Branch: refs/heads/master
Home: https://github.com/PathwayCommons/factoid
Commit: df5eee64629e1466b8b7b60cbf39dfd196decc1c
https://github.com/PathwayCommons/factoid/commit/df5eee64629e1466b8b7b60cbf39dfd196decc1c
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: 8e323496a547078a544a076eaa41404dafce11c6
https://github.com/PathwayCommons/factoid/commit/8e323496a547078a544a076eaa41404dafce11c6
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-26 (Tue, 26 Sep 2017)
Changed paths:
M package.json
M src/client/components/document-linkout.js
M src/client/components/editor/cy/index.js
A src/client/components/editor/cy/tippy.js
M src/client/components/entity-info.js
M src/client/components/popover.js
M src/client/components/tooltip.js
M src/client/defs.js
M src/styles/editor/editor.css
M src/styles/tippy.css
M src/util/cy.js
Log Message:
-----------
Converts Cytoscape graph to use Tippy instead of Qtip
Commit: 2cddc78a6ae0478cd2024e6aa5e63aca372da7cf
https://github.com/PathwayCommons/factoid/commit/2cddc78a6ae0478cd2024e6aa5e63aca372da7cf
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-26 (Tue, 26 Sep 2017)
Changed paths:
M src/client/components/entity-info.js
M src/client/defs.js
Log Message:
-----------
A (possibly) more reliable auto focus for "Entity name"
Commit: b7512fe330cba17aa6bf38c3f6f627dac5d0f205
https://github.com/PathwayCommons/factoid/commit/b7512fe330cba17aa6bf38c3f6f627dac5d0f205
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-27 (Wed, 27 Sep 2017)
Changed paths:
M src/client/components/editor/cy/tippy.js
Log Message:
-----------
Allow more than one tippy per node
Commit: e6b3af0bc2ff62e14b8a1403e579577278e2aa22
https://github.com/PathwayCommons/factoid/commit/e6b3af0bc2ff62e14b8a1403e579577278e2aa22
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-28 (Thu, 28 Sep 2017)
Changed paths:
A src/client/components/animate.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/editor/cy/tippy.js
M src/client/components/entity-info.js
M src/client/components/interaction-info.js
A src/client/components/participant-info.js
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
M src/util/dom.js
Log Message:
-----------
The interaction UI is spread out to a main interaction popover at the bottom
of the screen and participant popovers
Commit: 123581bac4626c4416c657ab45e442da7a4e9b98
https://github.com/PathwayCommons/factoid/commit/123581bac4626c4416c657ab45e442da7a4e9b98
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-28 (Thu, 28 Sep 2017)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/cy/layout.js
M src/client/components/tooltip.js
M src/styles/popover.css
M src/styles/tippy.css
M src/styles/tooltip.css
Log Message:
-----------
Improve tooltips #150
- Keys have a "KEY" label
- Clearer names for layout and fit
- All shortcut keys are nearby one another with the left hand (E, R, D, F)
Commit: 99f39ae98a06ec84148ea601fb9123894fec3e33
https://github.com/PathwayCommons/factoid/commit/99f39ae98a06ec84148ea601fb9123894fec3e33
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-28 (Thu, 28 Sep 2017)
Changed paths:
M src/client/components/editor/cy/defs.js
Log Message:
-----------
Restrict the min zoom a bit more to make it harder to lose your place in the
graph
Commit: 06c732f55a8855f413b5c3cf06f1fa7edb17e9a9
https://github.com/PathwayCommons/factoid/commit/06c732f55a8855f413b5c3cf06f1fa7edb17e9a9
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-09-28 (Thu, 28 Sep 2017)
Changed paths:
M src/client/components/editor/cy/edgehandles.js
A src/styles/image/ic_keyboard_tab_24px.svg
Log Message:
-----------
Add draw mode icon onto the blue edgehandle #149
Commit: da2e736efbd313de66c56668bd12021987aafd0d
https://github.com/PathwayCommons/factoid/commit/da2e736efbd313de66c56668bd12021987aafd0d
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-05 (Thu, 05 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
M src/client/debug.js
M src/styles/base.css
A src/styles/deps.css
M src/styles/index.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/views/404.html
M src/views/error.html
M src/views/index.html
M src/views/style-demo.html
A webpack.config.js
Log Message:
-----------
Tooling updates
- Switch to webpack
- Add bundle profiling
- Use unified browserlist
- Postcss must have safe:true
- Optimised fonts to reduce css bundle size
Commit: 6d37b44c1dbfbd12572298bdc611c000df34b949
https://github.com/PathwayCommons/factoid/commit/6d37b44c1dbfbd12572298bdc611c000df34b949
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-05 (Thu, 05 Oct 2017)
Changed paths:
R src/styles/qtip.css
Log Message:
-----------
qtip css not needed since we now use tippy for everything
Commit: 7f93f030458f8cfb6d9c6fa7aadb2d5be0dd061f
https://github.com/PathwayCommons/factoid/commit/7f93f030458f8cfb6d9c6fa7aadb2d5be0dd061f
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-05 (Thu, 05 Oct 2017)
Changed paths:
M src/styles/deps.css
M src/styles/index.css
Log Message:
-----------
tippy default stylesheet belongs in deps now
Commit: 16960bb94e9124d9a09462227ff54ea6b14271b4
https://github.com/PathwayCommons/factoid/commit/16960bb94e9124d9a09462227ff54ea6b14271b4
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-05 (Thu, 05 Oct 2017)
Changed paths:
M .babelrc
Log Message:
-----------
useBuiltins not reliable
Commit: dca1736b92db1de07fd223f54efc45561e2d6019
https://github.com/PathwayCommons/factoid/commit/dca1736b92db1de07fd223f54efc45561e2d6019
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-10 (Tue, 10 Oct 2017)
Changed paths:
M package.json
M src/client/components/editor/cy/doc.js
M webpack.config.js
Log Message:
-----------
Use inline-source-map and remove moment
Commit: 476b7ae47a00576f2f3e5757fec75813603589f7
https://github.com/PathwayCommons/factoid/commit/476b7ae47a00576f2f3e5757fec75813603589f7
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-10 (Tue, 10 Oct 2017)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/index.js
M src/styles/editor/editor.css
Log Message:
-----------
Make the linkout UI easier to find
- More visible
- 1 click vs 2
Commit: 0a1ea86d71dec0c85e134ff622435b50e4ed3a5f
https://github.com/PathwayCommons/factoid/commit/0a1ea86d71dec0c85e134ff622435b50e4ed3a5f
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-10 (Tue, 10 Oct 2017)
Changed paths:
M src/server/routes/api/document/reach.js
M src/server/routes/api/element-association/uniprot.js
Log Message:
-----------
Uniprot groundings/associations applied from Reach
Commit: 00e4e4b000665632ca7725242f3b5e659b6880b4
https://github.com/PathwayCommons/factoid/commit/00e4e4b000665632ca7725242f3b5e659b6880b4
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/model/element/entity.js
Log Message:
-----------
Associating an entity does not change its name
Commit: 4cb6b1a5b7b339a098a6929f751f44a15adbe555
https://github.com/PathwayCommons/factoid/commit/4cb6b1a5b7b339a098a6929f751f44a15adbe555
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/client/components/entity-info.js
Log Message:
-----------
Disassociating an entity does not clear its name textbox
Commit: 77461f4bc98f0b7586c5ef912b3ab4f41b272ee7
https://github.com/PathwayCommons/factoid/commit/77461f4bc98f0b7586c5ef912b3ab4f41b272ee7
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/client/components/editor/cy/defs.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/entity-info.js
M src/styles/editor/entity-info.css
M src/styles/vars.css
Log Message:
-----------
Include a message to encourage the user to associate an entity with a ground
Commit: a2f4e132a6ccdfe0bf12142a02277c04e186dbcc
https://github.com/PathwayCommons/factoid/commit/a2f4e132a6ccdfe0bf12142a02277c04e186dbcc
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/client/components/entity-info.js
A src/client/components/highlighter.js
M src/styles/editor/entity-info.css
A src/styles/highlighter.css
M src/styles/index.css
Log Message:
-----------
Highlight matches for entity association results
Commit: 8523f7e0968bfb7ac84c298fdad47e7376356466
https://github.com/PathwayCommons/factoid/commit/8523f7e0968bfb7ac84c298fdad47e7376356466
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/server/routes/api/element-association/uniprot.js
Log Message:
-----------
Restrict Uniprot searches to { geneName, proteinName } fields to improve
quality of results
- e.g. "cyclin e"
- e.g. "fazL"
Commit: 9e1df2241f13975bc3ec9e7602caaecb95cbbf98
https://github.com/PathwayCommons/factoid/commit/9e1df2241f13975bc3ec9e7602caaecb95cbbf98
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/server/routes/api/element-association/uniprot.js
Log Message:
-----------
Catch cases where Uniprot doesn't give any result and give an empty list
Commit: 0912aad091b7b56103e6da40211c623f81e48309
https://github.com/PathwayCommons/factoid/commit/0912aad091b7b56103e6da40211c623f81e48309
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/client/components/editor/cy/doc.js
Log Message:
-----------
Deleting an entity should remove its popup #151
Commit: ab93490c8597e07ee8131dcbaa9de3037636bbd2
https://github.com/PathwayCommons/factoid/commit/ab93490c8597e07ee8131dcbaa9de3037636bbd2
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/client/components/tooltip.js
M src/styles/tooltip.css
Log Message:
-----------
Improve keyboard shortcut indicator
Commit: a7ad045707f1c4f419f0fc02ef542c6216fcbc92
https://github.com/PathwayCommons/factoid/commit/a7ad045707f1c4f419f0fc02ef542c6216fcbc92
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/client/components/entity-info.js
M src/client/components/highlighter.js
M src/styles/editor/entity-info.css
Log Message:
-----------
The filtering should always use `oldName` (the last name sent to the server)
and the `Highlighter` should exit early when there is no search term
Commit: e4714ce4a8202c317e82efa0d7b7e999f00b7abc
https://github.com/PathwayCommons/factoid/commit/e4714ce4a8202c317e82efa0d7b7e999f00b7abc
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/client/components/highlighter.js
Log Message:
-----------
Allow `Highlighter` to match names with non-space separator differences (e.g.
'rad5' matches 'rad-5')
Commit: 90f5673c4af131501df730c57cafd0486b7f82bd
https://github.com/PathwayCommons/factoid/commit/90f5673c4af131501df730c57cafd0486b7f82bd
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/styles/highlighter.css
Log Message:
-----------
Mute the highlight colour a bit
Commit: c10925d632f4521292e091180baf068a4ece5d40
https://github.com/PathwayCommons/factoid/commit/c10925d632f4521292e091180baf068a4ece5d40
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-12 (Thu, 12 Oct 2017)
Changed paths:
M src/client/components/entity-info.js
Log Message:
-----------
Disable highlight for associated entities
Commit: 110b87e8794695398d033dabb843affc9fd48af9
https://github.com/PathwayCommons/factoid/commit/110b87e8794695398d033dabb843affc9fd48af9
Author: Max Franz <maxkfr...@gmail.com>
Date: 2017-10-16 (Mon, 16 Oct 2017)
Changed paths:
M test/document.js
Log Message:
-----------
We no longer expect association to change an entity's name
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
Compare:
https://github.com/PathwayCommons/factoid/compare/da0b609a3e49...9e6cd247b5df
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