
M src/client/components/editor/cy/edgehandles.js
Log Message:
-----------
Temporary workaround for blue highlight on source node tap
TODO Fix issue in edgehandles extension directly
Commit: f153925f94206675e6fe063de199263ec865509d
https://github.com/PathwayCommons/factoid/commit/f153925f94206675e6fe063de199263ec865509d
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-02-22 (Thu, 22 Feb 2018)
Changed paths:
M package-lock.json
M package.json
M src/client/components/editor/cy/edgehandles.js
Log Message:
-----------
Update to cytoscape-edgehandles@3.2.1 and remove workaround for lingering
blue highlight from b7058749b891c37f46cb94044eef7c3fb4d70f82
Commit: 83fefa943f3d1505a00ba39cf1b2fd1eff5cee23
https://github.com/PathwayCommons/factoid/commit/83fefa943f3d1505a00ba39cf1b2fd1eff5cee23
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-02-22 (Thu, 22 Feb 2018)
Changed paths:
M src/client/components/editor/cy/edgehandles.js
Log Message:
-----------
Show the interaction popover immediately after creating an interaction
Commit: cbee1b4c9a39ff746cc0def31b4d24eb6556fd6d
https://github.com/PathwayCommons/factoid/commit/cbee1b4c9a39ff746cc0def31b4d24eb6556fd6d
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-02-22 (Thu, 22 Feb 2018)
Changed paths:
M src/client/components/editor/cy/doc.js
Log Message:
-----------
The add element animations should be disabled for now to make sure that edge
creation feels snappy
Commit: 8073617d835c4d4e281dcc55293181692a0e5e0b
https://github.com/PathwayCommons/factoid/commit/8073617d835c4d4e281dcc55293181692a0e5e0b
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-02-22 (Thu, 22 Feb 2018)
Changed paths:
M src/client/components/editor/cy/edgehandles.js
Log Message:
-----------
Disable edgehandles for interaction source and target cases
Commit: 61ffd962be7b15cc31505e326b32d940702ea657
https://github.com/PathwayCommons/factoid/commit/61ffd962be7b15cc31505e326b32d940702ea657
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-02-27 (Tue, 27 Feb 2018)
Changed paths:
M Dockerfile
A ISSUE_TEMPLATE.md
M public/icon.png
A public/icon.svg
R src/client/components/conditional-tooltip.js
A src/client/components/debug.js
M src/client/components/document-filler.js
M src/client/components/document-linkout.js
M src/client/components/editor/buttons.js
M src/client/components/editor/cy/cxtmenu.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/edgehandles.js
M src/client/components/editor/cy/layout.js
R src/client/components/editor/cy/qtip.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/index.js
R src/client/components/element-info.js
A src/client/components/element-info/element-info.js
A src/client/components/element-info/entity-info.js
A src/client/components/element-info/interaction-info.js
A src/client/components/element-info/participant-info.js
R src/client/components/entity-info.js
A src/client/components/example-document.js
M src/client/components/home.js
R src/client/components/interaction-info.js
M src/client/components/organism-toggle.js
R src/client/components/participant-info.js
R src/client/components/popover.js
A src/client/components/popover/popover.js
A src/client/components/popover/tooltip.js
R src/client/components/tooltip.js
M src/client/router.js
M src/model/organism.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/reach.js
M src/server/routes/api/element-association/uniprot.js
M src/styles/app.css
M src/styles/base.css
A src/styles/debug.css
M src/styles/document-filler.css
M src/styles/editor/editor.css
R src/styles/editor/element-info.css
R src/styles/editor/entity-info.css
M src/styles/editor/index.css
R src/styles/editor/interaction-info.css
R src/styles/editor/organism-toggle.css
R src/styles/editor/participant-info.css
A src/styles/element-info/element-info.css
A src/styles/element-info/entity-info.css
A src/styles/element-info/index.css
A src/styles/element-info/interaction-info.css
A src/styles/element-info/participant-info.css
A src/styles/example-document.css
M src/styles/home.css
A src/styles/image/logo-full.svg
A src/styles/image/logo-no-slogan.svg
A src/styles/image/logo.svg
A src/styles/image/steps-figure.svg
M src/styles/index.css
A src/styles/organism-toggle.css
R src/styles/popover.css
A src/styles/popover/index.css
A src/styles/popover/popover.css
A src/styles/popover/tippy.css
A src/styles/popover/tooltip.css
R src/styles/tippy.css
R src/styles/tooltip.css
R src/styles/vendor/jquery.qtip.css
M test/syncher.js
Log Message:
-----------
Merge unstable into master : Iteration complete : Minor changes from user
testing
Commit: 8fe0019bdf1b98fddbd66b006ca9e3614a22519a
https://github.com/PathwayCommons/factoid/commit/8fe0019bdf1b98fddbd66b006ca9e3614a22519a
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Node text input 'x' icon does not clear existing text #165
Closes #165
Commit: 7d19ab7a35f74854debef1a3eb5b65591e5c03f0
https://github.com/PathwayCommons/factoid/commit/7d19ab7a35f74854debef1a3eb5b65591e5c03f0
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M src/server/routes/api/document/reach.js
Log Message:
-----------
Do not optimistically mark an entity as completed from reach. The entity is
marked as completed only if the association is successfully retrieved from the
element association services.
Commit: 3b538af5d0b339156b5db0b925d316d7ddd9fc3f
https://github.com/PathwayCommons/factoid/commit/3b538af5d0b339156b5db0b925d316d7ddd9fc3f
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M src/client/components/editor/cy/defs.js
Log Message:
-----------
Reduce the minimum zoom level from 1 to 0.5. This lets the user zoom out
twice as much as before.
Ref : Networks not initially 'fit to screen', elements offscreen #197
Commit: dd96d32d791b9cda2d71850545e426fee9643a2f
https://github.com/PathwayCommons/factoid/commit/dd96d32d791b9cda2d71850545e426fee9643a2f
Author: Max Franz <maxkfr...@gmail.com>
Date: 2018-03-21 (Wed, 21 Mar 2018)
Changed paths:
M src/server/routes/api/document/reach.js
Log Message:
-----------
Reach fails on "Since our results demonstrated that Hzf binds to p53 and
differentially modulates expression levels of the p53" #222
- Ignore all argument frames that do not specify an ID.
- Stricter check for arg types.
Commit: d804a42848b9b7209e89dc7dd851ca497596d32f
https://github.com/PathwayCommons/factoid/commit/d804a42848b9b7209e89dc7dd851ca497596d32f
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M src/client/components/form-editor/index.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
Separate forms for different templates.
Commit: 35d36630dbd2878007d918a313295a3dd57960a3
https://github.com/PathwayCommons/factoid/commit/35d36630dbd2878007d918a313295a3dd57960a3
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
A .idea/ClojureProjectResolveSettings.xml
A .idea/factoid.iml
A .idea/misc.xml
A .idea/modules.xml
M src/model/document/document.js
M src/model/element/element.js
M src/model/element/interaction.js
Log Message:
-----------
Interaction subtypes added.
Commit: 4dcd71a0dedc9c2bbd1b8a2aa38d7d6af245b475
https://github.com/PathwayCommons/factoid/commit/4dcd71a0dedc9c2bbd1b8a2aa38d7d6af245b475
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M src/client/components/form-editor/index.js
Log Message:
-----------
Remove interactions
Commit: 0a06efb7ad7a5147760b18f9794b05398faeab4d
https://github.com/PathwayCommons/factoid/commit/0a06efb7ad7a5147760b18f9794b05398faeab4d
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M src/client/components/form-editor/index.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
Remove interactions - bug fix
Commit: 25de9a53439b9f69d7af3cfb7f889e9dca6b70e2
https://github.com/PathwayCommons/factoid/commit/25de9a53439b9f69d7af3cfb7f889e9dca6b70e2
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M src/client/components/form-editor/index.js
Log Message:
-----------
Tooltips
Commit: 8df396cdc79cafd57a7474727bdec4a803f0a17c
https://github.com/PathwayCommons/factoid/commit/8df396cdc79cafd57a7474727bdec4a803f0a17c
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M src/model/document/document.js
Log Message:
-----------
Reverted back to original
Commit: a55f235cf38c5c3411a1e194af126b4624c7d535
https://github.com/PathwayCommons/factoid/commit/a55f235cf38c5c3411a1e194af126b4624c7d535
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M src/model/element/element.js
Log Message:
-----------
Reverted back to original
Commit: 398b8298f5c5acca905f4bd6542f30d3cecf5f65
https://github.com/PathwayCommons/factoid/commit/398b8298f5c5acca905f4bd6542f30d3cecf5f65
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M src/client/components/form-editor/index.js
Log Message:
-----------
Replaced interaction subtype with interaction description
Commit: 96207844fa8b3d44227aebc58c4dd0cd592c94fb
https://github.com/PathwayCommons/factoid/commit/96207844fa8b3d44227aebc58c4dd0cd592c94fb
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-03 (Tue, 03 Apr 2018)
Changed paths:
M src/client/components/form-editor/index.js
Log Message:
-----------
Title update
Commit: 22affccd71eec0242336659c5e22777cc112d369
https://github.com/PathwayCommons/factoid/commit/22affccd71eec0242336659c5e22777cc112d369
Author: fdurupinar <f.durupi...@gmail.com>
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 <f.durupi...@gmail.com>
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
Commit: 9ed471412153f24c0fec2cbeedb631804576207e
https://github.com/PathwayCommons/factoid/commit/9ed471412153f24c0fec2cbeedb631804576207e
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-04 (Wed, 04 Apr 2018)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Merge branch 'unstable' of https://github.com/PathwayCommons/factoid into
form-templates
Commit: 4b3b4a004ac1d8ec3f5c04481df738755ddb0e3c
https://github.com/PathwayCommons/factoid/commit/4b3b4a004ac1d8ec3f5c04481df738755ddb0e3c
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-05 (Thu, 05 Apr 2018)
Changed paths:
M .gitignore
M src/client/components/editor/cy/tippy.js
M src/client/components/form-editor/activation-inhibition-form.js
M src/client/components/form-editor/biochemical-reaction-form.js
M src/client/components/form-editor/complex-interaction-form.js
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/expression-regulation-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/client/components/form-editor/location-change-form.js
M src/client/components/form-editor/physical-interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
started entity grounding
Commit: d35f8adc0c49fbf07568e3b8af15436a12b6e35b
https://github.com/PathwayCommons/factoid/commit/d35f8adc0c49fbf07568e3b8af15436a12b6e35b
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-06 (Fri, 06 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/index.js
Log Message:
-----------
grounding cont'd
Commit: 20c951f0518e9babb7f87afea1aac3be8b3a2f76
https://github.com/PathwayCommons/factoid/commit/20c951f0518e9babb7f87afea1aac3be8b3a2f76
Author: Funda Durupinar Babur <durupina@Fundas-iMac.local>
Date: 2018-04-06 (Fri, 06 Apr 2018)
Changed paths:
M .gitignore
A .idea/ClojureProjectResolveSettings.xml
A .idea/codeStyles/Project.xml
A .idea/factoid.iml
A .idea/inspectionProfiles/Project_Default.xml
A .idea/misc.xml
A .idea/modules.xml
A .idea/vcs.xml
M .travis.yml
M README.md
M package-lock.json
M package.json
A src/client/components/debug-document-seeder.js
M src/client/components/debug.js
R src/client/components/document-filler.js
A src/client/components/document-seeder.js
A src/client/components/document-view-chooser.js
A src/client/components/document-wizard-stepper.js
M src/client/components/editor/cy/edgehandles.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/editor/cy/tippy.js
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
A 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/client/components/highlighter.js
M src/client/components/home.js
M src/client/components/notification/base.js
A src/client/components/page-not-found.js
M src/client/components/popover/tooltip.js
M src/client/router.js
M src/config.js
M src/model/document/document.js
M src/model/element/element.js
M src/model/element/interaction.js
M src/model/organism.js
M src/server/routes/api/document/index.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/server/routes/api/element-association/pubchem.js
M src/server/routes/api/element-association/search-string-conversion.js
M src/server/routes/api/element-association/uniprot.js
M src/styles/base.css
A src/styles/debug-document-seeder.css
R src/styles/document-filler.css
A src/styles/document-seeder.css
A src/styles/document-view-chooser.css
A src/styles/document-wizard-stepper.css
M src/styles/element-info/entity-info.css
A src/styles/form-editor/form-editor.css
A src/styles/form-editor/index.css
M src/styles/home.css
A src/styles/image/hero-splash-0.png
A src/styles/image/hero-splash.jpg
A src/styles/image/infographic-factoid.svg
M src/styles/index.css
M src/styles/notification.css
M src/styles/vars.css
M src/util/index.js
M src/util/memoize.js
M src/util/obj.js
A src/util/strings.js
M test/document.js
Log Message:
-----------
Merge branch 'form-templates' of https://github.com/PathwayCommons/factoid
into form-templates
Commit: a0463cd4ea387904fcefd0e2da4c987e4e9fad54
https://github.com/PathwayCommons/factoid/commit/a0463cd4ea387904fcefd0e2da4c987e4e9fad54
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-09 (Mon, 09 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/protein-modification-form.js
M src/client/components/popover/popover.js
Log Message:
-----------
interaction rows and grounded entities are updated after second click
Commit: df2a268daf025196b997e50f324655d5a1ef1244
https://github.com/PathwayCommons/factoid/commit/df2a268daf025196b997e50f324655d5a1ef1244
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-09 (Mon, 09 Apr 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-form.js
M src/client/components/form-editor/biochemical-reaction-form.js
M src/client/components/form-editor/complex-interaction-form.js
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/expression-regulation-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/client/components/form-editor/location-change-form.js
M src/client/components/form-editor/physical-interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
Log Message:
-----------
bug fix: interaction rows are updated after second click after delete
Commit: d867a923a7832a97faa85396775ef554de6de6db
https://github.com/PathwayCommons/factoid/commit/d867a923a7832a97faa85396775ef554de6de6db
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-09 (Mon, 09 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
Log Message:
-----------
bug: delete interaction removes the last interaction, but fixes after
reloading page
Commit: 7a80af8598587f3f492cac74849329e9d7312889
https://github.com/PathwayCommons/factoid/commit/7a80af8598587f3f492cac74849329e9d7312889
Author: Funda Durupinar Babur <durupina@Fundas-iMac.local>
Date: 2018-04-09 (Mon, 09 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/interaction-form.js
Log Message:
-----------
updates
Commit: c66b3044bf805d0ff17ac2d9ba7907e3cc373b67
https://github.com/PathwayCommons/factoid/commit/c66b3044bf805d0ff17ac2d9ba7907e3cc373b67
Author: Funda Durupinar Babur <durupina@Fundas-iMac.local>
Date: 2018-04-09 (Mon, 09 Apr 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-form.js
M src/client/components/form-editor/biochemical-reaction-form.js
M src/client/components/form-editor/complex-interaction-form.js
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/expression-regulation-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/client/components/form-editor/location-change-form.js
M src/client/components/form-editor/physical-interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
M src/client/components/popover/popover.js
Log Message:
-----------
new updates
Commit: facc863182a31ad5d65e5864a463d8fa994e0d10
https://github.com/PathwayCommons/factoid/commit/facc863182a31ad5d65e5864a463d8fa994e0d10
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-09 (Mon, 09 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
Log Message:
-----------
hideonclick false
Commit: 79710685b4651dcef9f3187f72e5e7e34a1cda13
https://github.com/PathwayCommons/factoid/commit/79710685b4651dcef9f3187f72e5e7e34a1cda13
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-09 (Mon, 09 Apr 2018)
Changed paths:
R .idea/ClojureProjectResolveSettings.xml
R .idea/codeStyles/Project.xml
R .idea/factoid.iml
R .idea/inspectionProfiles/Project_Default.xml
R .idea/misc.xml
R .idea/modules.xml
R .idea/vcs.xml
Log Message:
-----------
Removed folder from repository
Commit: 3fbc57b529a9d2679317559cfcc9d2ba29022eef
https://github.com/PathwayCommons/factoid/commit/3fbc57b529a9d2679317559cfcc9d2ba29022eef
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-10 (Tue, 10 Apr 2018)
Changed paths:
R .idea/ClojureProjectResolveSettings.xml
R .idea/codeStyles/Project.xml
R .idea/factoid.iml
R .idea/inspectionProfiles/Project_Default.xml
R .idea/misc.xml
R .idea/modules.xml
R .idea/vcs.xml
Log Message:
-----------
prev
Commit: 7542cf0f1e7d921723a6497ad02d6c8a59f36b78
https://github.com/PathwayCommons/factoid/commit/7542cf0f1e7d921723a6497ad02d6c8a59f36b78
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-10 (Tue, 10 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
M src/client/components/popover/popover.js
Log Message:
-----------
prev
Commit: e6317dbe5d42f2c8f3fb7940be0bedf16e46f14e
https://github.com/PathwayCommons/factoid/commit/e6317dbe5d42f2c8f3fb7940be0bedf16e46f14e
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-10 (Tue, 10 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/interaction-form.js
Log Message:
-----------
prev
Commit: 4bddc5b0838c24ef44f28671320b40484d12cfb7
https://github.com/PathwayCommons/factoid/commit/4bddc5b0838c24ef44f28671320b40484d12cfb7
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-10 (Tue, 10 Apr 2018)
Changed paths:
M src/client/components/form-editor/index.js
Log Message:
-----------
using dirty component instead. delete bug still exists.
Commit: a88a74673236f926e83312d4a97680446ea567c6
https://github.com/PathwayCommons/factoid/commit/a88a74673236f926e83312d4a97680446ea567c6
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-10 (Tue, 10 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
Log Message:
-----------
started merging entities
Commit: e872b28eaa078275af1898ac8c7e5ca2a829860a
https://github.com/PathwayCommons/factoid/commit/e872b28eaa078275af1898ac8c7e5ca2a829860a
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-10 (Tue, 10 Apr 2018)
Changed paths:
M src/client/components/popover/popover.js
Log Message:
-----------
updated to unstable version
Commit: 7a36c511d042c02e4864cad48a56083dbd6fd7ae
https://github.com/PathwayCommons/factoid/commit/7a36c511d042c02e4864cad48a56083dbd6fd7ae
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-11 (Wed, 11 Apr 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-form.js
M src/client/components/form-editor/biochemical-reaction-form.js
M src/client/components/form-editor/complex-interaction-form.js
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/expression-regulation-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/client/components/form-editor/location-change-form.js
M src/client/components/form-editor/physical-interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
Log Message:
-----------
delete and tooltip updates
Commit: a635f1806388a7d3eccc8f4352de063ce60799b2
https://github.com/PathwayCommons/factoid/commit/a635f1806388a7d3eccc8f4352de063ce60799b2
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-11 (Wed, 11 Apr 2018)
Changed paths:
M src/client/components/form-editor/interaction-form.js
Log Message:
-----------
delete and tooltip updates
Commit: 46b5dee10a7bc3ddd94daeb2cae54830866f2735
https://github.com/PathwayCommons/factoid/commit/46b5dee10a7bc3ddd94daeb2cae54830866f2735
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-11 (Wed, 11 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
Log Message:
-----------
merge working but participant type is not preserved
Commit: 1c81dfe7a0716daca1ae2e2b91ed9051ef02266e
https://github.com/PathwayCommons/factoid/commit/1c81dfe7a0716daca1ae2e2b91ed9051ef02266e
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-18 (Wed, 18 Apr 2018)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/client/components/form-editor/activation-inhibition-form.js
M src/client/components/form-editor/biochemical-reaction-form.js
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/expression-regulation-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/client/components/form-editor/location-change-form.js
M src/client/components/form-editor/protein-modification-form.js
M src/client/components/popover/popover.js
M src/model/document/document.js
M src/model/element-set.js
M src/model/element/element.js
M src/model/element/interaction.js
Log Message:
-----------
adding position in the interaction into entities
Commit: 5e234f5030cfbe9b327a3178c814513cf8094fb2
https://github.com/PathwayCommons/factoid/commit/5e234f5030cfbe9b327a3178c814513cf8094fb2
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-19 (Thu, 19 Apr 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/model/element/element.js
Log Message:
-----------
merging entities complete.
entity's location in the interaction is stored in the description field.
Commit: 6f60afc2a742ca25640223a12e6b7dcbb50b3c5e
https://github.com/PathwayCommons/factoid/commit/6f60afc2a742ca25640223a12e6b7dcbb50b3c5e
Author: fdurupinar <f.durupi...@gmail.com>
Date: 2018-04-19 (Thu, 19 Apr 2018)
Changed paths:
A src/client/components/action-logger/index.js
A src/client/components/app-bar.js
M src/client/components/editor/index.js
A src/client/components/my-factoids.js
M src/client/router.js
M src/server/routes/api/document/index.js
A src/styles/action-logger/action-logger.css
A src/styles/action-logger/index.css
A src/styles/app-bar.css
M src/styles/editor/editor.css
M src/styles/index.css
A src/styles/my-factoids.css
M src/styles/notification.css
Log Message:
-----------
Merge branch 'alpha' of https://github.com/PathwayCommons/factoid into
form-templates
Compare:
https://github.com/PathwayCommons/factoid/compare/a1f5b8a3913d...6f60afc2a742
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