Branch: refs/heads/master
Home: https://github.com/PathwayCommons/factoid
Commit: e5e363cb28e9969c79779e2710d5bb298ccc3c08
https://github.com/PathwayCommons/factoid/commit/e5e363cb28e9969c79779e2710d5bb298ccc3c08
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-03-26 (Thu, 26 Mar 2020)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
Update unstable package files to version 0.9.0-unstable
Commit: cf83b95a5dd6c799ee88e91f208bf4c077d7b6ce
https://github.com/PathwayCommons/factoid/commit/cf83b95a5dd6c799ee88e91f208bf4c077d7b6ce
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-06 (Mon, 06 Apr 2020)
Changed paths:
M src/styles/home.css
Log Message:
-----------
Make the title & caption more legible for some small screens
Commit: ef154a5c460861334f8e315cd2e060f306b9c6e1
https://github.com/PathwayCommons/factoid/commit/ef154a5c460861334f8e315cd2e060f306b9c6e1
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-06 (Mon, 06 Apr 2020)
Changed paths:
M src/styles/home.css
Log Message:
-----------
Revise the hover behaviour for the scroller
- The scroller card expands on hover to give more room for the title and author
list without overlapping the figure.
- The figure is no longer blurred out on hover, as there is no overlap.
- The scroller on the home page is shifted up to accommodate the extra space
needed for card expansion.
Commit: 7124a41ddc125994c3124d801ad5fc318d393350
https://github.com/PathwayCommons/factoid/commit/7124a41ddc125994c3124d801ad5fc318d393350
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-06 (Mon, 06 Apr 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
Log Message:
-----------
Improve the reliability of hovering w.r.t. scrolling
- Hovering is faster to activate on mobile.
- The hover state is removed when scrolling.
Commit: f8426fc089138bd0f186a6aa799bea2ed1d48e99
https://github.com/PathwayCommons/factoid/commit/f8426fc089138bd0f186a6aa799bea2ed1d48e99
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-06 (Mon, 06 Apr 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
The visibility of the pager icons is updated on window resize
Commit: 546ef51ab6a37ce3d1774b7def209ccf604c8ff9
https://github.com/PathwayCommons/factoid/commit/546ef51ab6a37ce3d1774b7def209ccf604c8ff9
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-06 (Mon, 06 Apr 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Links on the home page go out to new tabs
Commit: 8991c657170fbd8af9f7a15e6b27f07248b4a9eb
https://github.com/PathwayCommons/factoid/commit/8991c657170fbd8af9f7a15e6b27f07248b4a9eb
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-06 (Mon, 06 Apr 2020)
Changed paths:
M src/styles/home.css
Log Message:
-----------
Improve max screen size threshold for hiding the institution logos in the
footer
Commit: f7c9f8bdcafa479dda036386cda0dc223a47e628
https://github.com/PathwayCommons/factoid/commit/f7c9f8bdcafa479dda036386cda0dc223a47e628
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-09 (Thu, 09 Apr 2020)
Changed paths:
M src/model/element/interaction-type/interaction-type.js
Log Message:
-----------
For unnamed complexes, set the toString() to reference concatenated
participant names.
Commit: 244e0ff1ed1dda850a63b38aa2b77980b8e5029a
https://github.com/PathwayCommons/factoid/commit/244e0ff1ed1dda850a63b38aa2b77980b8e5029a
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-09 (Thu, 09 Apr 2020)
Changed paths:
M src/model/element/interaction-type/interaction-type.js
Log Message:
-----------
Rename participant names.
Commit: d890ed768d94fd8097fa7f21831411aed086ac8f
https://github.com/PathwayCommons/factoid/commit/d890ed768d94fd8097fa7f21831411aed086ac8f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-09 (Thu, 09 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
- api/document get: map the appropriate query params to correct type
- api/document get: filter out the demo before processing requests
Commit: 81f10273e86053b9cb8aa79c78433a51ae768576
https://github.com/PathwayCommons/factoid/commit/81f10273e86053b9cb8aa79c78433a51ae768576
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
Log Message:
-----------
Merge pull request #701 from PathwayCommons/home-style-tweaks
Home page style tweaks (expand on hover, etc.)
Commit: f4b5db7d6f79db99a0c1f2d7459d4663609a351b
https://github.com/PathwayCommons/factoid/commit/f4b5db7d6f79db99a0c1f2d7459d4663609a351b
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #705 from PathwayCommons/api-doc-get-params
API: Document query parameters
Commit: ebd12d4de02b062db32f50e20d20783c7e5d5f0a
https://github.com/PathwayCommons/factoid/commit/ebd12d4de02b062db32f50e20d20783c7e5d5f0a
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M package-lock.json
M package.json
M src/server/routes/api/document/index.js
M src/server/routes/api/index.js
Log Message:
-----------
Adding swagger packages and stub out api
Commit: 54a55d46bb150b08bcbd830e3828a82c651d3e8a
https://github.com/PathwayCommons/factoid/commit/54a55d46bb150b08bcbd830e3828a82c651d3e8a
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/index.js
Log Message:
-----------
- Upgrade to OAS3
- First draft of /api/document/ route
Commit: 0019a515e0ff2ab5355f1a7e5fdce8ce3da8a64a
https://github.com/PathwayCommons/factoid/commit/0019a515e0ff2ab5355f1a7e5fdce8ce3da8a64a
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
- Draft of Document object
Commit: 7812990091ec941860318656ab98883f08d54109
https://github.com/PathwayCommons/factoid/commit/7812990091ec941860318656ab98883f08d54109
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
- Adding format (text, biopax, sbgn) endpoints
Commit: 29822147ee3a606da696705bba14e4fb1a56207f
https://github.com/PathwayCommons/factoid/commit/29822147ee3a606da696705bba14e4fb1a56207f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
- Added description of Elements: either Entity or Interaction
Commit: cf637bacf13d8f7ac8c5752b84656da184afc05d
https://github.com/PathwayCommons/factoid/commit/cf637bacf13d8f7ac8c5752b84656da184afc05d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
- Added Author Affiliation descriptions
Commit: e9bdff52557f6014fdd59506eabd2d7007e73ef8
https://github.com/PathwayCommons/factoid/commit/e9bdff52557f6014fdd59506eabd2d7007e73ef8
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Improved summary for each path
Commit: ecf91a453f0c07414be4370b481542b29f17d8d6
https://github.com/PathwayCommons/factoid/commit/ecf91a453f0c07414be4370b481542b29f17d8d6
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Added authentication and API KEY authenicated routes.
Commit: 805aec3432dfdc314942926f699239c096fb91ac
https://github.com/PathwayCommons/factoid/commit/805aec3432dfdc314942926f699239c096fb91ac
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Remove authorization from /api-key-verify as redundant
Commit: 57409c84a18633d4c04c14f062c1543462f87392
https://github.com/PathwayCommons/factoid/commit/57409c84a18633d4c04c14f062c1543462f87392
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-13 (Mon, 13 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Documenting the PATCH status endpoint
Commit: 23c7b18faa6a558da54cdaa766f5d9eeb7df44b9
https://github.com/PathwayCommons/factoid/commit/23c7b18faa6a558da54cdaa766f5d9eeb7df44b9
Author: Jeffrey Wong <jvw...@outlook.com>
Date: 2020-04-14 (Tue, 14 Apr 2020)
Changed paths:
M package-lock.json
M src/server/routes/api/document/index.js
Log Message:
-----------
- Adding details for parameters like ID
Commit: b33a0ccffe56dd60af5c36d97a75938c5b566fad
https://github.com/PathwayCommons/factoid/commit/b33a0ccffe56dd60af5c36d97a75938c5b566fad
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-14 (Tue, 14 Apr 2020)
Changed paths:
M package-lock.json
M src/server/routes/api/document/index.js
Log Message:
-----------
- make emailType a component
- document association can be any of entity or interaction
Commit: e47322c0d4d934f210e3c1c6364461f7483c8790
https://github.com/PathwayCommons/factoid/commit/e47322c0d4d934f210e3c1c6364461f7483c8790
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-14 (Tue, 14 Apr 2020)
Changed paths:
M src/model/element/complex.js
M src/model/element/interaction-type/interaction-type.js
Log Message:
-----------
- revert changes to interaction
- add default name to complex if not named
Commit: a09867b502021bb4ec4e568c51178739709d717f
https://github.com/PathwayCommons/factoid/commit/a09867b502021bb4ec4e568c51178739709d717f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-14 (Tue, 14 Apr 2020)
Changed paths:
M src/model/element/complex.js
Log Message:
-----------
Call name getter from superclass
Commit: 5457971affa0353d1584840223337c916b24921e
https://github.com/PathwayCommons/factoid/commit/5457971affa0353d1584840223337c916b24921e
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-15 (Wed, 15 Apr 2020)
Changed paths:
M package-lock.json
M package.json
M src/server/routes/api/document/index.js
M src/server/routes/api/index.js
Log Message:
-----------
Merge pull request #706 from PathwayCommons/iss698_ws-api-docs
Swagger docs for (Document) web services
Commit: 09236eed5c4e8a21393803af1d471c866e281adf
https://github.com/PathwayCommons/factoid/commit/09236eed5c4e8a21393803af1d471c866e281adf
Author: Max Franz <max@Maxs-MacBook-Pro.local>
Date: 2020-04-15 (Wed, 15 Apr 2020)
Changed paths:
M src/client/components/editor/cy/doc.js
Log Message:
-----------
Handle the following cases for (inferred) complex renaming:
- Add a protein to complex
- Remove a protein from the complex
- Rename a protein that's already inside the complex
Commit: 0588e68d6c9a6c3ee2069770d13bd650c5283916
https://github.com/PathwayCommons/factoid/commit/0588e68d6c9a6c3ee2069770d13bd650c5283916
Author: Max Franz <max@Maxs-MacBook-Pro.local>
Date: 2020-04-15 (Wed, 15 Apr 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Complexes with the default (inferred) name don't get the name text box filled
in
The text box basically only has the explicit name that the user typed.
Otherwise, it's empty.
Commit: 3ad55fb2c5cbc9d7f350138923c2661eb74fa158
https://github.com/PathwayCommons/factoid/commit/3ad55fb2c5cbc9d7f350138923c2661eb74fa158
Author: Max Franz <max@Maxs-MacBook-Pro.local>
Date: 2020-04-15 (Wed, 15 Apr 2020)
Changed paths:
M src/styles/editor/undo-remove.css
Log Message:
-----------
Workaround for add'l erroneous complex node on delete
Commit: f523036f673d7a1393ee953ad405c774632c5621
https://github.com/PathwayCommons/factoid/commit/f523036f673d7a1393ee953ad405c774632c5621
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-15 (Wed, 15 Apr 2020)
Changed paths:
M src/client/components/editor/cy/doc.js
M src/client/components/element-info/entity-info.js
M src/model/element/complex.js
M src/styles/editor/undo-remove.css
Log Message:
-----------
Merge pull request #704 from PathwayCommons/iss693_default-complex-name
Default name of complex in interactions
Commit: 1d2ca4b22f0fd296f1cba5c1789fec0457b50db0
https://github.com/PathwayCommons/factoid/commit/1d2ca4b22f0fd296f1cba5c1789fec0457b50db0
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-17 (Fri, 17 Apr 2020)
Changed paths:
M src/client/components/editor/cy/doc.js
Log Message:
-----------
Remove unused param.
Commit: 2b4f313ebe1c08d08f07a6834bb32d9fd7c09e61
https://github.com/PathwayCommons/factoid/commit/2b4f313ebe1c08d08f07a6834bb32d9fd7c09e61
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-04-17 (Fri, 17 Apr 2020)
Changed paths:
M src/client/components/editor/cy/doc.js
Log Message:
-----------
Merge pull request #708 from PathwayCommons/lint-complex-name
Remove unused param.
Commit: 569cb804fcbe9f3b50706ebeb51c50ca3cc5e0b3
https://github.com/PathwayCommons/factoid/commit/569cb804fcbe9f3b50706ebeb51c50ca3cc5e0b3
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-17 (Fri, 17 Apr 2020)
Changed paths:
M src/config.js
M src/util/email.js
Log Message:
-----------
Working version of templated invitation. Removed the email subject config
variables.
Commit: 631e56ce6505e62dab3ebc280f262be476285785
https://github.com/PathwayCommons/factoid/commit/631e56ce6505e62dab3ebc280f262be476285785
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-17 (Fri, 17 Apr 2020)
Changed paths:
M src/util/email.js
Log Message:
-----------
Adding module variables for citation and URLs
Commit: 199104f3f64d0e4e81e5671357e20bfb6fb7a220
https://github.com/PathwayCommons/factoid/commit/199104f3f64d0e4e81e5671357e20bfb6fb7a220
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-20 (Mon, 20 Apr 2020)
Changed paths:
M src/util/email.js
Log Message:
-----------
- Drop extraineous subject variables
- Better names for email var defaults.
Commit: 4d880c29963cfedc4fbdfaa1b38811365a46d470
https://github.com/PathwayCommons/factoid/commit/4d880c29963cfedc4fbdfaa1b38811365a46d470
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-20 (Mon, 20 Apr 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
First draft with explore button, linkouts to Twitter, image and email
Commit: 6157cff7bc0f12f462dcd2f291efd728638e8e13
https://github.com/PathwayCommons/factoid/commit/6157cff7bc0f12f462dcd2f291efd728638e8e13
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-20 (Mon, 20 Apr 2020)
Changed paths:
M package-lock.json
M src/config.js
M src/server/routes/api/element-association/index.js
A src/server/routes/api/element-association/indra.js
Log Message:
-----------
Added web api to query documents for given two entities through indra
Commit: c84cf5bed0adf5fbab1260262759587bd05e54a0
https://github.com/PathwayCommons/factoid/commit/c84cf5bed0adf5fbab1260262759587bd05e54a0
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-21 (Tue, 21 Apr 2020)
Changed paths:
M src/server/routes/api/index.js
Log Message:
-----------
- Set api docs at base url
- No trailing slash required
Commit: a2819b24c6fa3e75bfa8b1bb3dbf8174b41466d4
https://github.com/PathwayCommons/factoid/commit/a2819b24c6fa3e75bfa8b1bb3dbf8174b41466d4
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-21 (Tue, 21 Apr 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
- Use a list for the linkouts
- Minor styling fixes
- Dropped unnecessary class for done task
Commit: 6e0a4bb2e1f16a140a43fa243eb2ca32b91d212f
https://github.com/PathwayCommons/factoid/commit/6e0a4bb2e1f16a140a43fa243eb2ca32b91d212f
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-21 (Tue, 21 Apr 2020)
Changed paths:
M src/model/document/document.js
M src/model/element/entity.js
M src/model/element/interaction-type/binding.js
M src/model/element/interaction-type/demethylation.js
M src/model/element/interaction-type/dephosphorylation.js
M src/model/element/interaction-type/deubiquitination.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction-type/interaction.js
M src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
M src/model/element/interaction-type/phosphorylation.js
M src/model/element/interaction-type/transcription-translation.js
M src/model/element/interaction-type/ubiquitination.js
M src/model/element/interaction.js
Log Message:
-----------
Export update (#709)
Biopax export related changes based on the facoid model updates.
Commit: 3b8dacad5ab721aa20058e3e818765ad00e8b7e4
https://github.com/PathwayCommons/factoid/commit/3b8dacad5ab721aa20058e3e818765ad00e8b7e4
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-21 (Tue, 21 Apr 2020)
Changed paths:
M src/server/routes/api/element-association/index.js
M src/server/routes/api/element-association/indra.js
Log Message:
-----------
Enable querying dcouments from indra for multiple entity pairs.
Commit: 8a926a7d2a1627288b6b35aec4b6f71de16b2212
https://github.com/PathwayCommons/factoid/commit/8a926a7d2a1627288b6b35aec4b6f71de16b2212
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-21 (Tue, 21 Apr 2020)
Changed paths:
M src/server/routes/api/element-association/index.js
M src/server/routes/api/element-association/indra.js
Log Message:
-----------
Updated input format for the service that searches documents through indra
Commit: e7bbdd8f7bbf37af50129f7ff3646defd2b4fe1a
https://github.com/PathwayCommons/factoid/commit/e7bbdd8f7bbf37af50129f7ff3646defd2b4fe1a
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-22 (Wed, 22 Apr 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
Add a factoid-converters service, used by webapp.
Commit: c0258fc8006fa79008a6c31d5c6925f4f9f429b7
https://github.com/PathwayCommons/factoid/commit/c0258fc8006fa79008a6c31d5c6925f4f9f429b7
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-04-22 (Wed, 22 Apr 2020)
Changed paths:
M src/server/routes/api/index.js
Log Message:
-----------
Merge pull request #712 from PathwayCommons/swagger-docs-routing
Swagger API docs routing
Commit: 0e171f06816f0768ba4e7e467d3adebe530b044d
https://github.com/PathwayCommons/factoid/commit/0e171f06816f0768ba4e7e467d3adebe530b044d
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-22 (Wed, 22 Apr 2020)
Changed paths:
M README.md
M src/client-env-vars.json
M src/client/components/editor/cy/viewport.js
A src/client/components/editor/help.js
M src/client/components/editor/index.js
A src/client/components/editor/info-panel.js
A src/client/components/editor/submit.js
A src/client/components/editor/title.js
M src/config.js
M src/styles/editor/editor.css
Log Message:
-----------
Add an info panel for the explore view
Design details:
- The panel is a sidebar on devices that have enough space.
- On small-screen devices, the panel takes up a small area at the bottom of the
screen by default.
- The panel can be scrolled.
- On small screens, scrolling the panel moves the panel up. This puts the
panel on top of the graph. This mechanism allows for the info panel to take up
the entire screen on phones, giving more space for content.
- The info panel currently contains a simple version of the paper metadata UI.
- This panel is where a related papers UI would go.
Technical details:
- The `GOOGLE_SCHOLAR_BASE_URL` has been added to facilitate links in the
explore view.
- Subcomponents within `Editor` have been put into separate files, including
`Help`, `Submit`, and `Title`.
- When the screen of a phone or tablet is rotated, the graph fits to the
screen. This prevents the user from losing the graph in the explore view.
Ref. #683 #681
Depends on #711 #672
Commit: d48809131d4aa46c7e0773cbb45e8d21231ce78e
https://github.com/PathwayCommons/factoid/commit/d48809131d4aa46c7e0773cbb45e8d21231ce78e
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-23 (Thu, 23 Apr 2020)
Changed paths:
M src/server/routes/api/element-association/indra.js
Log Message:
-----------
In indra service return an array of docuemnts instead of an object.
Commit: 9553af810172aa7a6f6593024096d550a8b9703d
https://github.com/PathwayCommons/factoid/commit/9553af810172aa7a6f6593024096d550a8b9703d
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-23 (Thu, 23 Apr 2020)
Changed paths:
M src/config.js
M src/server/routes/api/element-association/indra.js
Log Message:
-----------
Define INDRA_DB_BASE_URL in config file and make the subpaths from that.
Commit: 90648abf652e3f5af0230df5ed5b506f37b999ce
https://github.com/PathwayCommons/factoid/commit/90648abf652e3f5af0230df5ed5b506f37b999ce
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-04-24 (Fri, 24 Apr 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
Merge pull request #714 from PathwayCommons/iss713-factoid-converters-docker
Add a factoid-converters service, used by webapp.
Commit: e1f8ab30a8a8b49627678a338281e6fbe84b29e3
https://github.com/PathwayCommons/factoid/commit/e1f8ab30a8a8b49627678a338281e6fbe84b29e3
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-04-24 (Fri, 24 Apr 2020)
Changed paths:
M src/config.js
M src/util/email.js
Log Message:
-----------
Merge pull request #710 from PathwayCommons/iss700_app-sets-email-content
Email content set in app
Commit: d391f15cc51443d9f1101f0ca7499fc2c3470924
https://github.com/PathwayCommons/factoid/commit/d391f15cc51443d9f1101f0ca7499fc2c3470924
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-24 (Fri, 24 Apr 2020)
Changed paths:
M README.md
M src/client-env-vars.json
M src/client/components/editor/cy/viewport.js
A src/client/components/editor/help.js
M src/client/components/editor/index.js
A src/client/components/editor/info-panel.js
A src/client/components/editor/submit.js
A src/client/components/editor/title.js
M src/config.js
M src/styles/editor/editor.css
Log Message:
-----------
Merge pull request #715 from PathwayCommons/info-panel
Add an info panel for the explore view
Commit: 60d937bef7a688d6dadc6d85c8c805b7a2aedab9
https://github.com/PathwayCommons/factoid/commit/60d937bef7a688d6dadc6d85c8c805b7a2aedab9
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-24 (Fri, 24 Apr 2020)
Changed paths:
M src/server/routes/api/element-association/indra.js
Log Message:
-----------
While extracting indra interactions consider each evidence.
Commit: faab65e0071ad5cca6ed5626aa27d40f9b6ebf29
https://github.com/PathwayCommons/factoid/commit/faab65e0071ad5cca6ed5626aa27d40f9b6ebf29
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-24 (Fri, 24 Apr 2020)
Changed paths:
M src/server/routes/api/element-association/indra.js
Log Message:
-----------
Prevent duplication of the same interactions in a document for getting
documents from indra.
Commit: 1d9f0ef01732c223be3a66c6a579256170c0dc06
https://github.com/PathwayCommons/factoid/commit/1d9f0ef01732c223be3a66c6a579256170c0dc06
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-24 (Fri, 24 Apr 2020)
Changed paths:
M src/server/routes/api/element-association/indra.js
Log Message:
-----------
While getting the documents from indra skip evidences with no pmid.
Commit: d61cbbf001462282285156ee31531413cf06e547
https://github.com/PathwayCommons/factoid/commit/d61cbbf001462282285156ee31531413cf06e547
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-24 (Fri, 24 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
A src/server/routes/api/document/indra.js
M src/server/routes/api/element-association/index.js
R src/server/routes/api/element-association/indra.js
Log Message:
-----------
Replaced indra related services.
Commit: 7bab1f2d67971d97b19bcce5f20b30b7ecc87eb7
https://github.com/PathwayCommons/factoid/commit/7bab1f2d67971d97b19bcce5f20b30b7ecc87eb7
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-24 (Fri, 24 Apr 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
A little bug fix emerged while replacing a file.
Commit: 7b3856f1a27521e8ea293330306eab38d01bb0af
https://github.com/PathwayCommons/factoid/commit/7b3856f1a27521e8ea293330306eab38d01bb0af
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-27 (Mon, 27 Apr 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
- Spinner on submit
- Wait for submit/publish cycle before showing information to user
Commit: 2a63e8809e8b06337c4c5b62ec33386eccb8efbd
https://github.com/PathwayCommons/factoid/commit/2a63e8809e8b06337c4c5b62ec33386eccb8efbd
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-04-28 (Tue, 28 Apr 2020)
Changed paths:
M package-lock.json
M src/config.js
M src/server/routes/api/document/index.js
A src/server/routes/api/document/indra.js
Log Message:
-----------
Merge pull request #716 from PathwayCommons/related-papers
Related papers
Commit: 399dba3175ac49c2a045fad1be5a07e1a38a8d66
https://github.com/PathwayCommons/factoid/commit/399dba3175ac49c2a045fad1be5a07e1a38a8d66
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-28 (Tue, 28 Apr 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
Log Message:
-----------
Give ability for submit button to track submission status in TaskView
Commit: d2078c92cb2825a45d367dba5c233d624119ea3d
https://github.com/PathwayCommons/factoid/commit/d2078c92cb2825a45d367dba5c233d624119ea3d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-29 (Wed, 29 Apr 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
Log Message:
-----------
- Allow fetchPubmed to be customized via opts
- Remove default limit (retmax) for number of records returned by fetchPubmed
- POST to EFETCH EUTILS to allow large numbers of UIDs to be retrieved
Commit: 71eb74df21c3b93507bacb831c6da301b4c60168
https://github.com/PathwayCommons/factoid/commit/71eb74df21c3b93507bacb831c6da301b4c60168
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-29 (Wed, 29 Apr 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
Log Message:
-----------
- Set initial done state via doc attribute
- Don't wait for email sending to show done panel
Commit: 083da32b4578939ced1a2cc2b9de3eb65fe3d8b4
https://github.com/PathwayCommons/factoid/commit/083da32b4578939ced1a2cc2b9de3eb65fe3d8b4
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-29 (Wed, 29 Apr 2020)
Changed paths:
M README.md
M docker/.env
M docker/docker-compose.yml
M package-lock.json
M src/client-env-vars.json
M src/client/components/editor/cy/viewport.js
A src/client/components/editor/help.js
M src/client/components/editor/index.js
A src/client/components/editor/info-panel.js
A src/client/components/editor/submit.js
A src/client/components/editor/title.js
M src/client/components/tasks.js
M src/config.js
M src/model/document/document.js
M src/model/element/entity.js
M src/model/element/interaction-type/binding.js
M src/model/element/interaction-type/demethylation.js
M src/model/element/interaction-type/dephosphorylation.js
M src/model/element/interaction-type/deubiquitination.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction-type/interaction.js
M src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
M src/model/element/interaction-type/phosphorylation.js
M src/model/element/interaction-type/transcription-translation.js
M src/model/element/interaction-type/ubiquitination.js
M src/model/element/interaction.js
M src/server/routes/api/document/index.js
A src/server/routes/api/document/indra.js
M src/server/routes/api/index.js
M src/styles/editor/editor.css
M src/util/email.js
Log Message:
-----------
Merge branch 'unstable' into iss703_editor-submit-tweaks
# Conflicts:
# src/client/components/editor/index.js
Commit: 7b80580d6ed24d540b55ebfab396dcb9279faeec
https://github.com/PathwayCommons/factoid/commit/7b80580d6ed24d540b55ebfab396dcb9279faeec
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-29 (Wed, 29 Apr 2020)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
Remove unused prop to TaskView
Commit: 7e2ca0ec1f766ed2bfee1dc2656161a010fb89a7
https://github.com/PathwayCommons/factoid/commit/7e2ca0ec1f766ed2bfee1dc2656161a010fb89a7
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-29 (Wed, 29 Apr 2020)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
Walk back binding onDone function.
Commit: 0c1a388b0258001c83d56de2056b2adc7c3aa5a4
https://github.com/PathwayCommons/factoid/commit/0c1a388b0258001c83d56de2056b2adc7c3aa5a4
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-04-29 (Wed, 29 Apr 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
Log Message:
-----------
Merge pull request #718 from PathwayCommons/iss681_fetchpubmed-post
Related papers and PubMed: More flexibility in number of records retrieved
Commit: 454bd34b98bc6f366c1319feada8794596b8acf9
https://github.com/PathwayCommons/factoid/commit/454bd34b98bc6f366c1319feada8794596b8acf9
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-30 (Thu, 30 Apr 2020)
Changed paths:
M src/model/element/interaction-type/interaction-type.js
Log Message:
-----------
remove missing toString output elements
Commit: 63d2a531978c226df1c3d2056263a966550e13a1
https://github.com/PathwayCommons/factoid/commit/63d2a531978c226df1c3d2056263a966550e13a1
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-30 (Thu, 30 Apr 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
Download image link, explore link, and modified thanks text.
Commit: 32ede0b4e242ca7060b97be2659ef7bde74d0f76
https://github.com/PathwayCommons/factoid/commit/32ede0b4e242ca7060b97be2659ef7bde74d0f76
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-04-30 (Thu, 30 Apr 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
Updates to share links text.
Commit: 222c538edeadb7ec71928504bc2046d7095613ec
https://github.com/PathwayCommons/factoid/commit/222c538edeadb7ec71928504bc2046d7095613ec
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-04 (Mon, 04 May 2020)
Changed paths:
M src/client/components/editor/index.js
M src/styles/editor/editor.css
Log Message:
-----------
Workaround for mobile page size
- Apply a fixed pixel size to the editor page on load.
- Scroll to the top of the document upon loading the editor page.
- The fix is reapplied each time the page is resized.
Ref : #672
Commit: 0d9db80a92c466f51b0af17213d86724a1f48860
https://github.com/PathwayCommons/factoid/commit/0d9db80a92c466f51b0af17213d86724a1f48860
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-04 (Mon, 04 May 2020)
Changed paths:
M src/styles/editor/editor.css
Log Message:
-----------
Move the submit button to the bottom of the page #671
Commit: a334f8151de17b8bf936e7e0c67eb55a48e55e00
https://github.com/PathwayCommons/factoid/commit/a334f8151de17b8bf936e7e0c67eb55a48e55e00
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-04 (Mon, 04 May 2020)
Changed paths:
A src/client/components/editor/explore-share.js
M src/client/components/editor/index.js
A src/client/components/native-share.js
R src/client/components/share.js
A src/client/components/twitter-share.js
M src/styles/custom-icons.css
M src/styles/editor/editor.css
A src/styles/image/share-white.svg
A src/styles/image/share.svg
M src/styles/index.css
A src/styles/native-share.css
R src/styles/share.css
A src/styles/twitter-share.css
M src/styles/vars.css
Log Message:
-----------
Add mobile sharing button in the explore view #680
- Adds new button to the explore view
- Moves twitter sharing code to `twitter-share.js`
- Uses new `NativeShare` component
- `NativeShare` can be reused in multiple places in the UI
- The default content of `NativeShare` is a plain button with the traditional
share icon
- The content of `NativeShare` can be customised on a case-by-case basis
Commit: f437b35c00d141826469187657f6a123e4b2b44c
https://github.com/PathwayCommons/factoid/commit/f437b35c00d141826469187657f6a123e4b2b44c
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-04 (Mon, 04 May 2020)
Changed paths:
M src/client/components/editor/cy/tippy.js
Log Message:
-----------
Allow tippies to close when tapping the background or the info panel
- This requires a workaround, as the `hideOnClick: true` Tippy option doesn't
work out of the box.
- The cause is that the click events from `cy` have their callbacks called
before the native `click` event is emitted on the page's `<body>`, due to the
bubbling order.
- Using a `setTimeout()` with a duration of 0ms allows the `tippy.show()`
function to be called after the body's event callbacks complete.
Commit: 37257bb7cce5b2d2515d041a16cc2aa88470fc2a
https://github.com/PathwayCommons/factoid/commit/37257bb7cce5b2d2515d041a16cc2aa88470fc2a
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-04 (Mon, 04 May 2020)
Changed paths:
M src/styles/editor/editor.css
Log Message:
-----------
Panel separation improved
Commit: 9e268e9dffd20ac96f4be03255ca5a953a1e0239
https://github.com/PathwayCommons/factoid/commit/9e268e9dffd20ac96f4be03255ca5a953a1e0239
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-04 (Mon, 04 May 2020)
Changed paths:
M src/client/components/native-share.js
Log Message:
-----------
Disable debug `isNativeShareSupported()`
Commit: e7ecd4d5528a132e3ec3b520e0ccc991d6379970
https://github.com/PathwayCommons/factoid/commit/e7ecd4d5528a132e3ec3b520e0ccc991d6379970
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-05 (Tue, 05 May 2020)
Changed paths:
M src/model/element/interaction-type/interaction-type.js
Log Message:
-----------
Merge pull request #722 from PathwayCommons/iss720_to-text-bug
toText: Remove extra space
Commit: 8b2c15584b4442f6a44e61c05840c9d489383344
https://github.com/PathwayCommons/factoid/commit/8b2c15584b4442f6a44e61c05840c9d489383344
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-05-05 (Tue, 05 May 2020)
Changed paths:
M src/client/components/editor/cy/tippy.js
A src/client/components/editor/explore-share.js
M src/client/components/editor/index.js
A src/client/components/native-share.js
R src/client/components/share.js
A src/client/components/twitter-share.js
M src/styles/custom-icons.css
M src/styles/editor/editor.css
A src/styles/image/share-white.svg
A src/styles/image/share.svg
M src/styles/index.css
A src/styles/native-share.css
R src/styles/share.css
A src/styles/twitter-share.css
M src/styles/vars.css
Log Message:
-----------
Merge pull request #723 from PathwayCommons/mult-pr
Misc. improvements
Commit: 3def4cfd4246d93bc64f55212deaa7ebc83e919d
https://github.com/PathwayCommons/factoid/commit/3def4cfd4246d93bc64f55212deaa7ebc83e919d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-05 (Tue, 05 May 2020)
Changed paths:
M src/client/components/editor/cy/tippy.js
A src/client/components/editor/explore-share.js
M src/client/components/editor/index.js
A src/client/components/native-share.js
R src/client/components/share.js
A src/client/components/twitter-share.js
M src/model/element/interaction-type/interaction-type.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/styles/custom-icons.css
M src/styles/editor/editor.css
A src/styles/image/share-white.svg
A src/styles/image/share.svg
M src/styles/index.css
A src/styles/native-share.css
R src/styles/share.css
A src/styles/twitter-share.css
M src/styles/vars.css
Log Message:
-----------
Merge branch 'unstable' into iss703_editor-submit-tweaks
Commit: 3923fbaaed56925ae6208ceec37c017fbbcff132
https://github.com/PathwayCommons/factoid/commit/3923fbaaed56925ae6208ceec37c017fbbcff132
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-05 (Tue, 05 May 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
Log Message:
-----------
Use editor as single source of truth for sub-components (Submit, TaskView)
Commit: 71b1c38d74cc298e204b2a260d4f67247963707a
https://github.com/PathwayCommons/factoid/commit/71b1c38d74cc298e204b2a260d4f67247963707a
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-05 (Tue, 05 May 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
Prototyping the Share component.
Commit: c0448ea08c1ea6826edfc8d498a9c69387039b55
https://github.com/PathwayCommons/factoid/commit/c0448ea08c1ea6826edfc8d498a9c69387039b55
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-05 (Tue, 05 May 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
- Tweaked styling of all share links
Commit: 12e1ba0a002bd7a256ba5a27c4b3eff619eb2335
https://github.com/PathwayCommons/factoid/commit/12e1ba0a002bd7a256ba5a27c4b3eff619eb2335
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-06 (Wed, 06 May 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
- Removing native share (for now)
- Simplifying css and text
Commit: 3e817a0d32cb2cabfa4975801180afd828096ef7
https://github.com/PathwayCommons/factoid/commit/3e817a0d32cb2cabfa4975801180afd828096ef7
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-06 (Wed, 06 May 2020)
Changed paths:
M src/model/document/document.js
M src/model/element/entity.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Related papers (#721)
* Added a new indra service to query indra documents given a factoid document
id. Also, while making indra queries used id and namespace pair if the
namespace is hgnc or chebi #681.
* Fixed the duplication of lodash import happened after a merge
* Pick id and namespace for indra entity associations.
* For indra queries: Used TEXT instead of the namespace where the namespace is
missing #681
* - Allow fetchPubmed to be customized via opts
- Remove default limit (retmax) for number of records returned by fetchPubmed
- POST to EFETCH EUTILS to allow large numbers of UIDs to be retrieved
* Updated indra documents output format. Added pubmed metadate field and also
sorted the documents by the publication date.
* Remove moment.js and use the already existing date library instead
* Some changes were forgotten in the previous commit. Added them.
* Updates based on discussion at #721
* Updates based on the reviews from #721
* Remove old indra services
* Handled more of the exceptions for indra services.
* Do not convert indra search agents to uppercase
Co-authored-by: Jeffrey Wong <jvw...@gmail.com>
Commit: 37dc7e26610cd1ca092fbd81b9dcc823b904222a
https://github.com/PathwayCommons/factoid/commit/37dc7e26610cd1ca092fbd81b9dcc823b904222a
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-08 (Fri, 08 May 2020)
Changed paths:
M .gitignore
M package-lock.json
M package.json
M src/client/client-util/file.js
A src/server/routes/api/document/export.js
M src/server/routes/api/document/index.js
A src/util/document.js
M src/util/index.js
Log Message:
-----------
Offer contributed data as bulk file for download #717
Commit: 61c840cd832f64f97113a3a29c898debad2072e6
https://github.com/PathwayCommons/factoid/commit/61c840cd832f64f97113a3a29c898debad2072e6
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-11 (Mon, 11 May 2020)
Changed paths:
M src/server/routes/api/document/export.js
M src/util/document.js
Log Message:
-----------
Updates based on reviews at #725
Commit: aead49276544ed7ca3e821a77a99966bfb62aaa4
https://github.com/PathwayCommons/factoid/commit/aead49276544ed7ca3e821a77a99966bfb62aaa4
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-11 (Mon, 11 May 2020)
Changed paths:
M src/server/routes/api/document/export.js
Log Message:
-----------
Fixed lint error
Commit: 9ade27813fdd354b9db9338a013865ac813268d7
https://github.com/PathwayCommons/factoid/commit/9ade27813fdd354b9db9338a013865ac813268d7
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-12 (Tue, 12 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Added swagger documentation for bulk file service
Commit: 1bb703715c14ea5b3896b746fb28d6ee2b6ef5b9
https://github.com/PathwayCommons/factoid/commit/1bb703715c14ea5b3896b746fb28d6ee2b6ef5b9
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-13 (Wed, 13 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Updated descriptive text for swagger for /zip/dl.
Commit: 73f473cb19593273d34c3304391543f36bb68fe9
https://github.com/PathwayCommons/factoid/commit/73f473cb19593273d34c3304391543f36bb68fe9
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-13 (Wed, 13 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Relocated the bulk zip service
Commit: 4673d6cb35fe63a649a1510e8962728ac80ebb23
https://github.com/PathwayCommons/factoid/commit/4673d6cb35fe63a649a1510e8962728ac80ebb23
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-13 (Wed, 13 May 2020)
Changed paths:
M .gitignore
M package-lock.json
M package.json
M src/client/client-util/file.js
A src/server/routes/api/document/export.js
M src/server/routes/api/document/index.js
A src/util/document.js
M src/util/index.js
Log Message:
-----------
Merge pull request #725 from PathwayCommons/bulk-export
Offer contributed data as bulk file for download
Commit: 0006dc470f964ad2079b2e23ec04da1be3cdb7cf
https://github.com/PathwayCommons/factoid/commit/0006dc470f964ad2079b2e23ec04da1be3cdb7cf
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-14 (Thu, 14 May 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Use sementic search in sorting indra documents
Commit: c0537208700952c430ecb4e990a0513c01c3eade
https://github.com/PathwayCommons/factoid/commit/c0537208700952c430ecb4e990a0513c01c3eade
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-15 (Fri, 15 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Extended the timeout for related-papers service and also handled some minor
todos.
Commit: a94285267253291b47df54aa44d20622ce9d5b9c
https://github.com/PathwayCommons/factoid/commit/a94285267253291b47df54aa44d20622ce9d5b9c
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-20 (Wed, 20 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Trigger related papers when a document is submitted.
Commit: 74976b6a17831e7e2e6fee2c66a148db33051ee0
https://github.com/PathwayCommons/factoid/commit/74976b6a17831e7e2e6fee2c66a148db33051ee0
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-20 (Wed, 20 May 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
Docker changes for semantic search (not working yet)
Commit: 8fdae4564ffee4fb7412d85b7ab3c32d38bc13df
https://github.com/PathwayCommons/factoid/commit/8fdae4564ffee4fb7412d85b7ab3c32d38bc13df
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-20 (Wed, 20 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
A change in order of function calls after document submission.
Commit: 266cd6df260b82caede819e70400045df44dc0f1
https://github.com/PathwayCommons/factoid/commit/266cd6df260b82caede819e70400045df44dc0f1
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-20 (Wed, 20 May 2020)
Changed paths:
M package-lock.json
M src/client/components/home.js
M src/styles/base.css
M src/styles/home.css
M src/styles/image/home-figure-1.jpg
M src/styles/image/home-figure-2.jpg
R src/styles/image/home-figure-3.jpg
A src/styles/image/home-figure-fg-2.png
A src/styles/image/home-figure-old-2.jpg
A src/styles/image/home-figure-old-3.jpg
A src/styles/image/sample-editor-screen-fade.mp4
A src/styles/image/sample-editor-screen.m4v
M src/styles/vars.css
Log Message:
-----------
Homepage tweaks
- Added contact, twitter, and get started links at the top of the page.
- There is a 'get started' button in each section of the page.
- The 'how it works' section is clearer with an in-screen demo.
- Addition of the third section: Your pathway to share and explore. The figure
in this section can be updated by swapping the image.
- The 'read the paper' button doesn't point anywhere. It can be updated once
we have a biorxiv link.
- The text has been revised.
Ref. Feedback: Homepage tweaks #702
Commit: 8f6c6419583bd5b0148ad346e1f9a6988f6e8d7c
https://github.com/PathwayCommons/factoid/commit/8f6c6419583bd5b0148ad346e1f9a6988f6e8d7c
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-05-21 (Thu, 21 May 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/editor/submit.js
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
M src/styles/tasks.css
Log Message:
-----------
Merge pull request #719 from PathwayCommons/iss703_editor-submit-tweaks
Editor submit tweaks
Commit: 6a1a9a0fb7f0c191a4ac4b2568be3bab7a57ac49
https://github.com/PathwayCommons/factoid/commit/6a1a9a0fb7f0c191a4ac4b2568be3bab7a57ac49
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-05-21 (Thu, 21 May 2020)
Changed paths:
M package-lock.json
M src/client/components/home.js
M src/styles/base.css
M src/styles/home.css
M src/styles/image/home-figure-1.jpg
M src/styles/image/home-figure-2.jpg
R src/styles/image/home-figure-3.jpg
A src/styles/image/home-figure-fg-2.png
A src/styles/image/home-figure-old-2.jpg
A src/styles/image/home-figure-old-3.jpg
A src/styles/image/sample-editor-screen-fade.mp4
A src/styles/image/sample-editor-screen.m4v
M src/styles/vars.css
Log Message:
-----------
Merge pull request #728 from PathwayCommons/homepage-tweaks
Homepage tweaks
Commit: c62a5f23c152beca527b1a2842528775f492f29d
https://github.com/PathwayCommons/factoid/commit/c62a5f23c152beca527b1a2842528775f492f29d
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-21 (Thu, 21 May 2020)
Changed paths:
M docker/docker-compose.yml
Log Message:
-----------
Do not forward the semantic-search container port to host in docker-compose
Commit: 8e0f1569aae9af84dff0c23430aa5876170d514d
https://github.com/PathwayCommons/factoid/commit/8e0f1569aae9af84dff0c23430aa5876170d514d
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-21 (Thu, 21 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Fixes based on reviews at #727
Commit: 619849b681c8f6593704247644ae46b45205ffbb
https://github.com/PathwayCommons/factoid/commit/619849b681c8f6593704247644ae46b45205ffbb
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-22 (Fri, 22 May 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
Log Message:
-----------
Initial changes re. CTA redesign
- Auto-open editor URL
- Changes to text
- Remove spell check on email field
- Misc. presentational changes
Commit: ae1c56a4d807627d716341349dbf3708c1aa44a7
https://github.com/PathwayCommons/factoid/commit/ae1c56a4d807627d716341349dbf3708c1aa44a7
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-22 (Fri, 22 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Syntax change in a catch block #727
Commit: 1d0408ccc3c8e0e3e0c27015521ae94e806a29e9
https://github.com/PathwayCommons/factoid/commit/1d0408ccc3c8e0e3e0c27015521ae94e806a29e9
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-22 (Fri, 22 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Fixed some syntax error #727
Commit: 5e876b75f8bc93c88a1665fce30b4e02768803ab
https://github.com/PathwayCommons/factoid/commit/5e876b75f8bc93c88a1665fce30b4e02768803ab
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-25 (Mon, 25 May 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
Log Message:
-----------
- Removed unused code for 'context' declaration (signup, journal)
- Updated CTA to indicate rationale for inputs
Commit: ce0d008b64bb0b887c0132cfdef36e3bd04224f6
https://github.com/PathwayCommons/factoid/commit/ce0d008b64bb0b887c0132cfdef36e3bd04224f6
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-25 (Mon, 25 May 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
Log Message:
-----------
- Added the journal citation information to the success panel, to mimic what
will be seen in editor
Commit: cf37517010d35ef6924d51cbc6db61232bee8347
https://github.com/PathwayCommons/factoid/commit/cf37517010d35ef6924d51cbc6db61232bee8347
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-25 (Mon, 25 May 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Tweaked the email disclaimer
Commit: f32aaff9ea2eee65e324f14eeb5fe825f220f9bf
https://github.com/PathwayCommons/factoid/commit/f32aaff9ea2eee65e324f14eeb5fe825f220f9bf
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-25 (Mon, 25 May 2020)
Changed paths:
M README.md
Log Message:
-----------
- Added intro and 'getting data' section for researchers and devs
Commit: 0891099e726418a0fac7476606d52a285176178a
https://github.com/PathwayCommons/factoid/commit/0891099e726418a0fac7476606d52a285176178a
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-25 (Mon, 25 May 2020)
Changed paths:
M README.md
Log Message:
-----------
- hyperlink Biofactoid site
Commit: 0513cb4fe162e0c3d05abf09ccf710a3fabd591d
https://github.com/PathwayCommons/factoid/commit/0513cb4fe162e0c3d05abf09ccf710a3fabd591d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-25 (Mon, 25 May 2020)
Changed paths:
M src/config.js
Log Message:
-----------
Updated the PUBMED_LINK_BASE_URL config variable.
Commit: 3c78fe87028c07c524b940df968acae0e5786867
https://github.com/PathwayCommons/factoid/commit/3c78fe87028c07c524b940df968acae0e5786867
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-05-25 (Mon, 25 May 2020)
Changed paths:
M src/config.js
Log Message:
-----------
Merge pull request #733 from PathwayCommons/iss732_update-pubmed-url
Updated the PUBMED_LINK_BASE_URL config variable.
Commit: fee48155786d4417582f9a09e3fbf97f1d8eac4c
https://github.com/PathwayCommons/factoid/commit/fee48155786d4417582f9a09e3fbf97f1d8eac4c
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-25 (Mon, 25 May 2020)
Changed paths:
M package-lock.json
M package.json
M src/config.js
M src/server/index.js
A src/server/update-cron.js
Log Message:
-----------
Stubbed out cron job system on server.
Commit: ede98ace03ca65eafc4ec19a9dfeaa01cfe0c214
https://github.com/PathwayCommons/factoid/commit/ede98ace03ca65eafc4ec19a9dfeaa01cfe0c214
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-26 (Tue, 26 May 2020)
Changed paths:
M README.md
Log Message:
-----------
Merge pull request #731 from PathwayCommons/iss726_readme-data-resources
README: Getting data
Commit: f1acdc137f8e881e99d2d13f4fe3c73717a5252d
https://github.com/PathwayCommons/factoid/commit/f1acdc137f8e881e99d2d13f4fe3c73717a5252d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-26 (Tue, 26 May 2020)
Changed paths:
A src/server/routes/api/document/update.js
M src/server/update-cron.js
Log Message:
-----------
Function that selects docs to update from database. Currently based on
created Date.
Commit: 7905d94dea9f88e4f5007bebb82d82b0060689fd
https://github.com/PathwayCommons/factoid/commit/7905d94dea9f88e4f5007bebb82d82b0060689fd
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-26 (Tue, 26 May 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/update.js
Log Message:
-----------
Working prototype for Document updateArticle cron job.
Commit: beededdcdab40bb07c1539ed6d6b1dc1fb62724c
https://github.com/PathwayCommons/factoid/commit/beededdcdab40bb07c1539ed6d6b1dc1fb62724c
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-26 (Tue, 26 May 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/update.js
Log Message:
-----------
Update period granularity for frequency of Document article updates
Commit: 688371a20ef4d27926f82ead6b07f15213c233ad
https://github.com/PathwayCommons/factoid/commit/688371a20ef4d27926f82ead6b07f15213c233ad
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-26 (Tue, 26 May 2020)
Changed paths:
M src/config.js
M src/server/index.js
M src/server/routes/api/document/update.js
Log Message:
-----------
Set config variables for Document update scheduling
Commit: 4680d083b1738b3470d97e67c16cc88ccff19458
https://github.com/PathwayCommons/factoid/commit/4680d083b1738b3470d97e67c16cc88ccff19458
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-26 (Tue, 26 May 2020)
Changed paths:
M src/server/update-cron.js
Log Message:
-----------
Used more specific name for document update function.
Commit: cf09768db54c709015734ffb1acfabdd36b13107
https://github.com/PathwayCommons/factoid/commit/cf09768db54c709015734ffb1acfabdd36b13107
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-26 (Tue, 26 May 2020)
Changed paths:
M src/model/element/interaction-type/interaction-type.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Updates for #727
Commit: ec6b3c26542d176082224e37ce5b57591fc8e73c
https://github.com/PathwayCommons/factoid/commit/ec6b3c26542d176082224e37ce5b57591fc8e73c
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-27 (Wed, 27 May 2020)
Changed paths:
M src/styles/home.css
Log Message:
-----------
Make the figure bigger for small screens in the 'your pathway to share and
explore' section
Commit: 94b27b5ce1de2da19f3daae3d32dcce7780180dd
https://github.com/PathwayCommons/factoid/commit/94b27b5ce1de2da19f3daae3d32dcce7780180dd
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-27 (Wed, 27 May 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Add `playsInline` to allow iPhones to play the video in the background.
Commit: 82c5e8ddcd2e593b2169c4c8aaa5fbcd1d3aee6c
https://github.com/PathwayCommons/factoid/commit/82c5e8ddcd2e593b2169c4c8aaa5fbcd1d3aee6c
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-05-27 (Wed, 27 May 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
Log Message:
-----------
Merge pull request #734 from PathwayCommons/misc-homepage-fixes
Misc homepage fixes
Commit: 52cce211460ebbae76e066d0f1965c487c19d035
https://github.com/PathwayCommons/factoid/commit/52cce211460ebbae76e066d0f1965c487c19d035
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-27 (Wed, 27 May 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/update.js
M src/server/update-cron.js
Log Message:
-----------
- Bug in doc selection by ArticleIdList IdType
- Removed start date as a parameter.
Commit: 4afec22bd4ee8cc98f6f82e59f0b2099e2fa0345
https://github.com/PathwayCommons/factoid/commit/4afec22bd4ee8cc98f6f82e59f0b2099e2fa0345
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-27 (Wed, 27 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Drop the fetchPubmed debugging code
Commit: de536069a10211a84d5ade11bea196bb36bb1861
https://github.com/PathwayCommons/factoid/commit/de536069a10211a84d5ade11bea196bb36bb1861
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-27 (Wed, 27 May 2020)
Changed paths:
M src/server/routes/api/document/update.js
Log Message:
-----------
Drop comments for removed parameter.
Commit: 1a09844dfb3d3e87c0dff3727bec9cdd5f60cf0a
https://github.com/PathwayCommons/factoid/commit/1a09844dfb3d3e87c0dff3727bec9cdd5f60cf0a
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-27 (Wed, 27 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Update format of relatedPapers field in element table of database #727
Commit: a940cd7d9d006cda9044120eccea18781ff593f3
https://github.com/PathwayCommons/factoid/commit/a940cd7d9d006cda9044120eccea18781ff593f3
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-27 (Wed, 27 May 2020)
Changed paths:
M src/model/document/document.js
M src/model/element/interaction.js
Log Message:
-----------
Added document.relatedPapers() and interaction.relatedPapers() #727
Commit: db5e12c4c3852a5db1eb096dce496aade5c47888
https://github.com/PathwayCommons/factoid/commit/db5e12c4c3852a5db1eb096dce496aade5c47888
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-05-27 (Wed, 27 May 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Update relatedPapers fields of database tables from the model #727.
Commit: b5e368354910de2c72a6f12223e6ee756dd14dcc
https://github.com/PathwayCommons/factoid/commit/b5e368354910de2c72a6f12223e6ee756dd14dcc
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-28 (Thu, 28 May 2020)
Changed paths:
M src/server/routes/api/document/update.js
Log Message:
-----------
Bug in logic for determining if an update should be triggered.
Commit: df00ce33890a006d254463832bbaecef9eed4d1d
https://github.com/PathwayCommons/factoid/commit/df00ce33890a006d254463832bbaecef9eed4d1d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-28 (Thu, 28 May 2020)
Changed paths:
M README.md
M src/config.js
Log Message:
-----------
- Set default CRON_SCHEDULE to daily at 01:00
- Readme update for config variables.
Commit: 243e865353ecbb74b69465d56209fff477b548e5
https://github.com/PathwayCommons/factoid/commit/243e865353ecbb74b69465d56209fff477b548e5
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-28 (Thu, 28 May 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Clarify the email requirement text
Commit: d91d4ef8794b9a1359f2742127d67b2673cea27b
https://github.com/PathwayCommons/factoid/commit/d91d4ef8794b9a1359f2742127d67b2673cea27b
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-05-28 (Thu, 28 May 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
M src/config.js
M src/model/document/document.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Merge pull request #727 from PathwayCommons/related-papers-sort
Related papers sort and trigger
Commit: 7e665dc47cbc09a11518657d8f558085ec36dc4c
https://github.com/PathwayCommons/factoid/commit/7e665dc47cbc09a11518657d8f558085ec36dc4c
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-05-28 (Thu, 28 May 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
Log Message:
-----------
Merge pull request #730 from PathwayCommons/cta-redesign
CTA redesign
Commit: a9ebe0a4b74d899126680ccabd7285ae6ff986cb
https://github.com/PathwayCommons/factoid/commit/a9ebe0a4b74d899126680ccabd7285ae6ff986cb
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-05-29 (Fri, 29 May 2020)
Changed paths:
M README.md
M src/config.js
M src/server/routes/api/document/update.js
Log Message:
-----------
- Added 'DOCUMENT_CRON_REFRESH_ENABLED' boolean config which toggles
refreshing existing data
Commit: bf73bde310ca396f8d5fc96f02c7fe73972aff75
https://github.com/PathwayCommons/factoid/commit/bf73bde310ca396f8d5fc96f02c7fe73972aff75
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-05-29 (Fri, 29 May 2020)
Changed paths:
M README.md
M package-lock.json
M package.json
M src/config.js
M src/server/index.js
M src/server/routes/api/document/index.js
A src/server/routes/api/document/update.js
A src/server/update-cron.js
Log Message:
-----------
Merge pull request #735 from PathwayCommons/iss729_cron-article-metadata
Cron system: Update Article metadata
Commit: 9d2c59fbf6ae14e6c33305d7d865db1fe92a7f1c
https://github.com/PathwayCommons/factoid/commit/9d2c59fbf6ae14e6c33305d7d865db1fe92a7f1c
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-01 (Mon, 01 Jun 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
- Default Factoid image tag to be 'latest' rather than 'unstable'
- Publish the port for semantic-search, in anticipation of mapping it to a
domain
Commit: 7435380cb13b1da31ec8d73f116f981d057a3c81
https://github.com/PathwayCommons/factoid/commit/7435380cb13b1da31ec8d73f116f981d057a3c81
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-01 (Mon, 01 Jun 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
Merge pull request #739 from PathwayCommons/docker-compose-tweaks
Docker-compose updates
Commit: 1bffc331218fd43eb525830bd00da7fa69cebcf8
https://github.com/PathwayCommons/factoid/commit/1bffc331218fd43eb525830bd00da7fa69cebcf8
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-02 (Tue, 02 Jun 2020)
Changed paths:
M src/config.js
Log Message:
-----------
Config var for semantic-search service.
Commit: 7e4f99d85c5134310491c60229abb432b0dd4c7e
https://github.com/PathwayCommons/factoid/commit/7e4f99d85c5134310491c60229abb432b0dd4c7e
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-02 (Tue, 02 Jun 2020)
Changed paths:
M src/config.js
Log Message:
-----------
Merge pull request #740 from PathwayCommons/semantic-search-URL
Config var for semantic-search service.
Commit: 8f477774b67b1e36bb15b620fa12a07a10d1f20f
https://github.com/PathwayCommons/factoid/commit/8f477774b67b1e36bb15b620fa12a07a10d1f20f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-02 (Tue, 02 Jun 2020)
Changed paths:
M docker/docker-compose.yml
Log Message:
-----------
Missing space in docker-compose
Commit: 1a00d1f10fa7e55c2cf7d2da1d7ac1ea25e9358a
https://github.com/PathwayCommons/factoid/commit/1a00d1f10fa7e55c2cf7d2da1d7ac1ea25e9358a
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-04 (Thu, 04 Jun 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
Log Message:
-----------
- added missing 'await' on `tweetDoc()`
- TaskView waits for server response to show done panel
Commit: ba89393473f0333c10c72a4fa9af3e95b586a729
https://github.com/PathwayCommons/factoid/commit/ba89393473f0333c10c72a4fa9af3e95b586a729
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-04 (Thu, 04 Jun 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
-----------
Remove unused json conversion in status update response
Commit: 5503dbfb2311074dcdafb418c1668ba75725e86a
https://github.com/PathwayCommons/factoid/commit/5503dbfb2311074dcdafb418c1668ba75725e86a
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-09 (Tue, 09 Jun 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #744 from PathwayCommons/iss743_submit-wait-server
Submit: Wait for server response before showing 'done' panel
Commit: 00846d488294d13d2ed79ba51c43d08a2580132f
https://github.com/PathwayCommons/factoid/commit/00846d488294d13d2ed79ba51c43d08a2580132f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-09 (Tue, 09 Jun 2020)
Changed paths:
M package-lock.json
M package.json
M src/server/routes/api/document/pubmed/fetchPubmed.js
M test/pubmed/fetchPubmed.js
A test/pubmed/pmid_151222.xml
Log Message:
-----------
- New PubMed test file with MedlineDate
- Removed xml2js from packages
- Updated fetchPubMed tests
- Implemented fetchPubMed with xml-js library
Commit: 876bbf248faf7ce65f367288e795eaa2ed2db00d
https://github.com/PathwayCommons/factoid/commit/876bbf248faf7ce65f367288e795eaa2ed2db00d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-09 (Tue, 09 Jun 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
M test/pubmed/fetchPubmed.js
Log Message:
-----------
- Fixing bug in description of Chemical properties
Commit: 2ead7b8ef3cc1cad68019c1c3a351a4e148a71c2
https://github.com/PathwayCommons/factoid/commit/2ead7b8ef3cc1cad68019c1c3a351a4e148a71c2
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-10 (Wed, 10 Jun 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Log errors from fillDoc, which catches errors in underlying modules (e.g.
fetchPubmed)
Commit: 4ce085bc576fd756517d268671ee3cd0e2971f0e
https://github.com/PathwayCommons/factoid/commit/4ce085bc576fd756517d268671ee3cd0e2971f0e
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-10 (Wed, 10 Jun 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
Log Message:
-----------
Support Abstract Labels for structured abstracts.
Commit: 9ac54afc247e6c6b5993e28da1d7e5beeb597d9f
https://github.com/PathwayCommons/factoid/commit/9ac54afc247e6c6b5993e28da1d7e5beeb597d9f
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-06-10 (Wed, 10 Jun 2020)
Changed paths:
M .travis.yml
Log Message:
-----------
Disable rethinkdb in travis & use only node@10,12
Commit: fceefd5077d7a5ad32a9e9152386461179492282
https://github.com/PathwayCommons/factoid/commit/fceefd5077d7a5ad32a9e9152386461179492282
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-10 (Wed, 10 Jun 2020)
Changed paths:
M package-lock.json
M package.json
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M test/pubmed/fetchPubmed.js
A test/pubmed/pmid_151222.xml
Log Message:
-----------
Merge pull request #748 from PathwayCommons/iss745_xml-parsing-fetchPubmed
Import of PubMed EFETCH XML
Commit: a5b67235c2c6402dfdf748e68eda758a8c15422a
https://github.com/PathwayCommons/factoid/commit/a5b67235c2c6402dfdf748e68eda758a8c15422a
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-10 (Wed, 10 Jun 2020)
Changed paths:
M .travis.yml
Log Message:
-----------
Merge pull request #749 from PathwayCommons/erratic-travis
Disable rethinkdb in travis & use only node@10,12
Commit: 08cc57bdbe30b947fab696b6820783e6ea008c3b
https://github.com/PathwayCommons/factoid/commit/08cc57bdbe30b947fab696b6820783e6ea008c3b
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-06-10 (Wed, 10 Jun 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
-----------
No related papers results #742
Commit: fa6325b672b6863adf82287c5b981b8db4a56c14
https://github.com/PathwayCommons/factoid/commit/fa6325b672b6863adf82287c5b981b8db4a56c14
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-11 (Thu, 11 Jun 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
Log Message:
-----------
- Editor is sole source of truth for doc status
- Task submit, publish path is simplified
- DO not check status on server to attempt publish
Commit: 143ba5440806a0ba953bc824a713a1687ded48e6
https://github.com/PathwayCommons/factoid/commit/143ba5440806a0ba953bc824a713a1687ded48e6
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-11 (Thu, 11 Jun 2020)
Changed paths:
M src/client/components/editor/index.js
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #751 from PathwayCommons/iss743_submit-success-sync
Editor submit & success panel
Commit: c3590ddfa0ad86270d16863968e431769b22c07a
https://github.com/PathwayCommons/factoid/commit/c3590ddfa0ad86270d16863968e431769b22c07a
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-06-11 (Thu, 11 Jun 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
-----------
Catch unhandled dates and return the minimum possible integers while
calculating the publication time in ms in such cases #742
Commit: 999f3965c0f7f343fd1e15b5351f330dda13136a
https://github.com/PathwayCommons/factoid/commit/999f3965c0f7f343fd1e15b5351f330dda13136a
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-06-11 (Thu, 11 Jun 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Related Papers: Search aborts when (PubMed) metadata is missing #738
Commit: b3a08c18a40894581fef3f7ff6670e29c3f14e4a
https://github.com/PathwayCommons/factoid/commit/b3a08c18a40894581fef3f7ff6670e29c3f14e4a
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-12 (Fri, 12 Jun 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
-----------
Merge pull request #750 from PathwayCommons/related_papers_filter
No related papers results #742
Commit: 92b6380043093126fb0cd82a82ea3c7143e9dc04
https://github.com/PathwayCommons/factoid/commit/92b6380043093126fb0cd82a82ea3c7143e9dc04
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-06-12 (Fri, 12 Jun 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
-----------
Safer implementation for retrieving pmid for a document #752
Commit: df54b243498f40ef174101a1b1d491d9e0c3fb92
https://github.com/PathwayCommons/factoid/commit/df54b243498f40ef174101a1b1d491d9e0c3fb92
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-16 (Tue, 16 Jun 2020)
Changed paths:
M src/client-env-vars.json
M src/client/components/home.js
M src/config.js
Log Message:
-----------
Text only updates
Commit: 24fd003c5029adf536703dc4c628e749835676c2
https://github.com/PathwayCommons/factoid/commit/24fd003c5029adf536703dc4c628e749835676c2
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-06-16 (Tue, 16 Jun 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
-----------
Resolved merge conflicts for #752
Commit: fff46345a3b1af60517a1e12cfbc839752eec2eb
https://github.com/PathwayCommons/factoid/commit/fff46345a3b1af60517a1e12cfbc839752eec2eb
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/client/components/home.js
M src/config.js
Log Message:
-----------
Tweaking the email disclaimer.
Commit: 12b09f1e004be42cea20f9bb4bcdfd7d87f36252
https://github.com/PathwayCommons/factoid/commit/12b09f1e004be42cea20f9bb4bcdfd7d87f36252
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/styles/home.css
M src/styles/image/home-figure-fg-2.png
Log Message:
-----------
Updated section 3 figure.
Commit: 7b3ddb83e089b3ce050ad9bafb6c0e3ff63870eb
https://github.com/PathwayCommons/factoid/commit/7b3ddb83e089b3ce050ad9bafb6c0e3ff63870eb
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
A src/styles/image/logo_harvardu.png
A src/styles/image/logo_ohsu.jpg
A src/styles/image/logo_utoronto.png
R src/styles/image/uni-logos-bw.png
R src/styles/image/uni-logos.png
Log Message:
-----------
Individual images for universities and linkouts
Commit: ceeba37e6e4240d8f3ae0c7d21dc4421faf47113
https://github.com/PathwayCommons/factoid/commit/ceeba37e6e4240d8f3ae0c7d21dc4421faf47113
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/styles/home.css
Log Message:
-----------
Section 3: Reduce the size of image and flip background
Commit: fbb2a0b5796194caa25e85eddfa8b159a5b7d111
https://github.com/PathwayCommons/factoid/commit/fbb2a0b5796194caa25e85eddfa8b159a5b7d111
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Appended grant information to the Contact.
Commit: f8fe8893d460a32c89dc858bb33e7770c254130d
https://github.com/PathwayCommons/factoid/commit/f8fe8893d460a32c89dc858bb33e7770c254130d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Shorten the 'publish' popup text.
Commit: 8db3df102d3d12276470b841cce869e88c15c4b4
https://github.com/PathwayCommons/factoid/commit/8db3df102d3d12276470b841cce869e88c15c4b4
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Merge pull request #752 from PathwayCommons/no_abstract_handling
Related Papers: Search aborts when (PubMed) metadata is missing
Commit: 9be604f875f5fc9c5ec2cb60a07c820d0a087fce
https://github.com/PathwayCommons/factoid/commit/9be604f875f5fc9c5ec2cb60a07c820d0a087fce
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
M src/server/routes/api/document/pubmed/searchPubmed.js
Log Message:
-----------
- Add opts for searchPubmed
- getPubmedArticle explicitly searches for DOI, PMID or title.
Commit: b4b0a27f0ea2d726e4e1a1c4c26d090b326ced5f
https://github.com/PathwayCommons/factoid/commit/b4b0a27f0ea2d726e4e1a1c4c26d090b326ced5f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
Log Message:
-----------
Comment on need to sanitize titles.
Commit: 4c4158aff9a0ab6e04e033c6279584993dbfbc46
https://github.com/PathwayCommons/factoid/commit/4c4158aff9a0ab6e04e033c6279584993dbfbc46
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
Log Message:
-----------
When comparing titles, just eliminate any non word characters.
Commit: 58b97a476bc40afb2a670edac55f3d1603ebee05
https://github.com/PathwayCommons/factoid/commit/58b97a476bc40afb2a670edac55f3d1603ebee05
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-06-17 (Wed, 17 Jun 2020)
Changed paths:
A src/client/components/carousel.js
M src/client/components/editor/cy/defs.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/index.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/defs.js
M src/client/components/editor/explore-share.js
M src/client/components/editor/index.js
M src/client/components/editor/info-panel.js
M 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/home.js
A src/client/components/related-papers.js
M src/model/element/element.js
M src/model/element/interaction.js
M src/styles/base.css
A src/styles/carousel.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/index.css
M src/styles/element-info/interaction-info.css
M src/styles/home.css
M src/styles/index.css
A src/styles/related-papers.css
Log Message:
-----------
Related papers UI
- Adds related papers UI, labelled as "recommended articles", for the document,
each interaction, and each entity.
- Revises the carousel component to be generic. The carousel is an alternative
way to show the related papers that allows for showing more papers with
horizontal scrolling. This design can be swapped out in future, as needed.
- The information panel in the explore view always sits at the bottom of the
page, regardless of screen size.
- Large screens allow the related papers to be shown above the fold, by using a
two-column layout.
- Misc. fixes & improvements
- The information panel can be scrolled by scrolling over the network
visualisation.
- Improved entity information display in the explore view: It now reuses the
information panel rather than showing Tippy components.
- The use of Tippy components has been revised to address #736: Grounding:
Cannot 'Select better match for X'
- The `relatedPapers` method has been moved to the `Element` superclass to
support both `Entity`s and `Interaction`s. See
https://github.com/PathwayCommons/factoid/issues/742#issuecomment-644228132
- New nodes are always added around the same position to allow for more
consistency and to allow for a better experience on small screen sizes. (You
need the text box in the popover to be shown near the top of the screen.)
- Many gestures have been disabled in the visualisation of the explore view.
- There is a button in the explore view to access the corresponding tweet.
- And other minor usability improvements...
Commit: cbb4bf3238a56e077a3a4a5ba2edeab7cd290220
https://github.com/PathwayCommons/factoid/commit/cbb4bf3238a56e077a3a4a5ba2edeab7cd290220
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-18 (Thu, 18 Jun 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
Log Message:
-----------
Removed extraineous check on searchHit counts from PubMed.
Commit: f6a7113f365d5c90eef65c1d7cb57e613f884698
https://github.com/PathwayCommons/factoid/commit/f6a7113f365d5c90eef65c1d7cb57e613f884698
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-06-18 (Thu, 18 Jun 2020)
Changed paths:
M src/styles/editor/editor.css
Log Message:
-----------
Fixes twitter icon alignment in firefox
Commit: 9da3808f0bb62fe3c129d311147f11424d867c6d
https://github.com/PathwayCommons/factoid/commit/9da3808f0bb62fe3c129d311147f11424d867c6d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-19 (Fri, 19 Jun 2020)
Changed paths:
M src/client/components/editor/info-panel.js
M src/client/components/related-papers.js
M src/server/routes/api/document/indra.js
M src/util/pubmed.js
Log Message:
-----------
- Show doc text when Abstract unavailable
- Related papers uses live data
- Document stores citation of article
Commit: 7d0085775eef86116c62709fa478377d08dc2593
https://github.com/PathwayCommons/factoid/commit/7d0085775eef86116c62709fa478377d08dc2593
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-06-19 (Fri, 19 Jun 2020)
Changed paths:
A src/client/components/carousel.js
M src/client/components/editor/cy/defs.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/index.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/defs.js
M src/client/components/editor/explore-share.js
M src/client/components/editor/index.js
M src/client/components/editor/info-panel.js
M 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/home.js
A src/client/components/related-papers.js
M src/model/element/element.js
M src/model/element/interaction.js
M src/server/routes/api/document/indra.js
M src/styles/base.css
A src/styles/carousel.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/index.css
M src/styles/element-info/interaction-info.css
M src/styles/home.css
M src/styles/index.css
A src/styles/related-papers.css
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #755 from PathwayCommons/related-papers-ui
Related papers UI
Commit: f42bf0fac64114cb28a518eee922b6f2ed492514
https://github.com/PathwayCommons/factoid/commit/f42bf0fac64114cb28a518eee922b6f2ed492514
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-06-19 (Fri, 19 Jun 2020)
Changed paths:
A src/client/components/carousel.js
M src/client/components/editor/cy/defs.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/index.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/defs.js
M src/client/components/editor/explore-share.js
M src/client/components/editor/index.js
M src/client/components/editor/info-panel.js
M 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/home.js
A src/client/components/related-papers.js
M src/config.js
M src/model/element/element.js
M src/model/element/interaction.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
M src/styles/base.css
A src/styles/carousel.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/index.css
M src/styles/element-info/interaction-info.css
M src/styles/home.css
M src/styles/index.css
A src/styles/related-papers.css
M src/util/pubmed.js
Log Message:
-----------
Merge branch 'unstable' into iss753_homepage-tweaks-text
Commit: 125873d64ad8bd2ea2fd2364c5f91debde6f9e2a
https://github.com/PathwayCommons/factoid/commit/125873d64ad8bd2ea2fd2364c5f91debde6f9e2a
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-19 (Fri, 19 Jun 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
M src/server/routes/api/document/pubmed/searchPubmed.js
Log Message:
-----------
Merge pull request #756 from PathwayCommons/iss741_refactoring-find-PubMed
Pubmed articles by paperId
Commit: 8bf4980c0183d20c6cdb06ea4c409c436d02b08a
https://github.com/PathwayCommons/factoid/commit/8bf4980c0183d20c6cdb06ea4c409c436d02b08a
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-19 (Fri, 19 Jun 2020)
Changed paths:
M src/client/components/home.js
M src/styles/base.css
Log Message:
-----------
Punch up the text-decoration with bright white link
Commit: 2172cf55dfe82a372b8615bcf9d68d920a8d3a89
https://github.com/PathwayCommons/factoid/commit/2172cf55dfe82a372b8615bcf9d68d920a8d3a89
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-19 (Fri, 19 Jun 2020)
Changed paths:
A src/client/components/carousel.js
M src/client/components/editor/cy/defs.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/index.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/defs.js
M src/client/components/editor/explore-share.js
M src/client/components/editor/index.js
M src/client/components/editor/info-panel.js
M 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/home.js
A src/client/components/related-papers.js
M src/config.js
M src/model/element/element.js
M src/model/element/interaction.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
M src/styles/base.css
A src/styles/carousel.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/index.css
M src/styles/element-info/interaction-info.css
M src/styles/home.css
M src/styles/index.css
A src/styles/related-papers.css
M src/util/pubmed.js
Log Message:
-----------
Merge origin/iss753_homepage-tweaks-text into iss753_homepage-tweaks-text
Commit: 73b3c3bbb4d462331cf25a7ff2f3aeaccbb51028
https://github.com/PathwayCommons/factoid/commit/73b3c3bbb4d462331cf25a7ff2f3aeaccbb51028
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-22 (Mon, 22 Jun 2020)
Changed paths:
M src/client-env-vars.json
M src/client/components/home.js
M src/config.js
M src/styles/base.css
M src/styles/home.css
M src/styles/image/home-figure-fg-2.png
A src/styles/image/logo_harvardu.png
A src/styles/image/logo_ohsu.jpg
A src/styles/image/logo_utoronto.png
R src/styles/image/uni-logos-bw.png
R src/styles/image/uni-logos.png
Log Message:
-----------
Merge pull request #754 from PathwayCommons/iss753_homepage-tweaks-text
Iss753 homepage tweaks text
Commit: 763aeae4005cfc3e70584b2018e347da0e78b0a9
https://github.com/PathwayCommons/factoid/commit/763aeae4005cfc3e70584b2018e347da0e78b0a9
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-06-22 (Mon, 22 Jun 2020)
Changed paths:
M package-lock.json
M src/model/document/document.js
M src/model/element/entity-type.js
M src/model/element/entity.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Biopax additional attributes (#746)
* Updated biopax template format
* Consider dbxrefs for biopax
* A bug fix for reading organism id of entities during biopax export.
* Using ``typeOfGene`` property coming from grounding search service #737
* A little fix for #737
* Added pathwayName property to biopax template
Commit: 2c27f3b5290d6fe08a284e16eb9c947420b7d378
https://github.com/PathwayCommons/factoid/commit/2c27f3b5290d6fe08a284e16eb9c947420b7d378
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-23 (Tue, 23 Jun 2020)
Changed paths:
M src/client-env-vars.json
M src/client/components/document-management-components.js
M src/client/components/document-management.js
M src/client/components/editor/index.js
M src/client/components/home.js
M src/config.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/update.js
M src/util/email.js
Log Message:
-----------
- Drop context from email handling
- Fill doc functions retrieve their own information from provided
Commit: 1c6017ff6e971a603976b05e7e086ab476207e3f
https://github.com/PathwayCommons/factoid/commit/1c6017ff6e971a603976b05e7e086ab476207e3f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-23 (Tue, 23 Jun 2020)
Changed paths:
M src/util/email.js
Log Message:
-----------
Drop all nested variables and include only basic information required of
email.
Commit: b7a8b90867af9ca0e312082178f70e69436b80a4
https://github.com/PathwayCommons/factoid/commit/b7a8b90867af9ca0e312082178f70e69436b80a4
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-24 (Wed, 24 Jun 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Drop unused reference to ApiKey in RequestForm module
Commit: 67d6338feb6e338de8d506ada037717f2ea96562
https://github.com/PathwayCommons/factoid/commit/67d6338feb6e338de8d506ada037717f2ea96562
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-24 (Wed, 24 Jun 2020)
Changed paths:
M README.md
M src/config.js
Log Message:
-----------
Updated README for extra and missing environment variables
Commit: d786a051e7708782b65283bc4bd3e386e80a7d07
https://github.com/PathwayCommons/factoid/commit/d786a051e7708782b65283bc4bd3e386e80a7d07
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-24 (Wed, 24 Jun 2020)
Changed paths:
M README.md
M src/config.js
Log Message:
-----------
Revert "Updated README for extra and missing environment variables"
This reverts commit 67d6338feb6e338de8d506ada037717f2ea96562.
Whoops, intended to commit to the PR branch
Commit: c6b01679871fde8471afe135ca7427932723666d
https://github.com/PathwayCommons/factoid/commit/c6b01679871fde8471afe135ca7427932723666d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-06-24 (Wed, 24 Jun 2020)
Changed paths:
M README.md
Log Message:
-----------
Adding missing config variables and removing EMAIL_CONTEXT* entries.
Commit: 5b15f6461716d14f3e06a8ee7d3a009275bcf9df
https://github.com/PathwayCommons/factoid/commit/5b15f6461716d14f3e06a8ee7d3a009275bcf9df
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-06-25 (Thu, 25 Jun 2020)
Changed paths:
M README.md
M src/client-env-vars.json
M src/client/components/document-management-components.js
M src/client/components/document-management.js
M src/client/components/editor/index.js
M src/client/components/home.js
M src/config.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/update.js
M src/util/email.js
Log Message:
-----------
Merge pull request #761 from PathwayCommons/iss759_remove-context
Remove 'context'
Commit: c4f9e0ad8a9ade9fecfe60b1e42cf31b03ce4473
https://github.com/PathwayCommons/factoid/commit/c4f9e0ad8a9ade9fecfe60b1e42cf31b03ce4473
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-06-25 (Thu, 25 Jun 2020)
Changed paths:
M src/model/document/document.js
M src/model/element/entity.js
M src/model/element/interaction-type/interaction-type.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Entity related papers (#758)
* working on counting the entities in related papers calculations
* Handled some todos and fixed a typo
* Fixed a typo
* Fixes the bug for storing related papers mentioned in #758
Commit: 530a1ffbd9c8b3e4478e684099018856e4020b34
https://github.com/PathwayCommons/factoid/commit/530a1ffbd9c8b3e4478e684099018856e4020b34
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-06-26 (Fri, 26 Jun 2020)
Changed paths:
M src/client/components/editor/info-panel.js
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/interaction-info.js
M src/client/components/related-papers.js
M src/model/document/document.js
M src/model/element/element.js
M src/styles/editor/editor.css
M src/styles/related-papers.css
Log Message:
-----------
Related papers loading & notice
- Adds a notice to the related papers section when the calculation is in
progress.
- Automatically adds the related papers to the UI when the server sets them.
- Renames `relatedPaper` event to `relatedpaper`, to be consistent with all
other events.
- Limits the number of shown related papers to a maximum of six.
- Misc. fix to article title underline in the editor.
Commit: 722e8283272e2d9b9b2801d37898063b046c2883
https://github.com/PathwayCommons/factoid/commit/722e8283272e2d9b9b2801d37898063b046c2883
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-06-29 (Mon, 29 Jun 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/pubmed/searchPubmed.js
Log Message:
-----------
Use Crossref for more reliable Pubmed searches
Crossref searches get transformed into the Pubmed search result format, so no
other modules need to be changed.
Commit: f149a602c57bba30a9ff4fdc078ad69bc6477802
https://github.com/PathwayCommons/factoid/commit/f149a602c57bba30a9ff4fdc078ad69bc6477802
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-06-30 (Tue, 30 Jun 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/pubmed/searchPubmed.js
Log Message:
-----------
Revert "Use Crossref for more reliable Pubmed searches"
722e8283272e2d9b9b2801d37898063b046c2883
Commit: 1f0f9c84b394e9d8e3a1e560a5dae0447a04c1ed
https://github.com/PathwayCommons/factoid/commit/1f0f9c84b394e9d8e3a1e560a5dae0447a04c1ed
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-02 (Thu, 02 Jul 2020)
Changed paths:
M src/client/components/editor/info-panel.js
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/interaction-info.js
M src/client/components/related-papers.js
M src/model/document/document.js
M src/model/element/element.js
M src/styles/editor/editor.css
M src/styles/related-papers.css
Log Message:
-----------
Merge pull request #762 from PathwayCommons/relpprs-notice-refresh
Related papers loading & notice
Commit: 3de8fa7353669808098595f5cbad2f3e0ab08936
https://github.com/PathwayCommons/factoid/commit/3de8fa7353669808098595f5cbad2f3e0ab08936
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-02 (Thu, 02 Jul 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
Log Message:
-----------
Safe default if elements array does not exist.
Commit: eeb3dfb756a906e4b32184500eab109e5f6e3a7c
https://github.com/PathwayCommons/factoid/commit/eeb3dfb756a906e4b32184500eab109e5f6e3a7c
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-02 (Thu, 02 Jul 2020)
Changed paths:
M src/server/routes/api/document/pubmed/fetchPubmed.js
Log Message:
-----------
Merge pull request #766 from PathwayCommons/iss765_abstract-text-bug
Pubmed Article processing: Bug in processing text elements
Commit: 1774d3eae163f002b48ef1c511a0ae7bd41450fb
https://github.com/PathwayCommons/factoid/commit/1774d3eae163f002b48ef1c511a0ae7bd41450fb
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-02 (Thu, 02 Jul 2020)
Changed paths:
A .npmrc
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
Make the NODE_OPTION setting for max_old_space_size option configurable.
.npmrc has lower priority than environment= (docker).
Commit: e32fe3554c64b32602b382e733c9ea176a08a484
https://github.com/PathwayCommons/factoid/commit/e32fe3554c64b32602b382e733c9ea176a08a484
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-03 (Fri, 03 Jul 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
- Unify the PATCH endpoint to accept specific updates
- Admin
- call the POST endpoint for email (api key required)
- else call the modified PATCH endpoint (no api key required)
- Editor: Submit task calls modified PATCH. endpoint
Commit: 0ca4fc364b0ed8b64c5823b9526da1820da7ab92
https://github.com/PathwayCommons/factoid/commit/0ca4fc364b0ed8b64c5823b9526da1820da7ab92
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-06 (Mon, 06 Jul 2020)
Changed paths:
M src/client/components/document-management-components.js
Log Message:
-----------
Fixup the admin status icons; remove approved icon
Commit: e512becd0f38546ebcfbd473a7a2a1e842aa41e7
https://github.com/PathwayCommons/factoid/commit/e512becd0f38546ebcfbd473a7a2a1e842aa41e7
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-06 (Mon, 06 Jul 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
-----------
Drop debugging changes to indra.js
Commit: b494c7fb5b66ac53759f53d40b75df939ce6c66a
https://github.com/PathwayCommons/factoid/commit/b494c7fb5b66ac53759f53d40b75df939ce6c66a
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-06 (Mon, 06 Jul 2020)
Changed paths:
M src/client/components/document-management-components.js
M src/client/components/tasks.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #768 from PathwayCommons/iss760_refactor-api-patch
Admin: Refactoring PATCH endpoints
Commit: c7b7bc2fd9f95ccf276dc30759edcb32f73323bc
https://github.com/PathwayCommons/factoid/commit/c7b7bc2fd9f95ccf276dc30759edcb32f73323bc
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-06 (Mon, 06 Jul 2020)
Changed paths:
A .npmrc
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
Merge pull request #767 from
PathwayCommons/iss763_configure-max_old_space_size
Make the NODE_OPTION setting for max_old_space_size option configurable.
Commit: 6405118b75c5cf88e28d2b4d3bc8a5dbe37e1a93
https://github.com/PathwayCommons/factoid/commit/6405118b75c5cf88e28d2b4d3bc8a5dbe37e1a93
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-08 (Wed, 08 Jul 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
- Drop service for semantic search
- Use default SEMANTIC_SEARCH_BASE_URL
Commit: 3c8781ef0483572dcd38308d9e989c199fb7c54d
https://github.com/PathwayCommons/factoid/commit/3c8781ef0483572dcd38308d9e989c199fb7c54d
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-08 (Wed, 08 Jul 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
Merge pull request #772 from PathwayCommons/iss771_docker-semantic-search
Docker: Drop semantic search service
Commit: c5aa562ac267a8276f57fd82bdc5e7980f19eab5
https://github.com/PathwayCommons/factoid/commit/c5aa562ac267a8276f57fd82bdc5e7980f19eab5
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-07-09 (Thu, 09 Jul 2020)
Changed paths:
M src/client/components/editor/cy/tippy.js
Log Message:
-----------
Fixes tippy flipping behaviour, especially on small screens.
Previously, the popovers would fail to flip or would flip in a way that would
overlap the tapped node.
Commit: 2f4fecb383468e48486d037db62e4043ad42abef
https://github.com/PathwayCommons/factoid/commit/2f4fecb383468e48486d037db62e4043ad42abef
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-07-09 (Thu, 09 Jul 2020)
Changed paths:
M src/client/components/editor/title.js
M src/styles/editor/editor.css
Log Message:
-----------
Fixes the title spacing on the editor view
- This avoids the issue of the blue underline overstepping the bounds of the
text.
- This restores the ability of the text to be truncated with an ellipsis,
affecting articles with long titles.
Commit: 03d4c3e2031f9fab6de4ea47d120a70429a7e60f
https://github.com/PathwayCommons/factoid/commit/03d4c3e2031f9fab6de4ea47d120a70429a7e60f
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-15 (Wed, 15 Jul 2020)
Changed paths:
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/title.js
M src/styles/editor/editor.css
Log Message:
-----------
Merge pull request #773 from PathwayCommons/article-review
Article review
Commit: 4834cc003b00daac4d387e01e534129870218ad8
https://github.com/PathwayCommons/factoid/commit/4834cc003b00daac4d387e01e534129870218ad8
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-17 (Fri, 17 Jul 2020)
Changed paths:
M README.md
Log Message:
-----------
Related software section for other github and dockerhub remotes.
Commit: 47e2791c2e2094cd42fd84ffd3476cf49f0d3826
https://github.com/PathwayCommons/factoid/commit/47e2791c2e2094cd42fd84ffd3476cf49f0d3826
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-17 (Fri, 17 Jul 2020)
Changed paths:
M README.md
Log Message:
-----------
Update README.md
Co-authored-by: Max Franz <maxkfr...@gmail.com>
Commit: 31036a1cc281cc4a4b336a1ee1a1ca66afca2f7e
https://github.com/PathwayCommons/factoid/commit/31036a1cc281cc4a4b336a1ee1a1ca66afca2f7e
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-17 (Fri, 17 Jul 2020)
Changed paths:
M README.md
Log Message:
-----------
Update README.md
Co-authored-by: Max Franz <maxkfr...@gmail.com>
Commit: ed34c47d45b697aa2ee7b5bb71e1f31c6f41cc61
https://github.com/PathwayCommons/factoid/commit/ed34c47d45b697aa2ee7b5bb71e1f31c6f41cc61
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-17 (Fri, 17 Jul 2020)
Changed paths:
M README.md
Log Message:
-----------
Update README.md
Co-authored-by: Max Franz <maxkfr...@gmail.com>
Commit: 7e26228c81e3dea41c55cb77a340431a26aa2fd7
https://github.com/PathwayCommons/factoid/commit/7e26228c81e3dea41c55cb77a340431a26aa2fd7
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-17 (Fri, 17 Jul 2020)
Changed paths:
M README.md
Log Message:
-----------
Update README.md
Co-authored-by: Max Franz <maxkfr...@gmail.com>
Commit: 8149c21ec616e7643e1ef8a4758158e7d35ac48f
https://github.com/PathwayCommons/factoid/commit/8149c21ec616e7643e1ef8a4758158e7d35ac48f
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-17 (Fri, 17 Jul 2020)
Changed paths:
M README.md
Log Message:
-----------
Update README.md
Co-authored-by: Max Franz <maxkfr...@gmail.com>
Commit: c455c305e927a86870c7202e92fd448a3c42c058
https://github.com/PathwayCommons/factoid/commit/c455c305e927a86870c7202e92fd448a3c42c058
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-17 (Fri, 17 Jul 2020)
Changed paths:
M README.md
Log Message:
-----------
Update README.md
Co-authored-by: Max Franz <maxkfr...@gmail.com>
Commit: 994c4166502c330497666b1dc34e16320834c96f
https://github.com/PathwayCommons/factoid/commit/994c4166502c330497666b1dc34e16320834c96f
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-07-17 (Fri, 17 Jul 2020)
Changed paths:
M README.md
Log Message:
-----------
Update README.md
Co-authored-by: Max Franz <maxkfr...@gmail.com>
Commit: 6d614733a507263d3a5af24cab3c1f3617a63c28
https://github.com/PathwayCommons/factoid/commit/6d614733a507263d3a5af24cab3c1f3617a63c28
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-07-17 (Fri, 17 Jul 2020)
Changed paths:
M README.md
Log Message:
-----------
Merge pull request #781 from PathwayCommons/iss774_README-remote-links
README: Related software section ( github and dockerhub )
Commit: 8e1f8f99b8e4e1ba9e9d8e9d3aa79da90bc84980
https://github.com/PathwayCommons/factoid/commit/8e1f8f99b8e4e1ba9e9d8e9d3aa79da90bc84980
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-07-19 (Sun, 19 Jul 2020)
Changed paths:
M src/config.js
M src/model/element/element.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Related paper tweaks 775 (#777)
* Remove unused /related-papers/:id route
* use master grounding service by default, for testing
* el.toString
* use simple slice & comment out unused stuff
* quick and dirty first pass at #775; old mapping code commented out for
reference
* comment config
* apply double filtering of pmids for s.s. queries #775
1 - filter pmids from each template indra result
2 - filter pmid list just before sending to s.s. -- covers multitemplate case
(i.e. doc level)
chronological via pmid proxy (pmid is int, increasing over time)
* basic shuffle padding approach for low interaction results
@jvwong @metincansiper, could you test this?
* maybe this will filter out the bogus result from s.s. (same pmid as the
factoid)?
https://github.com/PathwayCommons/semantic-search/issues/16
@jvwong
* Clean up the console log and old commented out code segments.
* Handled some TODOs for making some constant variables configurable.
* Provide unique PMIDS for INDRA results before filtering.
* Update the default grounding search url which was temporarily changed for the
sake of testing.
Co-authored-by: metincansiper <metincansi...@gmail.com>
Co-authored-by: Jeffrey Wong <jvw...@gmail.com>
Commit: ec2a5684213a8360df5cbca50571414de47b58e9
https://github.com/PathwayCommons/factoid/commit/ec2a5684213a8360df5cbca50571414de47b58e9
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-07-22 (Wed, 22 Jul 2020)
Changed paths:
M README.md
M docker/.env
M package-lock.json
M package.json
M src/config.js
M src/server/index.js
Log Message:
-----------
AppSignal
Commit: 46a25d3ca71249ef06933aba7f4dcfa1811e1cb7
https://github.com/PathwayCommons/factoid/commit/46a25d3ca71249ef06933aba7f4dcfa1811e1cb7
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-29 (Wed, 29 Jul 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
- Tweak submit success: wrap text
- Bug in success explore link display
Commit: 5b9a9f976971159fca0a36bab7ecae1eabee1d67
https://github.com/PathwayCommons/factoid/commit/5b9a9f976971159fca0a36bab7ecae1eabee1d67
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-31 (Fri, 31 Jul 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
A src/styles/image/home-figure-2-slim.png
R src/styles/image/home-figure-2.jpg
A src/styles/image/home-figure-2.png
Log Message:
-----------
- Replaced background section 2 with detailed explore view image
- Alternate figure 2 for mobile
- Moved CTA #2 above footer; inverted color scheme
Commit: 59b84353f7fd154760833c7c8d9cc5ef5143eac7
https://github.com/PathwayCommons/factoid/commit/59b84353f7fd154760833c7c8d9cc5ef5143eac7
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-07-31 (Fri, 31 Jul 2020)
Changed paths:
M src/styles/image/home-figure-2-slim.png
M src/styles/image/home-figure-2.png
Log Message:
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Tweaking the text for figure 2
Commit: 420fd3de57c3bd081b8d24a9e831dd211f858030
https://github.com/PathwayCommons/factoid/commit/420fd3de57c3bd081b8d24a9e831dd211f858030
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-04 (Tue, 04 Aug 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
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Merge pull request #789 from PathwayCommons/iss787_popover-hangoer
Submit success: Wrapping url and text
Commit: ae92a2cf547fd1225fc8f697d7877358f94a6c0f
https://github.com/PathwayCommons/factoid/commit/ae92a2cf547fd1225fc8f697d7877358f94a6c0f
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-04 (Tue, 04 Aug 2020)
Changed paths:
M src/client/components/home.js
M src/styles/home.css
A src/styles/image/home-figure-2-slim.png
R src/styles/image/home-figure-2.jpg
A src/styles/image/home-figure-2.png
Log Message:
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Merge pull request #790 from PathwayCommons/iss786_homepage-how-to-explore
Homepage: How to explore; Reference audience
Commit: 5cd070ee75199935215d6f4b81cf2cb9af4191be
https://github.com/PathwayCommons/factoid/commit/5cd070ee75199935215d6f4b81cf2cb9af4191be
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-05 (Wed, 05 Aug 2020)
Changed paths:
M src/client/components/carousel.js
M src/model/document/document.js
M src/styles/carousel.css
Log Message:
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- Rearrange order of article text placed atop
- Shift background to bottom
- On hover, show document text and datestamp
Commit: 1e0d3d8d45e4f2006862bb02ab01b3def5e3a134
https://github.com/PathwayCommons/factoid/commit/1e0d3d8d45e4f2006862bb02ab01b3def5e3a134
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-05 (Wed, 05 Aug 2020)
Changed paths:
M src/styles/carousel.css
Log Message:
-----------
lint
Commit: 8690857537a4f31ff39cc3cffc67f9f81fa64d1d
https://github.com/PathwayCommons/factoid/commit/8690857537a4f31ff39cc3cffc67f9f81fa64d1d
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-05 (Wed, 05 Aug 2020)
Changed paths:
M src/styles/carousel.css
Log Message:
-----------
Hide background bleed-through on bottom hovered panel (left/right edge)
Commit: 334391c94d2f1d2c50c5ff53f8ffee2b1672af03
https://github.com/PathwayCommons/factoid/commit/334391c94d2f1d2c50c5ff53f8ffee2b1672af03
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-05 (Wed, 05 Aug 2020)
Changed paths:
M src/client/components/carousel.js
M src/model/document/document.js
M src/styles/carousel.css
Log Message:
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Merge pull request #792 from PathwayCommons/iss786_info-panel-text
Carousel panel: Text update
Commit: 45662830b8e17f22ac6f017d914c10f222d6d967
https://github.com/PathwayCommons/factoid/commit/45662830b8e17f22ac6f017d914c10f222d6d967
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-08-07 (Fri, 07 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Query related papers for each factoid element and the whole document
synchronously.
Commit: 7b0d539ffe5d9d179630c40e655cffc58bcda1b9
https://github.com/PathwayCommons/factoid/commit/7b0d539ffe5d9d179630c40e655cffc58bcda1b9
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-08-07 (Fri, 07 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
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Remove console.log statements
Commit: 0449a938f618af20fc9c98c11203a790cc19e6b1
https://github.com/PathwayCommons/factoid/commit/0449a938f618af20fc9c98c11203a790cc19e6b1
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-08-10 (Mon, 10 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Query related papers for the elements asynchronously as it is used to be.
Just query the related papers for the whole document as seperate from them.
Commit: d8436abdf2d59323a4fe526261a281b97d9c8a48
https://github.com/PathwayCommons/factoid/commit/d8436abdf2d59323a4fe526261a281b97d9c8a48
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-10 (Mon, 10 Aug 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
Log Message:
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Search PubMed with user's paperId then look through those (top 10)
corresponding articles for a match.
Commit: c549a069465648f0cec4f96af399cf6b7ea21733
https://github.com/PathwayCommons/factoid/commit/c549a069465648f0cec4f96af399cf6b7ea21733
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-11 (Tue, 11 Aug 2020)
Changed paths:
M src/server/routes/api/document/pubmed/index.js
Log Message:
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Merge pull request #796 from PathwayCommons/iss795_try-match-ESEARCH-results
Search PubMed search hit articles for match
Commit: 4659e93587bf78b0e93cea13d90465dc559d9c89
https://github.com/PathwayCommons/factoid/commit/4659e93587bf78b0e93cea13d90465dc559d9c89
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-08-11 (Tue, 11 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
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Merge pull request #793 from PathwayCommons/related_papers_fetch
Query related papers for the whole document after querying the related papers
for elements.
Commit: ff2d1b32fedb9cac000e88c1efa9a57065b4416d
https://github.com/PathwayCommons/factoid/commit/ff2d1b32fedb9cac000e88c1efa9a57065b4416d
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-08-11 (Tue, 11 Aug 2020)
Changed paths:
M README.md
M docker/.env
M package-lock.json
M package.json
M src/config.js
M src/server/index.js
Log Message:
-----------
Merge pull request #783 from PathwayCommons/appsignal
AppSignal
Commit: 8b5ee5e28f5e55754987021a64bdaccfd19f4915
https://github.com/PathwayCommons/factoid/commit/8b5ee5e28f5e55754987021a64bdaccfd19f4915
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-11 (Tue, 11 Aug 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
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Corresponding updates for changes in grounding search and APP signal support
Commit: 7b1f45fd8f32ff2ca7569ebb3021ed6f7b52f0a7
https://github.com/PathwayCommons/factoid/commit/7b1f45fd8f32ff2ca7569ebb3021ed6f7b52f0a7
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-11 (Tue, 11 Aug 2020)
Changed paths:
M docker/.env
Log Message:
-----------
Include the dev key
Commit: 7bd3369abe5601a0c6434960f3c75c185579c83f
https://github.com/PathwayCommons/factoid/commit/7bd3369abe5601a0c6434960f3c75c185579c83f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-11 (Tue, 11 Aug 2020)
Changed paths:
M docker/.env
Log Message:
-----------
Remove the dev key in .env
Commit: 055ece7eecd864b4f3291550f2edf2ad23e12434
https://github.com/PathwayCommons/factoid/commit/055ece7eecd864b4f3291550f2edf2ad23e12434
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-11 (Tue, 11 Aug 2020)
Changed paths:
M README.md
M docker/.env
M package-lock.json
M package.json
M src/config.js
M src/server/index.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge branch 'unstable' into docker-grounding-updates
# Conflicts:
# docker/.env
Commit: 0627f9d734a1bab0ddf4f98794ce9e9e3e85fc44
https://github.com/PathwayCommons/factoid/commit/0627f9d734a1bab0ddf4f98794ce9e9e3e85fc44
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-11 (Tue, 11 Aug 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
Merge pull request #797 from PathwayCommons/docker-grounding-updates
Docker grounding updates
Commit: d498d792bf788371526a639f5f821761521eada9
https://github.com/PathwayCommons/factoid/commit/d498d792bf788371526a639f5f821761521eada9
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-08-12 (Wed, 12 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #793 from PathwayCommons/related_papers_fetch
Query related papers for the whole document after querying the related papers
for elements.
Commit: f34823148f67c069dd81898cff2a523505a8071f
https://github.com/PathwayCommons/factoid/commit/f34823148f67c069dd81898cff2a523505a8071f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-12 (Wed, 12 Aug 2020)
Changed paths:
M README.md
M docker/.env
M package-lock.json
M package.json
M src/config.js
M src/server/index.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge branch 'unstable' into docker-grounding-updates
# Conflicts:
# docker/.env
Commit: f227c323369aabffc029d92a53082710149d91d1
https://github.com/PathwayCommons/factoid/commit/f227c323369aabffc029d92a53082710149d91d1
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-08-12 (Wed, 12 Aug 2020)
Changed paths:
M README.md
M docker/.env
M package-lock.json
M package.json
M src/config.js
M src/server/index.js
Log Message:
-----------
Merge pull request #783 from PathwayCommons/appsignal
AppSignal
Commit: 327d786df83a4735fe86029cdf23798c0a3fac47
https://github.com/PathwayCommons/factoid/commit/327d786df83a4735fe86029cdf23798c0a3fac47
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-12 (Wed, 12 Aug 2020)
Changed paths:
M docker/.env
M docker/docker-compose.yml
Log Message:
-----------
Merge pull request #797 from PathwayCommons/docker-grounding-updates
Docker grounding updates
Commit: 12e34e20c7bb1982deae1c28d054e892814f632b
https://github.com/PathwayCommons/factoid/commit/12e34e20c7bb1982deae1c28d054e892814f632b
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-12 (Wed, 12 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge branch 'iss798_ncbi-linkouts' of
https://github.com/PathwayCommons/factoid into iss798_ncbi-linkouts
Commit: b33381e7e503c71a67702fd11fe583a8c7d0d6f4
https://github.com/PathwayCommons/factoid/commit/b33381e7e503c71a67702fd11fe583a8c7d0d6f4
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-12 (Wed, 12 Aug 2020)
Changed paths:
M README.md
M src/client-env-vars.json
M src/client/components/element-info/entity-assoc-display.js
M src/config.js
M src/model/element/entity.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
- Make use of the grounding-search dbName and dbPrefix to linkout to source
via identifiers.org
- Related papers/indra;js makes use of dbName
Commit: 8b310ecc106b57e154e4f8f700f9f4af94a23838
https://github.com/PathwayCommons/factoid/commit/8b310ecc106b57e154e4f8f700f9f4af94a23838
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-14 (Fri, 14 Aug 2020)
Changed paths:
M README.md
M src/client-env-vars.json
M src/client/components/element-info/entity-assoc-display.js
M src/config.js
M src/model/element/entity.js
M src/server/routes/api/document/indra.js
Log Message:
-----------
Merge pull request #800 from PathwayCommons/iss798_ncbi-linkouts
Utilize the database information provided by grounding-search
Commit: 4e5ee6744da181578b21bd6194ca4a7eb7e6102c
https://github.com/PathwayCommons/factoid/commit/4e5ee6744da181578b21bd6194ca4a7eb7e6102c
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-14 (Fri, 14 Aug 2020)
Changed paths:
M docker/docker-compose.yml
Log Message:
-----------
Integrate the grounding and indexer services into one.
Commit: da166de5d87aee742b2b8f0906d1ef1b56e6eec3
https://github.com/PathwayCommons/factoid/commit/da166de5d87aee742b2b8f0906d1ef1b56e6eec3
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-17 (Mon, 17 Aug 2020)
Changed paths:
A src/server/routes/api/document/pubmed/linkPubmed.js
Log Message:
-----------
A wrapper module for the ELINK EUTIL.
Commit: 8e89bc6c57c1b7044654406d2c02cdac8956dd1f
https://github.com/PathwayCommons/factoid/commit/8e89bc6c57c1b7044654406d2c02cdac8956dd1f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-17 (Mon, 17 Aug 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
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Abstract the semantic search service in indra module.
Commit: 358e1b83502d4f2ad8d2df47506fbd3f7d8c8786
https://github.com/PathwayCommons/factoid/commit/358e1b83502d4f2ad8d2df47506fbd3f7d8c8786
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-17 (Mon, 17 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
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Prototype: Retrieve related papers for doc entirely from ELINK service
Commit: 88b6814179525baab85f26e0f978a7d203a29133
https://github.com/PathwayCommons/factoid/commit/88b6814179525baab85f26e0f978a7d203a29133
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-17 (Mon, 17 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Set the doc-level related papers on initial paperId submission.
Commit: 08fe4f3a70e32a666edf76f72f8aad9d5ca0540e
https://github.com/PathwayCommons/factoid/commit/08fe4f3a70e32a666edf76f72f8aad9d5ca0540e
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-17 (Mon, 17 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Bug in setting doc-level relatedPapers key for pmid
Commit: 5f6254a6f387d0bb065d7d7b00c50a23341f2ff2
https://github.com/PathwayCommons/factoid/commit/5f6254a6f387d0bb065d7d7b00c50a23341f2ff2
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-17 (Mon, 17 Aug 2020)
Changed paths:
M docker/docker-compose.yml
Log Message:
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Merge pull request #802 from PathwayCommons/iss76_grounding-search-boot
Integrate the grounding and indexer services into one.
Commit: 20f3f328f73a013bfc8382076c7b3a4d5e5efe82
https://github.com/PathwayCommons/factoid/commit/20f3f328f73a013bfc8382076c7b3a4d5e5efe82
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-17 (Mon, 17 Aug 2020)
Changed paths:
M ci.sh
Log Message:
-----------
Define a start script, default to 'start'
Commit: 56f12b8198358f381ff833dff2c719963b15af0a
https://github.com/PathwayCommons/factoid/commit/56f12b8198358f381ff833dff2c719963b15af0a
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-17 (Mon, 17 Aug 2020)
Changed paths:
M ci.sh
Log Message:
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Merge pull request #803 from PathwayCommons/pr802_define_start_script
Customize the ci.sh start script name
Commit: 535218ff2d6c23f6e5c5e3aad2b5764e379be599
https://github.com/PathwayCommons/factoid/commit/535218ff2d6c23f6e5c5e3aad2b5764e379be599
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-18 (Tue, 18 Aug 2020)
Changed paths:
M README.md
M ci.sh
M docker/docker-compose.yml
M src/client-env-vars.json
M src/client/components/element-info/entity-assoc-display.js
M src/config.js
M src/model/element/entity.js
M src/server/routes/api/document/indra.js
Log Message:
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Merge branch 'unstable' into iss801_elink-related-papers
# Conflicts:
# src/server/routes/api/document/indra.js
Commit: e9927644c339a82ade743c0eaf110891cd753455
https://github.com/PathwayCommons/factoid/commit/e9927644c339a82ade743c0eaf110891cd753455
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-18 (Tue, 18 Aug 2020)
Changed paths:
M src/server/routes/api/document/indra.js
Log Message:
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Resolve conflict in INDRA.js
Commit: 9e78a92e2e05496371cb1300a1dc4f5db2df647b
https://github.com/PathwayCommons/factoid/commit/9e78a92e2e05496371cb1300a1dc4f5db2df647b
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-19 (Wed, 19 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/server/routes/api/document/indra.js
A src/server/routes/api/document/pubmed/linkPubmed.js
Log Message:
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Merge pull request #805 from PathwayCommons/iss801_elink-related-papers
Retrieve doc-level related papers via ELINK
Commit: 17fa30686e5c29522a38cd667d70301f2b99e3f7
https://github.com/PathwayCommons/factoid/commit/17fa30686e5c29522a38cd667d70301f2b99e3f7
Author: metincansiper <metincansi...@gmail.com>
Date: 2020-08-19 (Wed, 19 Aug 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
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Omit chemicals while creating organisms dropdown component. (#804)
Commit: 881396bc8e079fd5275d31b5bcd5b1e8894d8a23
https://github.com/PathwayCommons/factoid/commit/881396bc8e079fd5275d31b5bcd5b1e8894d8a23
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-20 (Thu, 20 Aug 2020)
Changed paths:
M src/client/components/element-info/entity-assoc-display.js
Log Message:
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For chemicals, show the summary from ChEBI if available.
Commit: b6705f1150f25213e8300c6f9eb373068186d48e
https://github.com/PathwayCommons/factoid/commit/b6705f1150f25213e8300c6f9eb373068186d48e
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-08-20 (Thu, 20 Aug 2020)
Changed paths:
M src/client/components/editor/index.js
Log Message:
-----------
Resolves "Can't go home from explore view #788"
Commit: f73db8027ca106c1e917b1c760be4bda6b65a4df
https://github.com/PathwayCommons/factoid/commit/f73db8027ca106c1e917b1c760be4bda6b65a4df
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-20 (Thu, 20 Aug 2020)
Changed paths:
M src/client/components/element-info/entity-assoc-display.js
Log Message:
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Merge pull request #806 from PathwayCommons/iss799_chemical-summary-info
For chemicals, show the summary from ChEBI if available.
Commit: f92ff72a60734137ce99825f62875d559d66f6c1
https://github.com/PathwayCommons/factoid/commit/f92ff72a60734137ce99825f62875d559d66f6c1
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-08-20 (Thu, 20 Aug 2020)
Changed paths:
M src/client/components/editor/index.js
Log Message:
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Merge pull request #807 from PathwayCommons/back-home-788
Resolves "Can't go home from explore view #788"
Commit: a6f1a129663d76728053f9563112b578e57d29fa
https://github.com/PathwayCommons/factoid/commit/a6f1a129663d76728053f9563112b578e57d29fa
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-21 (Fri, 21 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
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Combine doc related papers with article fill .
Commit: 2ab31d22b4a14d509386980401b54609c64c207d
https://github.com/PathwayCommons/factoid/commit/2ab31d22b4a14d509386980401b54609c64c207d
Author: Jeffrey <jvw...@gmail.com>
Date: 2020-08-21 (Fri, 21 Aug 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
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Merge pull request #808 from PathwayCommons/iss801_related-papers-with-article
Fill related papers for doc with article info retrieval
Commit: d090b86b1999966976f1aaa38d7fcbcf5e49d99f
https://github.com/PathwayCommons/factoid/commit/d090b86b1999966976f1aaa38d7fcbcf5e49d99f
Author: Jeffrey Wong <jvw...@gmail.com>
Date: 2020-08-21 (Fri, 21 Aug 2020)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
0.9.0
Commit: 09bd90182d1a599fe9bf9aff4cbb0efeeb762fb3
https://github.com/PathwayCommons/factoid/commit/09bd90182d1a599fe9bf9aff4cbb0efeeb762fb3
Author: Max Franz <maxkfr...@gmail.com>
Date: 2020-08-21 (Fri, 21 Aug 2020)
Changed paths:
M .gitignore
A .npmrc
M .travis.yml
M README.md
M ci.sh
M docker/.env
M docker/docker-compose.yml
M package-lock.json
M package.json
M src/client-env-vars.json
M src/client/client-util/file.js
A src/client/components/carousel.js
M src/client/components/document-management-components.js
M src/client/components/document-management.js
M src/client/components/editor/cy/defs.js
M src/client/components/editor/cy/doc.js
M src/client/components/editor/cy/index.js
M src/client/components/editor/cy/tippy.js
M src/client/components/editor/cy/viewport.js
M src/client/components/editor/defs.js
A src/client/components/editor/explore-share.js
A src/client/components/editor/help.js
M src/client/components/editor/index.js
A src/client/components/editor/info-panel.js
A src/client/components/editor/submit.js
A src/client/components/editor/title.js
M 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/home.js
A src/client/components/native-share.js
A src/client/components/related-papers.js
R src/client/components/share.js
M src/client/components/tasks.js
A src/client/components/twitter-share.js
M src/config.js
M src/model/document/document.js
M src/model/element/complex.js
M src/model/element/element.js
M src/model/element/entity-type.js
M src/model/element/entity.js
M src/model/element/interaction-type/binding.js
M src/model/element/interaction-type/demethylation.js
M src/model/element/interaction-type/dephosphorylation.js
M src/model/element/interaction-type/deubiquitination.js
M src/model/element/interaction-type/interaction-type.js
M src/model/element/interaction-type/interaction.js
M src/model/element/interaction-type/methylation.js
M src/model/element/interaction-type/modification.js
M src/model/element/interaction-type/phosphorylation.js
M src/model/element/interaction-type/transcription-translation.js
M src/model/element/interaction-type/ubiquitination.js
M src/model/element/interaction.js
M src/server/index.js
A src/server/routes/api/document/export.js
M src/server/routes/api/document/index.js
A src/server/routes/api/document/indra.js
M src/server/routes/api/document/pubmed/fetchPubmed.js
M src/server/routes/api/document/pubmed/index.js
A src/server/routes/api/document/pubmed/linkPubmed.js
M src/server/routes/api/document/pubmed/searchPubmed.js
A src/server/routes/api/document/update.js
M src/server/routes/api/index.js
A src/server/update-cron.js
M src/styles/base.css
A src/styles/carousel.css
M src/styles/custom-icons.css
M src/styles/editor/editor.css
M src/styles/editor/undo-remove.css
M src/styles/element-info/element-info.css
M src/styles/element-info/entity-info.css
M src/styles/element-info/index.css
M src/styles/element-info/interaction-info.css
M src/styles/home.css
M src/styles/image/home-figure-1.jpg
A src/styles/image/home-figure-2-slim.png
R src/styles/image/home-figure-2.jpg
A src/styles/image/home-figure-2.png
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A src/styles/image/home-figure-fg-2.png
A src/styles/image/home-figure-old-2.jpg
A src/styles/image/home-figure-old-3.jpg
A src/styles/image/logo_harvardu.png
A src/styles/image/logo_ohsu.jpg
A src/styles/image/logo_utoronto.png
A src/styles/image/sample-editor-screen-fade.mp4
A src/styles/image/sample-editor-screen.m4v
A src/styles/image/share-white.svg
A src/styles/image/share.svg
R src/styles/image/uni-logos-bw.png
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M src/styles/index.css
A src/styles/native-share.css
A src/styles/related-papers.css
R src/styles/share.css
M src/styles/tasks.css
A src/styles/twitter-share.css
M src/styles/vars.css
A src/util/document.js
M src/util/email.js
M src/util/index.js
M src/util/pubmed.js
M test/pubmed/fetchPubmed.js
A test/pubmed/pmid_151222.xml
Log Message:
-----------
Merge pull request #809 from PathwayCommons/v0.9.0
Version 0.9.0
Compare:
https://github.com/PathwayCommons/factoid/compare/405ecbda280a...09bd90182d1a
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