Branch: refs/heads/master
Home: https://github.com/PathwayCommons/factoid
Commit: f6be9704a278bdf0d0bc766248e77e299d65653a
https://github.com/PathwayCommons/factoid/commit/f6be9704a278bdf0d0bc766248e77e299d65653a
Author: Max Franz <[email protected]>
Date: 2018-04-12 (Thu, 12 Apr 2018)
Changed paths:
A ci.sh
Log Message:
-----------
Add very simple ci.sh script for setting up continuous builds for a test
server
It's not fancy, but it should be fairly reliable. We've been using this script
for the factoid.baderlab.org CI testing server for a while now.
Commit: e4b09275800cdde351dbe5146e31407e8fc90772
https://github.com/PathwayCommons/factoid/commit/e4b09275800cdde351dbe5146e31407e8fc90772
Author: Max Franz <[email protected]>
Date: 2018-04-25 (Wed, 25 Apr 2018)
Changed paths:
M src/client/components/document-seeder.js
Log Message:
-----------
Lint : Add missing semicolons to DocumentSeeder
Commit: 543d9488fa029aac731817761ddfd5bdfab93c47
https://github.com/PathwayCommons/factoid/commit/543d9488fa029aac731817761ddfd5bdfab93c47
Author: Max Franz <[email protected]>
Date: 2018-04-25 (Wed, 25 Apr 2018)
Changed paths:
A src/client/components/data-component.js
M src/client/components/dirty-component.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/editor/cy/tippy.js
A src/client/components/element-info/chemical-formula.js
M src/client/components/element-info/element-info.js
A src/client/components/element-info/entity-assoc-display.js
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/interaction-info.js
M src/client/components/element-info/participant-info.js
A src/client/components/element-info/progression-stepper.js
A src/client/components/element-info/progression.js
M src/client/components/notification/base.js
M src/client/components/notification/corner.js
M src/client/components/notification/inline.js
M src/client/components/notification/list.js
M src/client/components/notification/notification.js
M src/client/components/notification/panel.js
M src/client/components/notification/popover.js
M src/client/defs.js
M src/model/element/element.js
M src/model/element/entity.js
M src/model/element/interaction-type/chemical-affects-protein.js
M src/model/element/interaction-type/enum.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction-type/modification.js
M src/model/element/interaction-type/protein-affects-chemical.js
M src/model/element/interaction.js
M src/styles/element-info/interaction-info.css
A src/util/cache.js
M src/util/index.js
Log Message:
-----------
Interaction completion wizard #199
Summary
- The interaction is specified in three stages: (1) Specify interaction type.
(2) Specify participant type. (3) Mark interaction as completed.
- Remote changes to interactions are animated with the yellow user highlight.
API changes
- Add `interaction.toString()` to get a human-readable phrase that represents
the interaction, e.g. 'A promotes the expression of B'.
- Automatically wrap most stateful components (at least the ones used by
`Editor`) to automatically use a React `key`.
- Improve the `DirtyComponent` class so subclasses don't have to use
'super.render()`.
- The `DirtyComponent` allows a callback to `dirty()` so you can know when
rendering happens.
- Add a `DataComponent` that uses `data` instead of state.
- Fixes to `InteractionType.prototype.isAllowedForInteraction()`.
- Move `complete()`, `completed()`, etc. from the `Entity` to the `Element`
class so interactions can use the same functions.
- Add `interaction.associated()`.
UI improvements
- Make selected edges go to the top of the z-order. This is useful in cases
where the label overlaps the edge arrow.
- Reduce the node label font size a bit. This is useful in cases where the
label overlaps the edge arrow.
- Improved arrowhead participant popover positioning.
- Manually specify the flipping and positioning of the main interaction popover
and the participant arrowhead popovers. This makes better use of screen space
while avoiding most cases that would cause overlap.
Misc. improvements
- Safer destroying of Tippy elements created on Cytoscape elements.
- Fix notification classes re. dangling listeners.
- Clean up the stylesheet re. interaction nodes.
- Improve default Tippy options for popovers that should update position on
page scroll.
- Update notification components to use DirtyComponent.
- Refactor `ElementInfo` to pull out common parts that are now re-used by
`InteractionInfo`.
Commit: d4b538ae4f95c5e13e7dce5105436520e9284a04
https://github.com/PathwayCommons/factoid/commit/d4b538ae4f95c5e13e7dce5105436520e9284a04
Author: Max Franz <[email protected]>
Date: 2018-05-02 (Wed, 02 May 2018)
Changed paths:
M test/interaction.js
Log Message:
-----------
Interaction tests should complete the interactions in order to use the
association
Commit: 37c3eebba66f168bb68a1b82fcc801df88686acc
https://github.com/PathwayCommons/factoid/commit/37c3eebba66f168bb68a1b82fcc801df88686acc
Author: Max Franz <[email protected]>
Date: 2018-05-02 (Wed, 02 May 2018)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/interaction-info.js
Log Message:
-----------
Correct id => key
Commit: f3a4d4a6db8630b80b936ccbc6366bfaefa78e19
https://github.com/PathwayCommons/factoid/commit/f3a4d4a6db8630b80b936ccbc6366bfaefa78e19
Author: Max Franz <[email protected]>
Date: 2018-05-03 (Thu, 03 May 2018)
Changed paths:
M package-lock.json
Log Message:
-----------
Upgrade to [email protected] in package-lock.json under dependency soap
Note that browser-sync still uses an old version of hoek, but this is just a
dev dependency.
$ npm ls hoek
├─┬ [email protected]
│·····················
│ ├─┬ [email protected]
│·····················
│ │ └─┬ [email protected]
│·····················
│ │ └─┬ [email protected]
│·····················
│ │ └─┬ [email protected]
│·····················
│ │ ├─┬ [email protected]
│·····················
│ │ │ └── [email protected] deduped
│·····················
│ │ ├── [email protected]
│·····················
│ │ └─┬ [email protected]
│·····················
│ │ └── [email protected] deduped
│·····················
│ └─┬ [email protected]
│·····················
│ └─┬ [email protected]
│·····················
│ └─┬ [email protected]
│·····················
│ ├─┬ [email protected]
│·····················
│ │ └── [email protected] deduped
│·····················
│ ├── [email protected]
│·····················
│ └─┬ [email protected]
│·····················
│ └── [email protected] deduped
└─┬ [email protected]
│·····················
└─┬ [email protected]
│·····················
└─┬ [email protected]
│·····················
├─┬ [email protected]
│·····················
│ └── [email protected] deduped
│·····················
├─┬ [email protected]
│·····················
│ └─┬ [email protected]
│·····················
│ └── [email protected] deduped
│·····················
├── [email protected]
│·····················
└─┬ [email protected]
│·····················
└── [email protected] deduped
Ref : Security vulnerability in hapijs/hoek #254
Commit: 3b68dbe6c3ba40b9e0d8ab45839d92657e682311
https://github.com/PathwayCommons/factoid/commit/3b68dbe6c3ba40b9e0d8ab45839d92657e682311
Author: Max Franz <[email protected]>
Date: 2018-05-03 (Thu, 03 May 2018)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
Add elements to the document optimistically in the Editor
- Do not wait for the element to be synched and created on the server side.
- Create element and add to document (ID ref) simultaneously.
- Should resolve case where network lag causes node to not show up right away
-- where the machine is waiting for the creation response before adding.
Ref : Lag in adding entities #251
Commit: 1f65f133b445e7fb37e5e673b7ea8dbce428e71c
https://github.com/PathwayCommons/factoid/commit/1f65f133b445e7fb37e5e673b7ea8dbce428e71c
Author: Dylan Fong <[email protected]>
Date: 2018-05-08 (Tue, 08 May 2018)
Changed paths:
M src/client/components/document-view-chooser.js
M src/styles/document-view-chooser.css
A src/styles/image/form-option-preview.png
A src/styles/image/network-option-preview.png
Log Message:
-----------
add image previews for each editor option
Commit: 8021ccff9b8fd08bfc8306f3e3b7f1feea97e009
https://github.com/PathwayCommons/factoid/commit/8021ccff9b8fd08bfc8306f3e3b7f1feea97e009
Author: Dylan Fong <[email protected]>
Date: 2018-05-08 (Tue, 08 May 2018)
Changed paths:
M src/styles/document-wizard-stepper.css
Log Message:
-----------
wizard stepper buttons are closer to the center of the screen / content
- refs #262
Commit: 06c1290b215cda6ae855f99268d05051525c92f3
https://github.com/PathwayCommons/factoid/commit/06c1290b215cda6ae855f99268d05051525c92f3
Author: fdurupinar <[email protected]>
Date: 2018-05-08 (Tue, 08 May 2018)
Changed paths:
A src/client/components/form-editor/activation-inhibition-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/molecular-interaction-form.js
A src/client/components/form-editor/protein-modification-form.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
form-editor components
Commit: 941b3f22b3553000e72a64d94c09362bc602dbf7
https://github.com/PathwayCommons/factoid/commit/941b3f22b3553000e72a64d94c09362bc602dbf7
Author: Dylan Fong <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/styles/document-wizard-stepper.css
Log Message:
-----------
fix lint error
Commit: c23227681d90bbbb59bcfbd9d56dc03603be18a8
https://github.com/PathwayCommons/factoid/commit/c23227681d90bbbb59bcfbd9d56dc03603be18a8
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
R src/client/components/form-editor/activation-inhibition-form.js
R src/client/components/form-editor/entity-form.js
R src/client/components/form-editor/expression-regulation-form.js
M src/client/components/form-editor/index.js
R src/client/components/form-editor/interaction-form.js
R src/client/components/form-editor/molecular-interaction-form.js
R src/client/components/form-editor/protein-modification-form.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
Revert "form-editor components"
06c1290b215cda6ae855f99268d05051525c92f3
This commit creates several errors that Travis is picking up. Please make PRs
so that code can be reviewed prior to merging. At the very least, make sure
that the test and lint tasks pass before making any changes on the unstable
branch that affect others.
Commit: 979406d99d28ae64cb0ef2cab56c18455196f378
https://github.com/PathwayCommons/factoid/commit/979406d99d28ae64cb0ef2cab56c18455196f378
Author: Dylan Fong <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/document-view-chooser.js
Log Message:
-----------
fix lint errors
Commit: 650b9b6941868d93f495a5800c900379f3c23197
https://github.com/PathwayCommons/factoid/commit/650b9b6941868d93f495a5800c900379f3c23197
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/styles/document-wizard-stepper.css
Log Message:
-----------
Merge pull request #263 from PathwayCommons/closer-wizard-stepper-buttons
wizard stepper buttons are closer to the center of the screen / content
Commit: ce1251022be28a3775c8cea64ad4dbcca5f37215
https://github.com/PathwayCommons/factoid/commit/ce1251022be28a3775c8cea64ad4dbcca5f37215
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/document-view-chooser.js
M src/styles/document-view-chooser.css
A src/styles/image/form-option-preview.png
A src/styles/image/network-option-preview.png
Log Message:
-----------
Merge pull request #261 from PathwayCommons/view-chooser-images
add image previews for each editor option
Commit: 3c4e75bbe4f119c31e283ae8e078655c7bbea2e6
https://github.com/PathwayCommons/factoid/commit/3c4e75bbe4f119c31e283ae8e078655c7bbea2e6
Author: Dylan Fong <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
A src/client/components/document-renamer.js
A src/styles/document-renamer.css
M src/styles/index.css
Log Message:
-----------
document renamer component
- requires a factoid doc as props
- had logic to rename the document
- google docs flavoured hover styling
Commit: 6d8b076586b4c3559dedaf5107ee5c98e2cf8ef1
https://github.com/PathwayCommons/factoid/commit/6d8b076586b4c3559dedaf5107ee5c98e2cf8ef1
Author: fdurupinar <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
A src/client/components/form-editor/activation-inhibition-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/molecular-interaction-form.js
A src/client/components/form-editor/protein-modification-form.js
Log Message:
-----------
form components
Commit: 4c2f542ac0e6dc72f6027adb6815cac207994160
https://github.com/PathwayCommons/factoid/commit/4c2f542ac0e6dc72f6027adb6815cac207994160
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/model/element/interaction-type/interaction-type.js
Log Message:
-----------
Loosen restrictions on getting source/target of interaction type/association.
Commit: 41b564c7cc89f0247d0cf697f41cb89593423ac8
https://github.com/PathwayCommons/factoid/commit/41b564c7cc89f0247d0cf697f41cb89593423ac8
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/model/element/interaction-type/interaction-type.js
M src/model/element/participant-type.js
Log Message:
-----------
Allow setting the target via an interaction association before the
interaction is complete via participant type UNSIGNED_TARGET.
Commit: e3b69d78b0dde53d930708b164605c084424c03c
https://github.com/PathwayCommons/factoid/commit/e3b69d78b0dde53d930708b164605c084424c03c
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/model/element/element-type.js
A src/model/element/entity-type.js
M src/model/element/interaction-type/chemical-affects-protein.js
M src/model/element/interaction-type/enum.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/interaction-type.js
A src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
A src/model/element/interaction-type/phosphorylation.js
A src/model/element/interaction-type/ubiquination.js
Log Message:
-----------
- Separate out entity types
- Clean up element types
- Add phosphorylation, methylation, and ubiquination subtypes of modification
interaction type/association
- Allow promotion, activation, and inhibition aliases on all interaction
subtypes
Commit: ab2967c2a3b7718d8a2b58166e7a641345699bb5
https://github.com/PathwayCommons/factoid/commit/ab2967c2a3b7718d8a2b58166e7a641345699bb5
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
R src/model/element/entity-mods.js
M src/model/element/entity.js
Log Message:
-----------
Remove model support for entity modification
Commit: ae6758656b102684d8c751cc2599dc4707ff4994
https://github.com/PathwayCommons/factoid/commit/ae6758656b102684d8c751cc2599dc4707ff4994
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/styles/element-info/entity-info.css
Log Message:
-----------
Remove modification support in the entity wizard
Commit: d986db3bd9ee940704f377669a06c4dc72cf02c7
https://github.com/PathwayCommons/factoid/commit/d986db3bd9ee940704f377669a06c4dc72cf02c7
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/editor/cy/stylesheet.js
M src/util/cy.js
Log Message:
-----------
Remove references to entity modification in Cytoscape visualisation
Commit: 3eff1f91d5aadf23bdb6b90535041915b97eec10
https://github.com/PathwayCommons/factoid/commit/3eff1f91d5aadf23bdb6b90535041915b97eec10
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/element-info/interaction-info.js
Log Message:
-----------
Skip the general modification interaction subtype in the interaction wizard
For now, only let users select the specific types (e.g. phosphorylation).
Commit: 295bbfa4e17e93abadd9bad8b8d54e7b0f136ba6
https://github.com/PathwayCommons/factoid/commit/295bbfa4e17e93abadd9bad8b8d54e7b0f136ba6
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
A src/client/components/document-renamer.js
A src/styles/document-renamer.css
M src/styles/index.css
Log Message:
-----------
Merge pull request #264 from PathwayCommons/document-renamer-component
document renamer component
Commit: 629528462c077a73b33a0d946b59656386cbf56b
https://github.com/PathwayCommons/factoid/commit/629528462c077a73b33a0d946b59656386cbf56b
Author: fdurupinar <[email protected]>
Date: 2018-05-09 (Wed, 09 May 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:
-----------
form components
Commit: d9edf6021d004f145619dae5abafa3efa706b53a
https://github.com/PathwayCommons/factoid/commit/d9edf6021d004f145619dae5abafa3efa706b53a
Author: fdurupinar <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Log Message:
-----------
Merge remote-tracking branch 'origin' into form-components
Commit: ad5a1470f8ddcd7f884c57078cf8314b6e40ba6d
https://github.com/PathwayCommons/factoid/commit/ad5a1470f8ddcd7f884c57078cf8314b6e40ba6d
Author: fdurupinar <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
A src/client/components/document-renamer.js
M src/client/components/editor/cy/stylesheet.js
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/interaction-info.js
M src/model/element/element-type.js
R src/model/element/entity-mods.js
A src/model/element/entity-type.js
M src/model/element/entity.js
M src/model/element/interaction-type/chemical-affects-protein.js
M src/model/element/interaction-type/enum.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/interaction-type.js
A src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
A src/model/element/interaction-type/phosphorylation.js
A src/model/element/interaction-type/ubiquination.js
M src/model/element/participant-type.js
A src/styles/document-renamer.css
M src/styles/element-info/entity-info.css
M src/styles/index.css
M src/util/cy.js
Log Message:
-----------
Merge branch 'unstable' of https://github.com/PathwayCommons/factoid into
form-components
Commit: 6256a44707f3230b0d8adddf9868f5a796925130
https://github.com/PathwayCommons/factoid/commit/6256a44707f3230b0d8adddf9868f5a796925130
Author: Dylan Fong <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/editor/index.js
A src/client/components/my-factoids.js
M src/client/router.js
M src/styles/index.css
A src/styles/my-factoids.css
Log Message:
-----------
re-implement the my factoids component using localstorage
Commit: 9081ee02501c7b1db6f2f293ff5142cce2ece8f9
https://github.com/PathwayCommons/factoid/commit/9081ee02501c7b1db6f2f293ff5142cce2ece8f9
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/element-info/progression-stepper.js
Log Message:
-----------
- Change the back and next icons in the entity and interaction wizards to be
chevrons to look less like the edge arrowheads.
Commit: 1e805ad14347853522542686d9c119bc3cb800b4
https://github.com/PathwayCommons/factoid/commit/1e805ad14347853522542686d9c119bc3cb800b4
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/element-info/interaction-info.js
Log Message:
-----------
Update the interaction wizard participant type notification to 'Activation or
inhibition?'.
Commit: 447670ea6d747fbecfe0fa46fc247e450a0503cd
https://github.com/PathwayCommons/factoid/commit/447670ea6d747fbecfe0fa46fc247e450a0503cd
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/element-info/progression-stepper.js
M src/styles/element-info/element-info.css
M src/styles/element-info/entity-info.css
Log Message:
-----------
Rename common entity/interaction wizard stepper styles to `element-info-*`
Commit: fa6159b04142a6f62fadfcdb2c92b83da4784892
https://github.com/PathwayCommons/factoid/commit/fa6159b04142a6f62fadfcdb2c92b83da4784892
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/element-info/progression-stepper.js
M src/styles/element-info/element-info.css
Log Message:
-----------
Fix tooltips for element wizard progression and simplify tooltip text
- Firefox didn't work at all, since it doesn't fire events for children of
buttons.
- Safari didn't work on disabled buttons.
- Both cases are fixed by using a wrapper div.
Commit: 194ee68630d942df649964307c326ef7aa194111
https://github.com/PathwayCommons/factoid/commit/194ee68630d942df649964307c326ef7aa194111
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/element-info/interaction-info.js
M src/styles/element-info/entity-info.css
M src/styles/element-info/interaction-info.css
Log Message:
-----------
Improve alignment of edit button on COMPLETED stage of element wizards
Commit: 9d0846dcb2c109db94948f1562ba0155e6d35ec3
https://github.com/PathwayCommons/factoid/commit/9d0846dcb2c109db94948f1562ba0155e6d35ec3
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/element-info/interaction-info.js
M src/client/components/element-info/participant-info.js
Log Message:
-----------
Interaction wizard: Allow quick skipping of stages by clicking the existing
selection
Commit: 6d21873b61083c7e732c8dcf6cc418e2b1c09430
https://github.com/PathwayCommons/factoid/commit/6d21873b61083c7e732c8dcf6cc418e2b1c09430
Author: Max Franz <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/components/editor/cy/tippy.js
Log Message:
-----------
Enable 'complete this' notification for interactions
- Interactions now have the same `complete()` API so it should just work
- Modify the text for the interaction case
- Make sure not to show the notification when hiding participant tippies
Commit: 5242dd326905560a9740ff21ebba7b0afd61a192
https://github.com/PathwayCommons/factoid/commit/5242dd326905560a9740ff21ebba7b0afd61a192
Author: fdurupinar <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
A src/client/components/form-editor/activation-inhibition-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/molecular-interaction-form.js
A src/client/components/form-editor/protein-modification-form.js
Log Message:
-----------
Form components (#269)
* `forever stopall` for `npm stop` to avoid forever non-zero exit codes
* Grounds in the map must be null checked because we now allow ungrounded
entities #145
* Fix joined input buttons, e.g. on textmining test page.
* 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.
* Avoid error when deleting an entity that has its entity popover shown.
* Temporary workaround for blue highlight on source node tap
TODO Fix issue in edgehandles extension directly
* Update to [email protected] and remove workaround for lingering
blue highlight from b7058749b891c37f46cb94044eef7c3fb4d70f82
* Show the interaction popover immediately after creating an interaction
* The add element animations should be disabled for now to make sure that edge
creation feels snappy
* Disable edgehandles for interaction source and target cases
* Node text input 'x' icon does not clear existing text #165
Closes #165
* 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.
* 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
* 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.
* Upgrade to [email protected] in package-lock.json under dependency soap
Note that browser-sync still uses an old version of hoek, but this is just a
dev dependency.
Ref #254
* form components
* form components
Commit: 96443276841e68fe1b1956e64b5f265d6f7f07a0
https://github.com/PathwayCommons/factoid/commit/96443276841e68fe1b1956e64b5f265d6f7f07a0
Author: Dylan Fong <[email protected]>
Date: 2018-05-09 (Wed, 09 May 2018)
Changed paths:
M src/client/router.js
Log Message:
-----------
change /my-factoids to /documents
Commit: 9823d001ca2e9f6a67a5ea4c7f6350150a0f6de2
https://github.com/PathwayCommons/factoid/commit/9823d001ca2e9f6a67a5ea4c7f6350150a0f6de2
Author: Dylan Fong <[email protected]>
Date: 2018-05-10 (Thu, 10 May 2018)
Changed paths:
M src/client/components/editor/index.js
M src/client/router.js
Log Message:
-----------
use lodash find instead of parsing my-factoids into a set to prevent
duplicate my factoid entries
Commit: a706092f8eb4f6b8d6a737715137b61e066f93dc
https://github.com/PathwayCommons/factoid/commit/a706092f8eb4f6b8d6a737715137b61e066f93dc
Author: fdurupinar <[email protected]>
Date: 2018-05-10 (Thu, 10 May 2018)
Changed paths:
M src/client/components/editor/cy/tippy.js
M src/client/components/element-info/interaction-info.js
M src/client/components/element-info/participant-info.js
M src/client/components/element-info/progression-stepper.js
M src/styles/element-info/element-info.css
M src/styles/element-info/entity-info.css
M src/styles/element-info/interaction-info.css
Log Message:
-----------
Merge branch 'unstable' of https://github.com/PathwayCommons/factoid into
form-components
Commit: eaffeb23db723d49b5893a8628af8b8bbc315fa9
https://github.com/PathwayCommons/factoid/commit/eaffeb23db723d49b5893a8628af8b8bbc315fa9
Author: fdurupinar <[email protected]>
Date: 2018-05-11 (Fri, 11 May 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-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/protein-modification-form.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction-type/protein-affects-chemical.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
model updates and bug fixes
Commit: 15f782a5bad1a1198d4d3358abc623eb0d243569
https://github.com/PathwayCommons/factoid/commit/15f782a5bad1a1198d4d3358abc623eb0d243569
Author: Max Franz <[email protected]>
Date: 2018-05-11 (Fri, 11 May 2018)
Changed paths:
M src/client/components/editor/index.js
A src/client/components/my-factoids.js
M src/client/router.js
M src/styles/index.css
A src/styles/my-factoids.css
Log Message:
-----------
Merge pull request #270 from PathwayCommons/my-factoids-local-storage
My factoids local storage
Commit: 9ccaabe1fc0cff5d2eedea8074969f37670a7443
https://github.com/PathwayCommons/factoid/commit/9ccaabe1fc0cff5d2eedea8074969f37670a7443
Author: Dylan Fong <[email protected]>
Date: 2018-05-11 (Fri, 11 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/index.js
Log Message:
-----------
Initial help system work
Commit: af5d6807b1adb2a253613ebb43a501456036999a
https://github.com/PathwayCommons/factoid/commit/af5d6807b1adb2a253613ebb43a501456036999a
Author: IgorRodchenkov <[email protected]>
Date: 2018-05-12 (Sat, 12 May 2018)
Changed paths:
M .gitignore
Log Message:
-----------
Added .idea/ to .gitignore.
Commit: 42a9baa7b9650883a0d7fed785af842cf8847fcf
https://github.com/PathwayCommons/factoid/commit/42a9baa7b9650883a0d7fed785af842cf8847fcf
Author: Dylan Fong <[email protected]>
Date: 2018-05-14 (Mon, 14 May 2018)
Changed paths:
A src/client/components/editor/help-network.json
M src/client/components/editor/index.js
Log Message:
-----------
on help button click, load a static help pathway
Commit: 37ae2326ea6ed3ecbd21e8e4952d90c25f5ea232
https://github.com/PathwayCommons/factoid/commit/37ae2326ea6ed3ecbd21e8e4952d90c25f5ea232
Author: Dylan Fong <[email protected]>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M package-lock.json
M package.json
M src/client/components/editor/buttons.js
M src/client/components/editor/help-network.json
M src/client/components/editor/index.js
M src/styles/editor/editor.css
M src/util/cy.js
Log Message:
-----------
help system continued
- use cytoscape popper for edge and node help tips
- use bus system for showing/hiding tooltips
- update dummy network json for better aesthetics
- add screen dimming overlay to show that the help system is active
Commit: 8733a307c5fb1f781666bd7d11ebf12ecb745a96
https://github.com/PathwayCommons/factoid/commit/8733a307c5fb1f781666bd7d11ebf12ecb745a96
Author: fdurupinar <[email protected]>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M src/client/components/form-editor/index.js
Log Message:
-----------
fixed a bug in interaction association
Commit: 74877897cbfd0b2810bcfbda3b891927cceb8392
https://github.com/PathwayCommons/factoid/commit/74877897cbfd0b2810bcfbda3b891927cceb8392
Author: Max Franz <[email protected]>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M src/model/element/interaction-type/interaction-type.js
Log Message:
-----------
Typo : InteractionType.prototype.isActivation()
Commit: 110c7a53c7a79cd47ddfc1e16fa941444885a0e6
https://github.com/PathwayCommons/factoid/commit/110c7a53c7a79cd47ddfc1e16fa941444885a0e6
Author: Max Franz <[email protected]>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
R src/model/element/interaction-type/chemical-affects-protein.js
M src/model/element/interaction-type/enum.js
M src/model/element/interaction-type/modification.js
R src/model/element/interaction-type/protein-affects-chemical.js
A src/model/element/interaction-type/protein-chemical.js
Log Message:
-----------
Use a common protein-checmical type to simplify the user selection of
interaction type
Ref : Tweaks to the interaction wizard #275
Commit: acb8456fd31aa37f0ed0ff064173bc62c1721f2a
https://github.com/PathwayCommons/factoid/commit/acb8456fd31aa37f0ed0ff064173bc62c1721f2a
Author: Max Franz <[email protected]>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M src/client/components/editor/cy/tippy.js
Log Message:
-----------
Use a slight animation to make the participant popovers more salient
Ref : Tweaks to the interaction wizard #275
Commit: 15b7cb89209a40da2e7df2a187c04f54612ed18b
https://github.com/PathwayCommons/factoid/commit/15b7cb89209a40da2e7df2a187c04f54612ed18b
Author: Dylan Fong <[email protected]>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
R src/client/components/editor/help-network.json
M src/client/components/editor/index.js
M src/client/defs.js
M src/styles/editor/editor.css
M src/styles/popover/tippy.css
Log Message:
-----------
Baseline help system
- use the current network to show help tips instead of a sample graph for now
- set zIndex default values for tippy
- comment out tippy zIndex override values in the css
- css transitions for the help overlay
Commit: 56b3c007db644a3045448bc9f84233eb8b83a0d6
https://github.com/PathwayCommons/factoid/commit/56b3c007db644a3045448bc9f84233eb8b83a0d6
Author: Dylan Fong <[email protected]>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M src/styles/editor/editor.css
M src/styles/popover/tippy.css
Log Message:
-----------
revert unnecessary changes to editor css for the help system, clearer comment
for tippy zindex
Commit: 5d7c72435b764b1b47310920037405beef60356a
https://github.com/PathwayCommons/factoid/commit/5d7c72435b764b1b47310920037405beef60356a
Author: metincansiper <[email protected]>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M src/client/components/document-seeder.js
M src/styles/document-seeder.css
Log Message:
-----------
Bold the interaction trigger word in the highlight mode #277
Commit: ffb2bc877a436c55eebef145ca35989982bb185b
https://github.com/PathwayCommons/factoid/commit/ffb2bc877a436c55eebef145ca35989982bb185b
Author: metincansiper <[email protected]>
Date: 2018-05-17 (Thu, 17 May 2018)
Changed paths:
M src/client/components/document-seeder.js
Log Message:
-----------
Removed unused variable #277
Commit: 8a47b479b00d245dc4d1caad3a6375c5888dd527
https://github.com/PathwayCommons/factoid/commit/8a47b479b00d245dc4d1caad3a6375c5888dd527
Author: Dylan Fong <[email protected]>
Date: 2018-05-17 (Thu, 17 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
R src/client/components/editor/menu.js
Log Message:
-----------
refactor out the help system into its own component
- use more accurate event names for opening/closing tooltips
- moved the help system code into the old help component
- removed the old unused menu component
Commit: 0bc47a6f6fb58fdda280ee540d79c651544a7e10
https://github.com/PathwayCommons/factoid/commit/0bc47a6f6fb58fdda280ee540d79c651544a7e10
Author: Dylan Fong <[email protected]>
Date: 2018-05-18 (Fri, 18 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
Log Message:
-----------
help button is viewable in either edit/view mode
- refactor toggleHelp function to be more readable
- slightly different tooltip content language based on whether the user is in
edit mode or view mode
- use controller to access cy instead of props as it is set in the editor data
asynchronously
Commit: b1bc706ba602f554962eddad574ee71a85812c8a
https://github.com/PathwayCommons/factoid/commit/b1bc706ba602f554962eddad574ee71a85812c8a
Author: metincansiper <[email protected]>
Date: 2018-05-21 (Mon, 21 May 2018)
Changed paths:
M package.json
M src/client/components/editor/buttons.js
M src/client/components/form-editor/index.js
M src/config.js
M src/model/document/document.js
A src/model/element/interaction-type/biopax-type.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/general.js
M src/model/element/interaction-type/interaction-type.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/protein-chemical.js
M src/model/element/interaction-type/ubiquination.js
M src/server/routes/api/document/index.js
M src/styles/form-editor/form-editor.css
A src/util/file.js
M src/util/index.js
Log Message:
-----------
Added biopax export buttons to form and network editors
Commit: b3437d1be6b9f69b9926b0d08b121e328c398383
https://github.com/PathwayCommons/factoid/commit/b3437d1be6b9f69b9926b0d08b121e328c398383
Author: metincansiper <[email protected]>
Date: 2018-05-22 (Tue, 22 May 2018)
Changed paths:
M src/model/element/interaction-type/modification.js
Log Message:
-----------
Fixed typo of "contollerProtein"
Commit: 900c1fdc765ee2e5ab8665e87cf4ba1bd890c810
https://github.com/PathwayCommons/factoid/commit/900c1fdc765ee2e5ab8665e87cf4ba1bd890c810
Author: metincansiper <[email protected]>
Date: 2018-05-22 (Tue, 22 May 2018)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Handle response error from biopax converter and throw error when response is
not ok.
Commit: 7bd63bda96ddfc6d5fe759b56211ec8fa9af61dd
https://github.com/PathwayCommons/factoid/commit/7bd63bda96ddfc6d5fe759b56211ec8fa9af61dd
Author: metincansiper <[email protected]>
Date: 2018-05-22 (Tue, 22 May 2018)
Changed paths:
M src/client/components/form-editor/index.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
Reverted changes for adding "Export to Biopax" button next to "Submit"
button. Exports to biopax on click of "Submit" button now. Funda will rename
"Submit".
Commit: 71b370c7da7ce16afd4b2753174897f279305517
https://github.com/PathwayCommons/factoid/commit/71b370c7da7ce16afd4b2753174897f279305517
Author: metincansiper <[email protected]>
Date: 2018-05-22 (Tue, 22 May 2018)
Changed paths:
M src/model/element/interaction-type/biopax-type.js
Log Message:
-----------
Indentation fix
Commit: 414d62032b1bb18a79647e4585beadb286ee08a4
https://github.com/PathwayCommons/factoid/commit/414d62032b1bb18a79647e4585beadb286ee08a4
Author: fdurupinar <[email protected]>
Date: 2018-05-22 (Tue, 22 May 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 fixes
Commit: e2e89d6afa613aeeb389b4f5917ce07f8103bc5e
https://github.com/PathwayCommons/factoid/commit/e2e89d6afa613aeeb389b4f5917ce07f8103bc5e
Author: Dylan Fong <[email protected]>
Date: 2018-05-23 (Wed, 23 May 2018)
Changed paths:
M src/client/components/editor/help.js
M src/styles/editor/editor.css
A src/styles/help.css
M src/styles/index.css
Log Message:
-----------
separate help css into its own file
Commit: ace7aec1aa9887984f1ee7ad995a032642b08fd1
https://github.com/PathwayCommons/factoid/commit/ace7aec1aa9887984f1ee7ad995a032642b08fd1
Author: fdurupinar <[email protected]>
Date: 2018-05-23 (Wed, 23 May 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-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/molecular-interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
hiding info for all entities
Commit: 468975cebfe73d0670cf36c0cb8481aeb3d1e2a8
https://github.com/PathwayCommons/factoid/commit/468975cebfe73d0670cf36c0cb8481aeb3d1e2a8
Author: Dylan Fong <[email protected]>
Date: 2018-05-23 (Wed, 23 May 2018)
Changed paths:
M src/client/components/document-view-chooser.js
M src/styles/document-view-chooser.css
Log Message:
-----------
add text for the editor chooser
Commit: 9cd41d3475c09006264040e6c332914cea09b197
https://github.com/PathwayCommons/factoid/commit/9cd41d3475c09006264040e6c332914cea09b197
Author: Dylan Fong <[email protected]>
Date: 2018-05-23 (Wed, 23 May 2018)
Changed paths:
M src/client/components/document-view-chooser.js
Log Message:
-----------
more concise wording for the chooser text
Commit: 0be9b8f907497cc5d674e1bc67fdc00969b34001
https://github.com/PathwayCommons/factoid/commit/0be9b8f907497cc5d674e1bc67fdc00969b34001
Author: fdurupinar <[email protected]>
Date: 2018-05-23 (Wed, 23 May 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/molecular-interaction-form.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
delete buttons for individual entities in molecular interaction template
Commit: cda3ef336c69e40a2f47328e82dc5755888a5f20
https://github.com/PathwayCommons/factoid/commit/cda3ef336c69e40a2f47328e82dc5755888a5f20
Author: fdurupinar <[email protected]>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M src/client/components/form-editor/molecular-interaction-form.js
Log Message:
-----------
delete buttons for individual entities in molecular interaction template
Commit: cd49876d1cebfb2aab4c56c981162b7f5b29b775
https://github.com/PathwayCommons/factoid/commit/cd49876d1cebfb2aab4c56c981162b7f5b29b775
Author: fdurupinar <[email protected]>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M src/client/components/editor/cy/tippy.js
R src/model/element/interaction-type/chemical-affects-protein.js
M src/model/element/interaction-type/enum.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction-type/modification.js
R src/model/element/interaction-type/protein-affects-chemical.js
A src/model/element/interaction-type/protein-chemical.js
Log Message:
-----------
Merge branch 'unstable' of https://github.com/PathwayCommons/factoid into
form-components
Commit: 4b5a6457ef17c1a866cc31412098fd340186b6a8
https://github.com/PathwayCommons/factoid/commit/4b5a6457ef17c1a866cc31412098fd340186b6a8
Author: fdurupinar <[email protected]>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-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/protein-modification-form.js
Log Message:
-----------
check for mounting status before hide/show
Commit: d32c289a65471dc9da38058b96d0317d04397316
https://github.com/PathwayCommons/factoid/commit/d32c289a65471dc9da38058b96d0317d04397316
Author: Max Franz <[email protected]>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M src/client/components/document-seeder.js
M src/styles/document-seeder.css
Log Message:
-----------
Merge pull request #281 from metincansiper/highlight-text-updates
Bold the interaction trigger word in the highlight mode
Commit: d0b0237401e7109fc3a89e519e1b2b7408bf87c7
https://github.com/PathwayCommons/factoid/commit/d0b0237401e7109fc3a89e519e1b2b7408bf87c7
Author: Dylan Fong <[email protected]>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M src/client/components/editor/help.js
Log Message:
-----------
Fix help system tooltip typos
Commit: af6eef0ce3baaa35871fbeeb6d2afe701f8fcf4c
https://github.com/PathwayCommons/factoid/commit/af6eef0ce3baaa35871fbeeb6d2afe701f8fcf4c
Author: Max Franz <[email protected]>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M src/client/components/document-view-chooser.js
M src/styles/document-view-chooser.css
Log Message:
-----------
Merge pull request #285 from PathwayCommons/editor-chooser-text
add text for the editor chooser
Commit: 3798040aeff212683a96c9d90ef2c0ce843c14e4
https://github.com/PathwayCommons/factoid/commit/3798040aeff212683a96c9d90ef2c0ce843c14e4
Author: Max Franz <[email protected]>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M package-lock.json
M package.json
M src/client/components/editor/buttons.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
R src/client/components/editor/menu.js
M src/client/defs.js
A src/styles/help.css
M src/styles/index.css
M src/styles/popover/tippy.css
M src/util/cy.js
Log Message:
-----------
Merge pull request #282 from PathwayCommons/help-system
Help system
Commit: d7820f0b97e1071bf83b7728243a7377abdbb89c
https://github.com/PathwayCommons/factoid/commit/d7820f0b97e1071bf83b7728243a7377abdbb89c
Author: fdurupinar <[email protected]>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
Log Message:
-----------
update mounting status manually
Commit: 3de4d5804796bfd5cca028fd219b73ee4e365902
https://github.com/PathwayCommons/factoid/commit/3de4d5804796bfd5cca028fd219b73ee4e365902
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/client/defs.js
Log Message:
-----------
Update Tippy options
- performance:true could be useful
- touchHold:false by default -- only useful for hover tooltips
Note : Updating to latest version of Tippy.js causes popovers to stutter when
resized.
Ref : Issues with touch device support #273
Commit: 6bedec10ca26fa7162b2648c531247f4c9c707ba
https://github.com/PathwayCommons/factoid/commit/6bedec10ca26fa7162b2648c531247f4c9c707ba
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/client/components/popover/tooltip.js
Log Message:
-----------
Remove click event in Tooltip options for Tippy
The click event causes the hover/help tooltips to misbehave on touch devices
Ref : Issues with touch device support #273
Commit: ba95b600c8859b54b07fde6354efdfbbaa449eed
https://github.com/PathwayCommons/factoid/commit/ba95b600c8859b54b07fde6354efdfbbaa449eed
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/client/components/editor/cy/tippy.js
Log Message:
-----------
Remove debug window ref
Commit: ff7b6dab8d2b06c435dd57e28824986bf6e550df
https://github.com/PathwayCommons/factoid/commit/ff7b6dab8d2b06c435dd57e28824986bf6e550df
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/styles/element-info/element-info.css
Log Message:
-----------
Reduce element popover min width to better accommodate touch devices
Commit: 82d92e3cc69830c500305132e5ce10c9c8e86932
https://github.com/PathwayCommons/factoid/commit/82d92e3cc69830c500305132e5ce10c9c8e86932
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/client/components/editor/cy/tippy.js
Log Message:
-----------
Place the entity popovers above or below the node rather than left or right
on small screens
Commit: 266e864f4c572dde7cc5a0e206037166606e0315
https://github.com/PathwayCommons/factoid/commit/266e864f4c572dde7cc5a0e206037166606e0315
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/styles/notification.css
Log Message:
-----------
Make the notifications make better use of space
- On larger screens, make sure the corner notification does not overlap the
toolbar.
- On smaller screens, reduce the font size of the notification body text.
Commit: 4030bd7d274d53b025a74011888c29675f2664d7
https://github.com/PathwayCommons/factoid/commit/4030bd7d274d53b025a74011888c29675f2664d7
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/styles/element-info/element-info.css
Log Message:
-----------
Max out the element popover width at 400px
- The new range is [300px, 400px]
- The old range was [300px, 33vw] -- 33vw can get very large on large screens
Commit: 4a27685a1b009225233379a9a7acf7479556d084
https://github.com/PathwayCommons/factoid/commit/4a27685a1b009225233379a9a7acf7479556d084
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/styles/element-info/element-info.css
Log Message:
-----------
Reduce the max width of the element info to better fit small screens
Commit: e5f42634b50f364ac785569d6e9b8659952ec858
https://github.com/PathwayCommons/factoid/commit/e5f42634b50f364ac785569d6e9b8659952ec858
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/styles/notification.css
Log Message:
-----------
Use a bit less space in the notification action area -- better for smaller
screens
Commit: 77f4940c10597ce1d83e666e99320d6cede350e1
https://github.com/PathwayCommons/factoid/commit/77f4940c10597ce1d83e666e99320d6cede350e1
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/styles/element-info/entity-info.css
Log Message:
-----------
Adjust the entity tooltip max height to be smaller on smaller screens
Commit: 741e8ebcb1c665660236120ed2028d63249d0eef
https://github.com/PathwayCommons/factoid/commit/741e8ebcb1c665660236120ed2028d63249d0eef
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/client/components/editor/cy/tippy.js
Log Message:
-----------
Always make interaction popovers consider the edge as horizontal to avoid
overlap with participant popovers
Commit: d5e9a1790197f8e0667ee761d44d719e7db3f191
https://github.com/PathwayCommons/factoid/commit/d5e9a1790197f8e0667ee761d44d719e7db3f191
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/styles/base.css
Log Message:
-----------
Remove nowrap restriction on plain links for better small screen support
This prevents a plain link making the page overflow horizontally, e.g. on the
home page.
Commit: 8489c02d065061d00a54fbf5f3f483714e5d53fe
https://github.com/PathwayCommons/factoid/commit/8489c02d065061d00a54fbf5f3f483714e5d53fe
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/styles/editor/editor.css
M src/styles/init-app.css
Log Message:
-----------
Avoid use of vw and vh units, especially for the 100vh case
iOS does not return the proper value for 100vh. This change should make the
page fit better on iOS devices, and it should prevent the case where the page
does slight scrolling and gets stuck. The scrolling bug can be reproduced
without this change by swiping on the toolbar. Sometimes popovers can
reproduce the bug on show.
Commit: c5abc7b0e6472988115d2bfec0c626587fc7d2dc
https://github.com/PathwayCommons/factoid/commit/c5abc7b0e6472988115d2bfec0c626587fc7d2dc
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/styles/popover/tippy.css
Log Message:
-----------
May make tippies easier to use on home page and form editor
Commit: 669915e039d2303d44f4ffac43d6c3028379b94c
https://github.com/PathwayCommons/factoid/commit/669915e039d2303d44f4ffac43d6c3028379b94c
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/client/components/editor/cy/tippy.js
M src/client/defs.js
Log Message:
-----------
Turn off sticky and live placement
Commit: 722b0b982c1d5d9382f2afbe939b3da18359c853
https://github.com/PathwayCommons/factoid/commit/722b0b982c1d5d9382f2afbe939b3da18359c853
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/client/components/editor/help.js
Log Message:
-----------
Fixes help tooltips on graph elements
Commit: e225f4c6124b279549b5c9fdfc972f78098feb6a
https://github.com/PathwayCommons/factoid/commit/e225f4c6124b279549b5c9fdfc972f78098feb6a
Author: Max Franz <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
Log Message:
-----------
Fixes toolbar help tooltips
Commit: 47d3e7680976e2963f86e0a233c2b769803ea738
https://github.com/PathwayCommons/factoid/commit/47d3e7680976e2963f86e0a233c2b769803ea738
Author: fdurupinar <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M .gitignore
A ci.sh
A src/client/components/data-component.js
M src/client/components/dirty-component.js
A src/client/components/document-renamer.js
M src/client/components/document-view-chooser.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/element-info/chemical-formula.js
M src/client/components/element-info/element-info.js
A src/client/components/element-info/entity-assoc-display.js
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/interaction-info.js
M src/client/components/element-info/participant-info.js
A src/client/components/element-info/progression-stepper.js
A src/client/components/element-info/progression.js
A src/client/components/form-editor/activation-inhibition-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/molecular-interaction-form.js
A src/client/components/form-editor/protein-modification-form.js
A src/client/components/my-factoids.js
M src/client/components/notification/base.js
M src/client/components/notification/corner.js
M src/client/components/notification/inline.js
M src/client/components/notification/list.js
M src/client/components/notification/notification.js
M src/client/components/notification/panel.js
M src/client/components/notification/popover.js
M src/client/defs.js
M src/client/router.js
M src/model/element/element-type.js
M src/model/element/element.js
R src/model/element/entity-mods.js
A src/model/element/entity-type.js
M src/model/element/entity.js
R src/model/element/interaction-type/chemical-affects-protein.js
M src/model/element/interaction-type/enum.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/interaction-type.js
A src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
A src/model/element/interaction-type/phosphorylation.js
R src/model/element/interaction-type/protein-affects-chemical.js
A src/model/element/interaction-type/protein-chemical.js
A src/model/element/interaction-type/ubiquination.js
M src/model/element/interaction.js
M src/model/element/participant-type.js
A src/styles/document-renamer.css
M src/styles/document-view-chooser.css
M src/styles/document-wizard-stepper.css
M src/styles/element-info/element-info.css
M src/styles/element-info/entity-info.css
M src/styles/element-info/interaction-info.css
M src/styles/form-editor/form-editor.css
A src/styles/image/form-option-preview.png
A src/styles/image/network-option-preview.png
M src/styles/index.css
A src/styles/my-factoids.css
A src/util/cache.js
M src/util/cy.js
M src/util/index.js
M test/interaction.js
Log Message:
-----------
Merge branch 'form-components' of https://github.com/PathwayCommons/factoid
into form-components
Commit: ef818ef64a5ead08e559063f6d8831bb79d4c6b9
https://github.com/PathwayCommons/factoid/commit/ef818ef64a5ead08e559063f6d8831bb79d4c6b9
Author: fdurupinar <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M package-lock.json
M package.json
M src/client/components/document-seeder.js
M src/client/components/document-view-chooser.js
M src/client/components/editor/buttons.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
R src/client/components/editor/menu.js
M src/client/defs.js
M src/styles/document-seeder.css
M src/styles/document-view-chooser.css
A src/styles/help.css
M src/styles/index.css
M src/styles/popover/tippy.css
M src/util/cy.js
Log Message:
-----------
Merge branch 'unstable' of https://github.com/PathwayCommons/factoid into
form-components
Commit: 8578b72e1a049076d124a1eb5be5e538dd729a74
https://github.com/PathwayCommons/factoid/commit/8578b72e1a049076d124a1eb5be5e538dd729a74
Author: fdurupinar <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/molecular-interaction-form.js
Log Message:
-----------
fix for molecular interaction entity delete problem for clones
Commit: 587d3b3e4864d5fe0287405f07aba7fc81c2e5c0
https://github.com/PathwayCommons/factoid/commit/587d3b3e4864d5fe0287405f07aba7fc81c2e5c0
Author: metincansiper <[email protected]>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M src/server/routes/api/document/reach.js
Log Message:
-----------
Add interaction type to reach created elements #252
Commit: f68e576c7f3149983f992c07c28100b0b78709c3
https://github.com/PathwayCommons/factoid/commit/f68e576c7f3149983f992c07c28100b0b78709c3
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/help.js
M src/client/components/popover/tooltip.js
M src/client/defs.js
M src/styles/base.css
M src/styles/editor/editor.css
M src/styles/element-info/element-info.css
M src/styles/element-info/entity-info.css
M src/styles/init-app.css
M src/styles/notification.css
M src/styles/popover/tippy.css
Log Message:
-----------
Merge pull request #286 from PathwayCommons/touch
Issues with touch device support
Commit: 1e18951103c2e89efd2bbf3fa26ac8d3331bf5d0
https://github.com/PathwayCommons/factoid/commit/1e18951103c2e89efd2bbf3fa26ac8d3331bf5d0
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/styles/editor/editor.css
Log Message:
-----------
add task list button that displays the number of entities to complete as a
todo indicator
Commit: 93534043f44518c7caa2b870e2331bfcd9675ec5
https://github.com/PathwayCommons/factoid/commit/93534043f44518c7caa2b870e2331bfcd9675ec5
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
A src/client/components/editor/task-list.js
M src/styles/editor/editor.css
M src/styles/index.css
A src/styles/task-list.css
Log Message:
-----------
task list component files
Commit: 9f4b048203e20055a0a1f4ec58a7924995cdc954
https://github.com/PathwayCommons/factoid/commit/9f4b048203e20055a0a1f4ec58a7924995cdc954
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/index.js
M src/client/components/editor/task-list.js
M src/styles/task-list.css
Log Message:
-----------
toggle implementation for the task list notification button
Commit: 4263a40e44e241aa28f4d0a640a260990a0a2607
https://github.com/PathwayCommons/factoid/commit/4263a40e44e241aa28f4d0a640a260990a0a2607
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/task-list.js
Log Message:
-----------
basic element event listening to update the task list
Commit: afd8db773c7e1e968aadee0204c18d6ed877f678
https://github.com/PathwayCommons/factoid/commit/afd8db773c7e1e968aadee0204c18d6ed877f678
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/task-list.js
Log Message:
-----------
Proper event binding for the task list and button
Commit: 9b8c6f104d649c0b3525d612d7af57229db8eefd
https://github.com/PathwayCommons/factoid/commit/9b8c6f104d649c0b3525d612d7af57229db8eefd
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/task-list.js
M src/client/components/notification/list.js
M src/client/components/notification/panel.js
Log Message:
-----------
notification list and panel for the task list
Commit: 4d6dc8dc26a7ad69aefbe317f516381da9572a7c
https://github.com/PathwayCommons/factoid/commit/4d6dc8dc26a7ad69aefbe317f516381da9572a7c
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/task-list.js
M src/client/components/notification/panel.js
M src/styles/notification.css
M src/styles/task-list.css
Log Message:
-----------
use inline notifications instead of the base notification
- on opening the notification, opens the entity info for the corresponding
entity
- TODO might need to change the behaviour of emitting 'opentip' and 'closetip'
(currently it is a toggle).
Commit: 3748c01cb88b48bafbf53e121a14e0e9f4502926
https://github.com/PathwayCommons/factoid/commit/3748c01cb88b48bafbf53e121a14e0e9f4502926
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/task-list.js
M src/client/components/notification/base.js
M src/client/components/notification/notification.js
Log Message:
-----------
Add a dismissable option for notifications
- notifications with dismissable set to false will not be able to be dismissed
- notifications in the task list set this option to false
Commit: c17967ba52661c2fccb3f386617f5ac631ef9b15
https://github.com/PathwayCommons/factoid/commit/c17967ba52661c2fccb3f386617f5ac631ef9b15
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/styles/task-list.css
Log Message:
-----------
task list css styling
Commit: 081bb04e6dd52e46991ce14c10ba45a1908c3c8f
https://github.com/PathwayCommons/factoid/commit/081bb04e6dd52e46991ce14c10ba45a1908c3c8f
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/index.js
M src/styles/editor/editor.css
M src/styles/task-list.css
Log Message:
-----------
task list slides in from the side of the screen mac os style
- turn editor buttons into a react component and add another prop for classname
- create shifted styles for the button and editor
Commit: 60a1b96412d0739b468986fcc0ed0731abe06a4a
https://github.com/PathwayCommons/factoid/commit/60a1b96412d0739b468986fcc0ed0731abe06a4a
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/help.js
M src/client/components/editor/index.js
Log Message:
-----------
hide the task list, and remove the edge draw mode toggle when activating the
help system
Commit: 477711ddcfc28849efcb1eb65e2762e81921916b
https://github.com/PathwayCommons/factoid/commit/477711ddcfc28849efcb1eb65e2762e81921916b
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/styles/task-list.css
Log Message:
-----------
fix missed css lint error
Commit: ac23cf3b2d31503edce479c0a3916440969bf9fd
https://github.com/PathwayCommons/factoid/commit/ac23cf3b2d31503edce479c0a3916440969bf9fd
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/styles/editor/editor.css
Log Message:
-----------
hide overflow when the task list is being shown
Commit: 38eefee3dc800df945076ab0971201e5a7fb3077
https://github.com/PathwayCommons/factoid/commit/38eefee3dc800df945076ab0971201e5a7fb3077
Author: Dylan Fong <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/styles/task-list.css
Log Message:
-----------
scroll the task list for overflow
Commit: 29ad6895683739b06393a252719a278e82bd7524
https://github.com/PathwayCommons/factoid/commit/29ad6895683739b06393a252719a278e82bd7524
Author: fdurupinar <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/help.js
M src/client/components/popover/tooltip.js
M src/client/defs.js
M src/styles/base.css
M src/styles/editor/editor.css
M src/styles/element-info/element-info.css
M src/styles/element-info/entity-info.css
M src/styles/init-app.css
M src/styles/notification.css
M src/styles/popover/tippy.css
Log Message:
-----------
Merge branch 'unstable' of https://github.com/PathwayCommons/factoid into
form-components
Commit: 1f021f95e2ad9deec0d417f8d24107b745b0b800
https://github.com/PathwayCommons/factoid/commit/1f021f95e2ad9deec0d417f8d24107b745b0b800
Author: metincansiper <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/config.js
Log Message:
-----------
Updated biopax converter url.
Commit: b692726365b1095c6a7d7c7ac4a70bf3c62ab4ec
https://github.com/PathwayCommons/factoid/commit/b692726365b1095c6a7d7c7ac4a70bf3c62ab4ec
Author: fdurupinar <[email protected]>
Date: 2018-05-29 (Tue, 29 May 2018)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/element-info/entity-info.js
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/model/element/interaction-type/interaction-type.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
entity info update when clones are updated
Commit: dbb2a3921b2835c7ffebcbbe29a312889ba43c4a
https://github.com/PathwayCommons/factoid/commit/dbb2a3921b2835c7ffebcbbe29a312889ba43c4a
Author: metincansiper <[email protected]>
Date: 2018-05-30 (Wed, 30 May 2018)
Changed paths:
M src/server/routes/api/document/reach.js
Log Message:
-----------
Add interaction type to reach created elements #252 (Added group field to
target entries)
Commit: 375147283e11e8b6ad3a0ecd802e455b0d9a4915
https://github.com/PathwayCommons/factoid/commit/375147283e11e8b6ad3a0ecd802e455b0d9a4915
Author: metincansiper <[email protected]>
Date: 2018-05-30 (Wed, 30 May 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/form-editor/index.js
M src/server/routes/api/document/index.js
M src/util/file.js
Log Message:
-----------
Use Get /biopax/:id instead of POST /convert-to-biopax for biopax converter
service. Also, used underscore for string.endsWith() instead of
string.prototype.endsWith() for cross browser compability issues.
Commit: 15c5b0445b8cfe2ec70cd42036d819e9edeb595e
https://github.com/PathwayCommons/factoid/commit/15c5b0445b8cfe2ec70cd42036d819e9edeb595e
Author: fdurupinar <[email protected]>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/client/components/form-editor/molecular-interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
Log Message:
-----------
interaction synch
Commit: a331e706d68a320bcc8205e2e9543d124cac3996
https://github.com/PathwayCommons/factoid/commit/a331e706d68a320bcc8205e2e9543d124cac3996
Author: Dylan Fong <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/client/components/editor/help.js
M src/client/components/editor/index.js
M src/client/components/editor/task-list.js
Log Message:
-----------
task list and help system cleanup
- removed uneccessary events to listen to in the task list
- made the toggle help code more readable
- turned the resetMenuState function into a promise
- resetMenuState waits 250ms for the menu animations to be completed
- toggleTaskList is implemented similarly to toggleDrawMode
Commit: fc26457900a2e43d8bded481cfd6511b203d9a42
https://github.com/PathwayCommons/factoid/commit/fc26457900a2e43d8bded481cfd6511b203d9a42
Author: fdurupinar <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/client/components/form-editor/index.js
Log Message:
-----------
interaction synchronization fixed
Commit: 5f882e7b28614b21e4046b294d2ab3acfec2b6ad
https://github.com/PathwayCommons/factoid/commit/5f882e7b28614b21e4046b294d2ab3acfec2b6ad
Author: fdurupinar <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
fixed typo
Commit: 12436a551bde5cad135f53c6e61d43eab329bb19
https://github.com/PathwayCommons/factoid/commit/12436a551bde5cad135f53c6e61d43eab329bb19
Author: metincansiper <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/model/document/document.js
M src/model/element/entity.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/general.js
M src/model/element/interaction-type/modification.js
M src/model/element/interaction-type/protein-chemical.js
M src/model/element/interaction.js
Log Message:
-----------
Add entity xrefs as well to biopax templates.
Commit: a47092aaed9746b542f1d6121c38992e1b6f685e
https://github.com/PathwayCommons/factoid/commit/a47092aaed9746b542f1d6121c38992e1b6f685e
Author: Dylan Fong <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/editor/task-list.js
Log Message:
-----------
Task list now supports interactions
- also use Promise.delay for resetMenuState
Commit: 421c3835e174d10ba0a41703837f3c5efc633d6a
https://github.com/PathwayCommons/factoid/commit/421c3835e174d10ba0a41703837f3c5efc633d6a
Author: Dylan Fong <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/client/components/editor/task-list.js
Log Message:
-----------
order entities before interactions for the task list
Commit: de36d09dbb7fb666d36e9fbb1e40df0844159508
https://github.com/PathwayCommons/factoid/commit/de36d09dbb7fb666d36e9fbb1e40df0844159508
Author: Dylan Fong <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/client/components/editor/task-list.js
Log Message:
-----------
update the num tasks indicator to include incomplete interactions
Commit: 7e3f15228e4b07c4de50b26c681a52252cf918fc
https://github.com/PathwayCommons/factoid/commit/7e3f15228e4b07c4de50b26c681a52252cf918fc
Author: Dylan Fong <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
close network tooltips in reset menu state
- fixes edge case of floating tooltips when a user opens the help system
Commit: 33facdd1c262c87c063b68d3efa50573bbfd008e
https://github.com/PathwayCommons/factoid/commit/33facdd1c262c87c063b68d3efa50573bbfd008e
Author: Dylan Fong <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
hide button tooltips if they are open when calling resetMenuState
Commit: 4ac4c327a28d64535cd7822d721f4eca7256077a
https://github.com/PathwayCommons/factoid/commit/4ac4c327a28d64535cd7822d721f4eca7256077a
Author: metincansiper <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M package-lock.json
Log Message:
-----------
Updated package-lock.json by re-installing file-saver library.
Commit: 3ce244fb8062cf81d9daf63bd11d0f33407ee199
https://github.com/PathwayCommons/factoid/commit/3ce244fb8062cf81d9daf63bd11d0f33407ee199
Author: fdurupinar <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-form.js
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/index.js
Log Message:
-----------
only one entityinfo per form is allowed
Commit: 7337478d0411c395c63325e6645e1a371c3b8b0b
https://github.com/PathwayCommons/factoid/commit/7337478d0411c395c63325e6645e1a371c3b8b0b
Author: fdurupinar <[email protected]>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M package-lock.json
M src/client/components/form-editor/entity-form.js
Log Message:
-----------
only one entityinfo per form is allowed
Commit: aab2467c0a3a1f311f7770c984bbfafff5f121f9
https://github.com/PathwayCommons/factoid/commit/aab2467c0a3a1f311f7770c984bbfafff5f121f9
Author: fdurupinar <[email protected]>
Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths:
R package-lock.json
Log Message:
-----------
updates
Commit: 5a701973a8a6d4e1dfa36fdf05989a7f660b1072
https://github.com/PathwayCommons/factoid/commit/5a701973a8a6d4e1dfa36fdf05989a7f660b1072
Author: fdurupinar <[email protected]>
Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths:
A package-lock.json
M src/client/components/editor/index.js
M src/client/components/form-editor/activation-inhibition-form.js
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/molecular-interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
Log Message:
-----------
updates
Commit: 6c6568f38e0be93a8e5f22349748f7428d0d812d
https://github.com/PathwayCommons/factoid/commit/6c6568f38e0be93a8e5f22349748f7428d0d812d
Author: fdurupinar <[email protected]>
Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/molecular-interaction-form.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
entityinfo with popover
Commit: d2bd08ecfb48296a15f17134978ac78f977812c6
https://github.com/PathwayCommons/factoid/commit/d2bd08ecfb48296a15f17134978ac78f977812c6
Author: fdurupinar <[email protected]>
Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
M src/client/components/form-editor/index.js
Log Message:
-----------
entityinfo directly with tippy
Commit: 65d556583901893e8f25fe4ee19f4b34d84adc87
https://github.com/PathwayCommons/factoid/commit/65d556583901893e8f25fe4ee19f4b34d84adc87
Author: fdurupinar <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
Log Message:
-----------
tippy placement update
Commit: 2571fbdc9ade9370a7bdf785b8a6d926a371ca4b
https://github.com/PathwayCommons/factoid/commit/2571fbdc9ade9370a7bdf785b8a6d926a371ca4b
Author: Max Franz <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
A src/client/components/editor/task-list.js
M src/client/components/notification/base.js
M src/client/components/notification/list.js
M src/client/components/notification/notification.js
M src/client/components/notification/panel.js
M src/styles/editor/editor.css
M src/styles/index.css
M src/styles/notification.css
A src/styles/task-list.css
Log Message:
-----------
Merge notification-list into unstable
- Local testing successful
- Closes PR #288
Commit: d6a61179d7e23ebf72a81f868ada3747e7e840c1
https://github.com/PathwayCommons/factoid/commit/d6a61179d7e23ebf72a81f868ada3747e7e840c1
Author: Max Franz <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/server/routes/api/document/reach.js
Log Message:
-----------
Merge branch 'reach-element-type' of https://github.com/metincansiper/factoid
into metincansiper-reach-element-type
Commit: ba3c794b0be700e4d2502bb42d29132170baff83
https://github.com/PathwayCommons/factoid/commit/ba3c794b0be700e4d2502bb42d29132170baff83
Author: Max Franz <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M package-lock.json
M src/server/routes/api/document/reach.js
Log Message:
-----------
Cleanup
Commit: a801c6bfd2f03f2bf3346e27f55a73883850afe5
https://github.com/PathwayCommons/factoid/commit/a801c6bfd2f03f2bf3346e27f55a73883850afe5
Author: Max Franz <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M package-lock.json
M src/server/routes/api/document/reach.js
Log Message:
-----------
Merge metincansiper-reach-element-type into unstable
- Local tests successful for 'p53 phosphorylates mdm2'
- Do some cleanup re. completed state
- Closes PR #287
Commit: 82463716ba4a4e4ab62b1f8f3b12a9f40bd482ff
https://github.com/PathwayCommons/factoid/commit/82463716ba4a4e4ab62b1f8f3b12a9f40bd482ff
Author: Max Franz <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/index.js
M src/client/router.js
M src/styles/editor/editor.css
Log Message:
-----------
Add 'More tools' button to toolbar
- New Factoid
- My factoids
- Form-based editor
- About & contact
Commit: 0ce56ca8913c2f9bc92a001c2f1d241d43c7ad97
https://github.com/PathwayCommons/factoid/commit/0ce56ca8913c2f9bc92a001c2f1d241d43c7ad97
Author: Max Franz <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
Log Message:
-----------
Re-organise the button groups to be more analogous to the future LHS/RHS
separation
Commit: 61e2bce8834a2dae541fe05a37728231505c921e
https://github.com/PathwayCommons/factoid/commit/61e2bce8834a2dae541fe05a37728231505c921e
Author: Max Franz <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M package-lock.json
M package.json
M src/client/components/editor/buttons.js
M src/client/components/form-editor/index.js
M src/config.js
M src/model/document/document.js
M src/model/element/entity.js
A src/model/element/interaction-type/biopax-type.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/general.js
M src/model/element/interaction-type/interaction-type.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/protein-chemical.js
M src/model/element/interaction-type/ubiquination.js
M src/model/element/interaction.js
M src/server/routes/api/document/index.js
A src/util/file.js
M src/util/index.js
Log Message:
-----------
Merge branch 'export-to-biopax' of https://github.com/metincansiper/factoid
into metincansiper-export-to-biopax
# Conflicts:
# src/client/components/editor/buttons.js
Commit: 13ccc104b2f3430cdc3c1c063e066766281785a8
https://github.com/PathwayCommons/factoid/commit/13ccc104b2f3430cdc3c1c063e066766281785a8
Author: Max Franz <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M package-lock.json
M package.json
M src/client/components/editor/buttons.js
M src/client/components/form-editor/index.js
M src/config.js
M src/model/document/document.js
M src/model/element/entity.js
A src/model/element/interaction-type/biopax-type.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/general.js
M src/model/element/interaction-type/interaction-type.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/protein-chemical.js
M src/model/element/interaction-type/ubiquination.js
M src/model/element/interaction.js
M src/server/routes/api/document/index.js
A src/util/file.js
M src/util/index.js
Log Message:
-----------
Merge metincansiper-export-to-biopax into unstable
- Local test successful for 'pcna phosphorylates mdm2'
- Fixes save button
- Closes PR #284
Commit: 0fdb01a21fbed1a300756a316d6dabd3b3c2b5ba
https://github.com/PathwayCommons/factoid/commit/0fdb01a21fbed1a300756a316d6dabd3b3c2b5ba
Author: Dylan Fong <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
Log Message:
-----------
Port over the editor toggle + extras button
Commit: 51434403add28e29fb930b510d882c3d86675f82
https://github.com/PathwayCommons/factoid/commit/51434403add28e29fb930b510d882c3d86675f82
Author: Dylan Fong <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/form-editor/index.js
M src/client/router.js
A src/styles/app-bar.css
M src/styles/form-editor/form-editor.css
M src/styles/index.css
Log Message:
-----------
port over minimal app bar for the form editor
Commit: a5aaaf76e0ed7896c940577c2c0847d5b6305ac3
https://github.com/PathwayCommons/factoid/commit/a5aaaf76e0ed7896c940577c2c0847d5b6305ac3
Author: Dylan Fong <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
M src/styles/editor/editor.css
M src/styles/task-list.css
Log Message:
-----------
organize menu and editor buttons into different button sets
- remove close help button because it obstructs the right menu
Commit: fd6332fab828489ce7cfc0833eec5fec933a46fc
https://github.com/PathwayCommons/factoid/commit/fd6332fab828489ce7cfc0833eec5fec933a46fc
Author: Dylan Fong <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/editor/help.js
M src/client/components/editor/index.js
Log Message:
-----------
temporarily use cy from controller.data
- current issues with passing cy as props to the component
Commit: ef1f1b728e4bc802b8d50d50481b99239e676b51
https://github.com/PathwayCommons/factoid/commit/ef1f1b728e4bc802b8d50d50481b99239e676b51
Author: Dylan Fong <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/styles/notification.css
Log Message:
-----------
move the corner notification out of the way of the right menu
Commit: e003f8f710c033d7c2abdb59767c11c6bd772d04
https://github.com/PathwayCommons/factoid/commit/e003f8f710c033d7c2abdb59767c11c6bd772d04
Author: Dylan Fong <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
disable corner notification for now
Commit: c27c2a21f13d1d7b7af272c7a6357d47e7741366
https://github.com/PathwayCommons/factoid/commit/c27c2a21f13d1d7b7af272c7a6357d47e7741366
Author: Dylan Fong <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/task-list.js
M src/styles/editor/editor.css
Log Message:
-----------
display 50+ when there are more than 50 todo items
- task number indicator position fixes
Commit: 363c76a21db237f9da2ee07793df16bfa5ea069d
https://github.com/PathwayCommons/factoid/commit/363c76a21db237f9da2ee07793df16bfa5ea069d
Author: Dylan Fong <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/editor/index.js
M src/styles/editor/editor.css
M src/styles/notification.css
Log Message:
-----------
Revert experiemental changes
Commit: 7a391a98b8314b3c128c1211c301818fb02272fe
https://github.com/PathwayCommons/factoid/commit/7a391a98b8314b3c128c1211c301818fb02272fe
Author: fdurupinar <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M src/client/components/form-editor/entity-form.js
Log Message:
-----------
entity info sync with initial grounding on graph interface
Commit: 1f9be760ef48ac0667646f2b47c25bd81586ead8
https://github.com/PathwayCommons/factoid/commit/1f9be760ef48ac0667646f2b47c25bd81586ead8
Author: fdurupinar <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M package-lock.json
M package.json
M src/client/components/editor/buttons.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
A src/client/components/editor/task-list.js
M src/client/components/form-editor/index.js
M src/client/components/notification/base.js
M src/client/components/notification/list.js
M src/client/components/notification/notification.js
M src/client/components/notification/panel.js
M src/client/router.js
M src/config.js
M src/model/document/document.js
M src/model/element/entity.js
A src/model/element/interaction-type/biopax-type.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/general.js
M src/model/element/interaction-type/interaction-type.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/protein-chemical.js
M src/model/element/interaction-type/ubiquination.js
M src/model/element/interaction.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/reach.js
M src/styles/editor/editor.css
M src/styles/index.css
M src/styles/notification.css
A src/styles/task-list.css
A src/util/file.js
M src/util/index.js
Log Message:
-----------
merge with unstable
Commit: bbcdbd161292302c585b4547fc20c835a3c3e148
https://github.com/PathwayCommons/factoid/commit/bbcdbd161292302c585b4547fc20c835a3c3e148
Author: fdurupinar <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M package.json
Log Message:
-----------
updated modules
Commit: 8832965ab1746f037c559906f5b4ebecb320a588
https://github.com/PathwayCommons/factoid/commit/8832965ab1746f037c559906f5b4ebecb320a588
Author: fdurupinar <[email protected]>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
R package-lock.json
Log Message:
-----------
updated modules
Commit: 5712dec0d5034ea61a2318f86965b80b7bdc7460
https://github.com/PathwayCommons/factoid/commit/5712dec0d5034ea61a2318f86965b80b7bdc7460
Author: Dylan Fong <[email protected]>
Date: 2018-06-05 (Tue, 05 Jun 2018)
Changed paths:
M src/styles/app-bar.css
Log Message:
-----------
fix lint error
Commit: d426172e454260dd3d461b739569e9ef0b2732a0
https://github.com/PathwayCommons/factoid/commit/d426172e454260dd3d461b739569e9ef0b2732a0
Author: Dylan Fong <[email protected]>
Date: 2018-06-05 (Tue, 05 Jun 2018)
Changed paths:
M src/client/components/editor/task-list.js
Log Message:
-----------
fix comparison logic error for the task list indicator
Commit: 41269d391d7ab330a32709b25f4923a4fd8534a7
https://github.com/PathwayCommons/factoid/commit/41269d391d7ab330a32709b25f4923a4fd8534a7
Author: Max Franz <[email protected]>
Date: 2018-06-05 (Tue, 05 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
M src/client/components/editor/task-list.js
M src/client/components/form-editor/index.js
M src/client/router.js
A src/styles/app-bar.css
M src/styles/editor/editor.css
M src/styles/form-editor/form-editor.css
M src/styles/index.css
M src/styles/task-list.css
Log Message:
-----------
Merge pull request #294 from PathwayCommons/alpha
Split editor and app buttons
Commit: d2e872b1b7b82984f2fc075a77d24c7bb84376c9
https://github.com/PathwayCommons/factoid/commit/d2e872b1b7b82984f2fc075a77d24c7bb84376c9
Author: Max Franz <[email protected]>
Date: 2018-06-05 (Tue, 05 Jun 2018)
Changed paths:
M src/styles/editor/editor.css
Log Message:
-----------
Misc lint
Commit: bb3387ca0d64917a1418f823d98cde2b891f2025
https://github.com/PathwayCommons/factoid/commit/bb3387ca0d64917a1418f823d98cde2b891f2025
Author: Max Franz <[email protected]>
Date: 2018-06-05 (Tue, 05 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/styles/app.css
Log Message:
-----------
Add home button with logo icon on the right-hand toolbar
Commit: cced62a7ba20176464738b2b103b002e804843c9
https://github.com/PathwayCommons/factoid/commit/cced62a7ba20176464738b2b103b002e804843c9
Author: Dylan Fong <[email protected]>
Date: 2018-06-06 (Wed, 06 Jun 2018)
Changed paths:
M src/client/components/document-seeder.js
M src/server/routes/api/document/index.js
M src/styles/document-seeder.css
Log Message:
-----------
add document title input in the document seeder page
Commit: 17923c688f652348facaf2da82cc349130c98c5c
https://github.com/PathwayCommons/factoid/commit/17923c688f652348facaf2da82cc349130c98c5c
Author: Dylan Fong <[email protected]>
Date: 2018-06-06 (Wed, 06 Jun 2018)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
rename the doc in the main post function instead of in the lower level
functions
Commit: d4da2ee6e10df35f80ef4dd83cdf248f6b2c4e1b
https://github.com/PathwayCommons/factoid/commit/d4da2ee6e10df35f80ef4dd83cdf248f6b2c4e1b
Author: Max Franz <[email protected]>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M src/client/components/editor/cy/doc.js
M src/client/components/element-info/entity-info.js
M src/client/components/form-editor/index.js
M src/client/components/form-editor/interaction-form.js
M src/model/element-set.js
M src/model/element/interaction.js
Log Message:
-----------
Form fixes (#306)
* Fix form ui from passing invalid association data on interaction init
- Can't pass class-instantiated objects to json store
- Add guard in Interaction for when garbage association data is sent
- Fixes 'can not create new Type of null' error from the form
* Fix mis-use of remoterename changes to EntityInfo
* Changes re. form-graph synch re. 'can not create edge' and 'can not read
property completed' errors
- Do not animate removed elements, as a conservative safety check.
- Make sure the form is using bluebird promises.
- Fix/rewrite addInteractionRow(), as its previous flow did not make sense.
Other code in the form should be following this pattern.
- Cleans up getInputParticipant() and getOutputParticipant().
- Add safety check in ElementSet for entry mapping. There is the possibility
that some code like react could query the list while background loading is
happening.
- Enqueue events for remote changes of ElementSet and emit all events in batch
after the remote update. This isn't strictly necessary, but it could
potentially help some client code that has small mistakes.
Commit: b7ec39ad3ed9fe956718fde4567937a8d939642b
https://github.com/PathwayCommons/factoid/commit/b7ec39ad3ed9fe956718fde4567937a8d939642b
Author: Dylan Fong <[email protected]>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M src/styles/document-seeder.css
Log Message:
-----------
minor style changes to the doc seeder title and doc text input height
Commit: 275724aa7758aa9fc320bedebe2852fec317a656
https://github.com/PathwayCommons/factoid/commit/275724aa7758aa9fc320bedebe2852fec317a656
Author: Dylan Fong <[email protected]>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M src/client/components/document-seeder.js
Log Message:
-----------
More descriptive doc seeder title
Commit: ba42f04c6f7481699ca5730fb823e77d11c003ef
https://github.com/PathwayCommons/factoid/commit/ba42f04c6f7481699ca5730fb823e77d11c003ef
Author: Dylan Fong <[email protected]>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M src/client/components/document-seeder.js
M src/styles/document-seeder.css
Log Message:
-----------
access/store document title and text using react state
- fix minor issue where the highlighting version of the doc text was of
different height than the plain version
Commit: f053fc682cf5c6d761231d52e1655c4ebbf7e9bf
https://github.com/PathwayCommons/factoid/commit/f053fc682cf5c6d761231d52e1655c4ebbf7e9bf
Author: Max Franz <[email protected]>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M src/client/components/document-seeder.js
M src/server/routes/api/document/index.js
M src/styles/document-seeder.css
Log Message:
-----------
Merge pull request #305 from PathwayCommons/doc-title-seeder
Doc title seeder
Commit: d9f48add77817f6de3de2470f2cfe15cb0a0ff8b
https://github.com/PathwayCommons/factoid/commit/d9f48add77817f6de3de2470f2cfe15cb0a0ff8b
Author: Max Franz <[email protected]>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M src/client/components/element-info/entity-assoc-display.js
M src/styles/element-info/entity-info.css
Log Message:
-----------
Add support for Pathway Commons linkouts on entities
- PC search uses `q=${fullOfficialName}`, since PC UI does not yet support
`q=${ns:id}` queries for `uniprot` and `chebi` namespaces.
- Use PubChem linkouts for chemicals, even though we use Chebi grounding for
now. It works OK, and the PubChem page is a bit nicer.
Ref : PC entity linkouts #299
Commit: 3e1d3f24237581df33744425a17672f02c3849be
https://github.com/PathwayCommons/factoid/commit/3e1d3f24237581df33744425a17672f02c3849be
Author: d2fong <[email protected]>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M src/client/components/document-seeder.js
Log Message:
-----------
fix doc seeder state function typo
Commit: 9fb13118d090d28dd3934299f11cbe5235205930
https://github.com/PathwayCommons/factoid/commit/9fb13118d090d28dd3934299f11cbe5235205930
Author: d2fong <[email protected]>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
store my factoids local storage on doc load
Commit: 8ba90ea14d367327d65c54f658b848a348a6c32d
https://github.com/PathwayCommons/factoid/commit/8ba90ea14d367327d65c54f658b848a348a6c32d
Author: Dylan Fong <[email protected]>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/styles/app.css
M src/styles/editor/editor.css
Log Message:
-----------
Merge pull request #308 from PathwayCommons/logo
Add Factoid logo to right side toolbar
Commit: 633a641e76534e41857072cc3f08cccdda57c2be
https://github.com/PathwayCommons/factoid/commit/633a641e76534e41857072cc3f08cccdda57c2be
Author: Max Franz <[email protected]>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M README.md
M src/client/components/element-info/entity-assoc-display.js
M src/config.js
Log Message:
-----------
Add PC_LINK_BASE_URL env var & minor cleanup
Commit: 8e08c9e08957900aed077caee53d285e6bb839d7
https://github.com/PathwayCommons/factoid/commit/8e08c9e08957900aed077caee53d285e6bb839d7
Author: Max Franz <[email protected]>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M src/client/components/document-seeder.js
M src/client/components/editor/index.js
Log Message:
-----------
Merge pull request #310 from PathwayCommons/doc-title-seeder
Doc title seeder
Commit: fb0f030d52ba1b612eb135be14de510667e50e09
https://github.com/PathwayCommons/factoid/commit/fb0f030d52ba1b612eb135be14de510667e50e09
Author: Dylan Fong <[email protected]>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M README.md
M src/client/components/element-info/entity-assoc-display.js
M src/config.js
M src/styles/element-info/entity-info.css
Log Message:
-----------
Merge pull request #309 from PathwayCommons/linkouts
Add support for Pathway Commons linkouts on entities
Commit: f272272f1f2d720d49a13b1a4258a6f185effd7f
https://github.com/PathwayCommons/factoid/commit/f272272f1f2d720d49a13b1a4258a6f185effd7f
Author: metincansiper <[email protected]>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/form-editor/index.js
A src/client/util/file.js
A src/client/util/index.js
R src/util/file.js
M src/util/index.js
Log Message:
-----------
Move util code for biopax export to /client #300
Commit: 6d5fa343bdd514807cb99822fb6ae13bfd9162fb
https://github.com/PathwayCommons/factoid/commit/6d5fa343bdd514807cb99822fb6ae13bfd9162fb
Author: Max Franz <[email protected]>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M src/client/components/editor/buttons.js
M src/client/components/form-editor/index.js
A src/client/util/file.js
A src/client/util/index.js
R src/util/file.js
M src/util/index.js
Log Message:
-----------
Merge pull request #312 from metincansiper/move-file-util
Move util code for biopax export to /client
Commit: 2486abd8439dde4d6994f6f7a4a8d0fead5bc481
https://github.com/PathwayCommons/factoid/commit/2486abd8439dde4d6994f6f7a4a8d0fead5bc481
Author: Max Franz <[email protected]>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M README.md
M src/client/components/document-seeder.js
M src/client/components/editor/buttons.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
M src/client/components/editor/task-list.js
M src/client/components/element-info/entity-assoc-display.js
M src/client/components/form-editor/index.js
M src/client/router.js
A src/client/util/file.js
A src/client/util/index.js
M src/config.js
M src/server/routes/api/document/index.js
A src/styles/app-bar.css
M src/styles/app.css
M src/styles/document-seeder.css
M src/styles/editor/editor.css
M src/styles/element-info/entity-info.css
M src/styles/form-editor/form-editor.css
M src/styles/index.css
M src/styles/task-list.css
R src/util/file.js
M src/util/index.js
Log Message:
-----------
Merge unstable into form-cleanup
Commit: 952e8a505a1b917066d942cb1af548e59c36a5c0
https://github.com/PathwayCommons/factoid/commit/952e8a505a1b917066d942cb1af548e59c36a5c0
Author: Max Franz <[email protected]>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
A package-lock.json
M package.json
Log Message:
-----------
Reset package-lock.json and package.json changes
Commit: 755032a52e88750c2f0993d3aa2d5c99598653f8
https://github.com/PathwayCommons/factoid/commit/755032a52e88750c2f0993d3aa2d5c99598653f8
Author: Max Franz <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
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:
-----------
Some initial cleanup of the form code
- N.b. only the base form component and the phosphorylation component are
corrected. The molecular interaction, activation-inhibition, and expression
components need to also be cleaned up.
- Use DirtyComponent and DataComponent subclassing instead of trying to
manually do the same pattern.
- Don't mix `state` and `data`.
- Proper use of the bus for re-rendering the child components of the form base.
- Use a better list of model events for rendering the form.
- Make sure the form cleans up its listeners on unmount so it doesn't create
memory leaks and errors over time.
- More reliable and readable implementations of `deleteInteractionRow()`,
`updateModificationType()`, and `updateActivationInhibition()`.
- Don't try to `complete()` an interaction when it doesn't have all the data
needed in order to complete it..
Remove more junk
Commit: 328eca5e7781e5d6b09480e93d1e6186d7524c5d
https://github.com/PathwayCommons/factoid/commit/328eca5e7781e5d6b09480e93d1e6186d7524c5d
Author: Max Franz <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M src/model/syncher.js
Log Message:
-----------
Enable squashing in RethinkDB. This helps to avoid out of order operation
receipt via socket.io.
Commit: 9f4d2dd7eae8bac87337069013fb28ee3642a8f1
https://github.com/PathwayCommons/factoid/commit/9f4d2dd7eae8bac87337069013fb28ee3642a8f1
Author: Max Franz <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M src/model/element-set.js
Log Message:
-----------
More manual control of order of livening elements within an ElementSet. Also
add the loadelements event to indicate when the elements in the set have been
filled.
Commit: 88dd492ba3fc1378f8ad2488d96d7fce2788b40c
https://github.com/PathwayCommons/factoid/commit/88dd492ba3fc1378f8ad2488d96d7fce2788b40c
Author: Max Franz <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
Stricter restriction on ordering of operations for adding in the network
editor
Commit: 5b24d6dd56af95f2efb1169506203276b851bf48
https://github.com/PathwayCommons/factoid/commit/5b24d6dd56af95f2efb1169506203276b851bf48
Author: Max Franz <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M src/client/components/editor/cy/edgehandles.js
Log Message:
-----------
Interactions created by using edgehandles are created atomically w.r.t. the
participant list, where possible. This can only be applied to new
interactions. This assumption currently holds for the network editor, because
all interactions are binary.
Commit: ce58517a6ef83d8ac565713c49727810852f2cb9
https://github.com/PathwayCommons/factoid/commit/ce58517a6ef83d8ac565713c49727810852f2cb9
Author: Max Franz <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M src/client/components/editor/cy/doc.js
Log Message:
-----------
Add loadelements handler in the graph elements synchronisation for the
network editor. This helps when operations come in out of order.
Commit: eeb9132501dbc4b8119adba411d68b550cab35c8
https://github.com/PathwayCommons/factoid/commit/eeb9132501dbc4b8119adba411d68b550cab35c8
Author: Max Franz <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
Remove bus listeners on Editor on unmount
Commit: 1a5775321af625321960f919ed2e1c3989639862
https://github.com/PathwayCommons/factoid/commit/1a5775321af625321960f919ed2e1c3989639862
Author: Dylan Fong <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 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/styles/form-editor/form-editor.css
Log Message:
-----------
form ui rework
- use overlay for element info
- clean up form ui
- changed delete icon
- fixed form doc event listeners for pre existing doc elements
Commit: 6470d2c96731beb359fa6bad400515f0005ff258
https://github.com/PathwayCommons/factoid/commit/6470d2c96731beb359fa6bad400515f0005ff258
Author: Dylan Fong <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M src/model/element/interaction-type/interaction-type.js
Log Message:
-----------
fix bug where interaction becomes unsigned when changing the interaction sign
Commit: a4ca6e5554ac0da8454a01bea17d00ac39191fca
https://github.com/PathwayCommons/factoid/commit/a4ca6e5554ac0da8454a01bea17d00ac39191fca
Author: Dylan Fong <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M src/styles/popover/tippy.css
Log Message:
-----------
fix tooltips for pages that scroll
- they will be fixed to the element they are apart of
Commit: 3502548f89cf5625e3593490021a224635c4ad68
https://github.com/PathwayCommons/factoid/commit/3502548f89cf5625e3593490021a224635c4ad68
Author: metincansiper <[email protected]>
Date: 2018-06-14 (Thu, 14 Jun 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-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/molecular-interaction-form.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
Updated form types other than protein modification
Commit: 0d5020204359c01841ec882a5d4e5455e8f254b2
https://github.com/PathwayCommons/factoid/commit/0d5020204359c01841ec882a5d4e5455e8f254b2
Author: metincansiper <[email protected]>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M src/client/components/form-editor/index.js
Log Message:
-----------
Removed unused log() function
Commit: 937146cc4989763397ed05c23b53d79e38312dfb
https://github.com/PathwayCommons/factoid/commit/937146cc4989763397ed05c23b53d79e38312dfb
Author: Max Franz <[email protected]>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M src/model/syncher.js
Log Message:
-----------
Disable squashing for the add/change distinction in the changefeed
Commit: e88fb5166d051783553365f9067d63ebfe8e1034
https://github.com/PathwayCommons/factoid/commit/e88fb5166d051783553365f9067d63ebfe8e1034
Author: Max Franz <[email protected]>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M src/model/syncher.js
Log Message:
-----------
Simplify the PUSH/PULL database operations by using `expr.default()` instead
of `r.branch()`
Commit: 5e170154031aad1f3423bc937efad09683086db8
https://github.com/PathwayCommons/factoid/commit/5e170154031aad1f3423bc937efad09683086db8
Author: Max Franz <[email protected]>
Date: 2018-06-15 (Fri, 15 Jun 2018)
Changed paths:
M test/syncher.js
Log Message:
-----------
Apply the debounce pattern used in the pull by value test to the pull by id
test
Commit: de62b3c7c5cfce85660690b1698247af191c3353
https://github.com/PathwayCommons/factoid/commit/de62b3c7c5cfce85660690b1698247af191c3353
Author: metincansiper <[email protected]>
Date: 2018-06-18 (Mon, 18 Jun 2018)
Changed paths:
M src/client/components/form-editor/molecular-interaction-form.js
Log Message:
-----------
Do not allow adding more than 2 participants from the form editor #317.
Commit: 815eb37326772d2b0bde0b15f2279f80f7281e0a
https://github.com/PathwayCommons/factoid/commit/815eb37326772d2b0bde0b15f2279f80f7281e0a
Author: metincansiper <[email protected]>
Date: 2018-06-18 (Mon, 18 Jun 2018)
Changed paths:
M src/client/components/form-editor/molecular-interaction-form.js
Log Message:
-----------
Remove the line that becomes unused after removing add participant button #317
Commit: db45d002c8037b946bb4b83676ece2c9ca24dbab
https://github.com/PathwayCommons/factoid/commit/db45d002c8037b946bb4b83676ece2c9ca24dbab
Author: metincansiper <[email protected]>
Date: 2018-06-18 (Mon, 18 Jun 2018)
Changed paths:
M src/client/components/form-editor/molecular-interaction-form.js
Log Message:
-----------
In form editor represented molecular interactions as "A interacts with B"
Commit: 15a2799c64dd21f49da752c04400b220f92afb51
https://github.com/PathwayCommons/factoid/commit/15a2799c64dd21f49da752c04400b220f92afb51
Author: Max Franz <[email protected]>
Date: 2018-06-19 (Tue, 19 Jun 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-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/molecular-interaction-form.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
Merge branch 'form-types' of https://github.com/metincansiper/factoid into
metincansiper-form-types
Commit: a8120abac0c196e5f25121915b49570fc0ff0117
https://github.com/PathwayCommons/factoid/commit/a8120abac0c196e5f25121915b49570fc0ff0117
Author: Max Franz <[email protected]>
Date: 2018-06-19 (Tue, 19 Jun 2018)
Changed paths:
M src/client/components/form-editor/activation-inhibition-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/molecular-interaction-form.js
M src/styles/form-editor/form-editor.css
Log Message:
-----------
Merge branch 'metincansiper-form-types' into synch-fix
Commit: 099cea65fbff5a08ff4ea9922a48505f9c84b2c5
https://github.com/PathwayCommons/factoid/commit/099cea65fbff5a08ff4ea9922a48505f9c84b2c5
Author: Max Franz <[email protected]>
Date: 2018-06-19 (Tue, 19 Jun 2018)
Changed paths:
M src/client/components/form-editor/index.js
Log Message:
-----------
Remove `data` self assignment
Commit: 4bf9a86c0b315457672a0e18a29e4250d8a5bad6
https://github.com/PathwayCommons/factoid/commit/4bf9a86c0b315457672a0e18a29e4250d8a5bad6
Author: Max Franz <[email protected]>
Date: 2018-06-19 (Tue, 19 Jun 2018)
Changed paths:
M package-lock.json
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/edgehandles.js
M src/client/components/editor/index.js
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/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/molecular-interaction-form.js
M src/client/components/form-editor/protein-modification-form.js
M src/model/element-set.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction.js
M src/model/syncher.js
M src/styles/form-editor/form-editor.css
M src/styles/popover/tippy.css
M test/syncher.js
Log Message:
-----------
Merge pull request #318 from PathwayCommons/synch-fix
Merge synch-fix into unstable
Commit: 7b1f8e93cdb7f4a206580a3564dbf078e3a1385a
https://github.com/PathwayCommons/factoid/commit/7b1f8e93cdb7f4a206580a3564dbf078e3a1385a
Author: Max Franz <[email protected]>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
M .gitignore
M README.md
A ci.sh
M package-lock.json
M package.json
A src/client/components/data-component.js
M src/client/components/dirty-component.js
A src/client/components/document-renamer.js
M src/client/components/document-seeder.js
M src/client/components/document-view-chooser.js
M src/client/components/editor/buttons.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/help.js
M src/client/components/editor/index.js
R src/client/components/editor/menu.js
A src/client/components/editor/task-list.js
A src/client/components/element-info/chemical-formula.js
M src/client/components/element-info/element-info.js
A src/client/components/element-info/entity-assoc-display.js
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/interaction-info.js
M src/client/components/element-info/participant-info.js
A src/client/components/element-info/progression-stepper.js
A src/client/components/element-info/progression.js
A src/client/components/form-editor/activation-inhibition-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/molecular-interaction-form.js
A src/client/components/form-editor/protein-modification-form.js
A src/client/components/my-factoids.js
M src/client/components/notification/base.js
M src/client/components/notification/corner.js
M src/client/components/notification/inline.js
M src/client/components/notification/list.js
M src/client/components/notification/notification.js
M src/client/components/notification/panel.js
M src/client/components/notification/popover.js
M src/client/components/popover/tooltip.js
M src/client/defs.js
M src/client/router.js
A src/client/util/file.js
A src/client/util/index.js
M src/config.js
M src/model/document/document.js
M src/model/element-set.js
M src/model/element/element-type.js
M src/model/element/element.js
R src/model/element/entity-mods.js
A src/model/element/entity-type.js
M src/model/element/entity.js
A src/model/element/interaction-type/biopax-type.js
R src/model/element/interaction-type/chemical-affects-protein.js
M src/model/element/interaction-type/enum.js
M src/model/element/interaction-type/expression.js
M src/model/element/interaction-type/general.js
M src/model/element/interaction-type/interaction-type.js
A src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
A src/model/element/interaction-type/phosphorylation.js
R src/model/element/interaction-type/protein-affects-chemical.js
A src/model/element/interaction-type/protein-chemical.js
A src/model/element/interaction-type/ubiquination.js
M src/model/element/interaction.js
M src/model/element/participant-type.js
M src/model/syncher.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/reach.js
A src/styles/app-bar.css
M src/styles/app.css
M src/styles/base.css
A src/styles/document-renamer.css
M src/styles/document-seeder.css
M src/styles/document-view-chooser.css
M src/styles/document-wizard-stepper.css
M src/styles/editor/editor.css
M src/styles/element-info/element-info.css
M src/styles/element-info/entity-info.css
M src/styles/element-info/interaction-info.css
M src/styles/form-editor/form-editor.css
A src/styles/help.css
A src/styles/image/form-option-preview.png
A src/styles/image/network-option-preview.png
M src/styles/index.css
M src/styles/init-app.css
A src/styles/my-factoids.css
M src/styles/notification.css
M src/styles/popover/tippy.css
A src/styles/task-list.css
A src/util/cache.js
M src/util/cy.js
M src/util/index.js
M test/interaction.js
M test/syncher.js
Log Message:
-----------
Merge pull request #320 from PathwayCommons/unstable
Merge unstable into master for 0.1.0
Compare:
https://github.com/PathwayCommons/factoid/compare/abdd89df76a1...7b1f8e93cdb7
**NOTE:** This service been marked for deprecation:
https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
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