Branch: refs/heads/master
  Home:   https://github.com/PathwayCommons/factoid
  Commit: 8e48819a79be69553ff7911618a5571e639190e4
      
https://github.com/PathwayCommons/factoid/commit/8e48819a79be69553ff7911618a5571e639190e4
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-01 (Thu, 01 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  Node text input 'x' icon does not clear existing text #165

Closes #165


  Commit: ad9bd5fb11220ac6e27d17b032e7e029270a166a
      
https://github.com/PathwayCommons/factoid/commit/ad9bd5fb11220ac6e27d17b032e7e029270a166a
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-01 (Thu, 01 Mar 2018)

  Changed paths:
    M src/model/document/document.js
    M src/server/routes/api/document/index.js

  Log Message:
  -----------
  Refactor layout running from POST:/api/document to document.applyLayout()

As before, the layout is run on a headless Cytoscape instance.  The final 
positions are applied to the document elements after the layout has finished 
running (async).  Thus, document.applyLayout() is mostly useful for serverside 
usecases.  For example, it could be useful as a clean-up step for a document 
that was created outside of UI or in a non-graph UI.


  Commit: 4b34d3b4589c6c6c3a2c591c12ebeaedf03a49cc
      
https://github.com/PathwayCommons/factoid/commit/4b34d3b4589c6c6c3a2c591c12ebeaedf03a49cc
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-01 (Thu, 01 Mar 2018)

  Log Message:
  -----------
  Do not optimistically mark an entity as completed from reach.  The entity is 
marked as completed only if the association is successfully retrieved from the 
element association services.


  Commit: 4497a132ae3382d9324d461385de2d8421fc2ec1
      
https://github.com/PathwayCommons/factoid/commit/4497a132ae3382d9324d461385de2d8421fc2ec1
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-01 (Thu, 01 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/base.css

  Log Message:
  -----------
  Modify home page for new landing page design


  Commit: 4e2807722ab59ea60141d3a38ed031369c93e440
      
https://github.com/PathwayCommons/factoid/commit/4e2807722ab59ea60141d3a38ed031369c93e440
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-02 (Fri, 02 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/base.css
    M src/styles/home.css
    A src/styles/image/factoid-hero-splash.jpg

  Log Message:
  -----------
  Landing page hero section styling/design


  Commit: 8f92aaa907251c519a2e68ff1190dcb0c3c96a90
      
https://github.com/PathwayCommons/factoid/commit/8f92aaa907251c519a2e68ff1190dcb0c3c96a90
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-02 (Fri, 02 Mar 2018)

  Changed paths:
    R src/styles/image/factoid-hero-splash.jpg
    A src/styles/image/hero-splash.jpg

  Log Message:
  -----------
  add the correct splash, delete the wrong one


  Commit: e36e293b4b44a07bc579002e5d2f68e28f29e6d1
      
https://github.com/PathwayCommons/factoid/commit/e36e293b4b44a07bc579002e5d2f68e28f29e6d1
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-02 (Fri, 02 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  Minor text changes


  Commit: a5608df9aea0869a7461976219e4c2b99e2c3d1f
      
https://github.com/PathwayCommons/factoid/commit/a5608df9aea0869a7461976219e4c2b99e2c3d1f
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-05 (Mon, 05 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  Minor layout changes to the 'how does factoid work' section


  Commit: 5952ef80c7a220afdb6d59bf84c90cbfe036e1d1
      
https://github.com/PathwayCommons/factoid/commit/5952ef80c7a220afdb6d59bf84c90cbfe036e1d1
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-05 (Mon, 05 Mar 2018)

  Changed paths:
    M src/client/components/home.js

  Log Message:
  -----------
  Team and contact section skeletons


  Commit: f8cfe6cd8e3e51bfb14fef79c191c5e8b8b0a509
      
https://github.com/PathwayCommons/factoid/commit/f8cfe6cd8e3e51bfb14fef79c191c5e8b8b0a509
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-05 (Mon, 05 Mar 2018)

  Changed paths:
    M src/client/components/home.js

  Log Message:
  -----------
  generic contact description text


  Commit: 4a0de04ed8a93848eea8a1b293af2f27a46b79b0
      
https://github.com/PathwayCommons/factoid/commit/4a0de04ed8a93848eea8a1b293af2f27a46b79b0
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-05 (Mon, 05 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  Better layout and css for the team and contact pages


  Commit: 87e83425e129660e5e87b3a01afc587c376f487d
      
https://github.com/PathwayCommons/factoid/commit/87e83425e129660e5e87b3a01afc587c376f487d
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-05 (Mon, 05 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  navbar links move to correct ids


  Commit: a90497766589d2dea097dfbe458ba5c04ea1c3c2
      
https://github.com/PathwayCommons/factoid/commit/a90497766589d2dea097dfbe458ba5c04ea1c3c2
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-06 (Tue, 06 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  Change contact link to the pathway commons support group


  Commit: fa54f42cb0bf37f60b23ab074221c7b76d9ce55a
      
https://github.com/PathwayCommons/factoid/commit/fa54f42cb0bf37f60b23ab074221c7b76d9ce55a
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-06 (Tue, 06 Mar 2018)

  Changed paths:
    M src/styles/home.css

  Log Message:
  -----------
  nav link font size is now the same as regular landing page text


  Commit: ef7d143c04519d6284f241c7172f283db2dc22dc
      
https://github.com/PathwayCommons/factoid/commit/ef7d143c04519d6284f241c7172f283db2dc22dc
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-06 (Tue, 06 Mar 2018)

  Changed paths:
    M src/styles/base.css
    M src/styles/home.css

  Log Message:
  -----------
  general css width/height changes for the landing page


  Commit: 70f58b530133a48adf0607d8b90b31eeb3014027
      
https://github.com/PathwayCommons/factoid/commit/70f58b530133a48adf0607d8b90b31eeb3014027
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-07 (Wed, 07 Mar 2018)

  Changed paths:
    M src/client/components/editor/cy/defs.js

  Log Message:
  -----------
  Reduce the minimum zoom level from 1 to 0.5.  This lets the user zoom out 
twice as much as before.

Ref : Networks not initially 'fit to screen', elements offscreen #197


  Commit: 455b87ba6e207f6acb9c767bd076cdf0e286250f
      
https://github.com/PathwayCommons/factoid/commit/455b87ba6e207f6acb9c767bd076cdf0e286250f
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-07 (Wed, 07 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/styles/element-info/entity-info.css
    M src/styles/vars.css

  Log Message:
  -----------
  Add a green check in place of the forward icon for completed entities.

Ref : Explicit indication that entity is 'complete' #194


  Commit: bf1c2b6d8662817599cc440f042b3cac83b722ba
      
https://github.com/PathwayCommons/factoid/commit/bf1c2b6d8662817599cc440f042b3cac83b722ba
  Author: metincansiper <metincansi...@gmail.com>
  Date:   2018-03-08 (Thu, 08 Mar 2018)

  Changed paths:
    M src/server/routes/api/document/reach.js

  Log Message:
  -----------
  Use PubChem results for grounding small molecules in entity tooltip search 
#201


  Commit: 8750ea878a5e9fee6830cfe89a990cb522b70cb9
      
https://github.com/PathwayCommons/factoid/commit/8750ea878a5e9fee6830cfe89a990cb522b70cb9
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-08 (Thu, 08 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/client/components/popover/tooltip.js

  Log Message:
  -----------
  Add back tooltips for back and forward buttons in entity grounding wizard.

- Add tooltips.
- Increase default tooltip delay from 500ms to 1000ms to make them less 
annoying.

Explicit indication that entity is 'complete' #194


  Commit: c8dba0b1ef1da9b2333bb4898f28f2563f1340ed
      
https://github.com/PathwayCommons/factoid/commit/c8dba0b1ef1da9b2333bb4898f28f2563f1340ed
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-08 (Thu, 08 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/base.css
    M src/styles/home.css
    A src/styles/image/hero-splash.jpg

  Log Message:
  -----------
  Merge pull request #198 from PathwayCommons/landing-page

Landing page skeleton


  Commit: 3c1b7a3a2b0d2d48cacc71c8fac120839ad8148f
      
https://github.com/PathwayCommons/factoid/commit/3c1b7a3a2b0d2d48cacc71c8fac120839ad8148f
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-08 (Thu, 08 Mar 2018)

  Changed paths:
    M src/server/routes/api/element-association/pubchem.js

  Log Message:
  -----------
  Clean up pubchem service

- Make sure namespace is available for aggregate service
- Add synonyms for both table and plain json queries
- Use first synonym as backup name -- sometimes pubchem gives no main name for 
a chemical
- Cleans up case of names -- always use 'Title case'.  Sometimes pubchem uses 
'ALL CAPS' or 'lower case'.  They're not consistent.
- Use traditional iupac name by default

See also #201


  Commit: 13b488d457f15d290646060823e2343b73ba4be3
      
https://github.com/PathwayCommons/factoid/commit/13b488d457f15d290646060823e2343b73ba4be3
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-08 (Thu, 08 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/config.js
    M src/server/routes/api/element-association/aggregate.js
    M src/server/routes/api/element-association/pubchem.js

  Log Message:
  -----------
  Switch chebi to pubchem in user-generated groundings #201


  Commit: 47f8f657db6c4a81ccea951d7ceb0b70115abab3
      
https://github.com/PathwayCommons/factoid/commit/47f8f657db6c4a81ccea951d7ceb0b70115abab3
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-08 (Thu, 08 Mar 2018)

  Changed paths:
    M src/server/routes/api/element-association/index.js

  Log Message:
  -----------
  Send HTTP 500 on failed element association queries


  Commit: 04c1f01d6eb3b36a431ab13eb259e3b1adbdb455
      
https://github.com/PathwayCommons/factoid/commit/04c1f01d6eb3b36a431ab13eb259e3b1adbdb455
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-08 (Thu, 08 Mar 2018)

  Changed paths:
    M src/server/routes/api/element-association/aggregate.js

  Log Message:
  -----------
  Log failed aggregate requests


  Commit: 7cad206747b485d3ecaaed2d57c2375ed007b3e5
      
https://github.com/PathwayCommons/factoid/commit/7cad206747b485d3ecaaed2d57c2375ed007b3e5
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-09 (Fri, 09 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  our mission section for the landing page, css refactor


  Commit: 1773d9a50281efa3ac149a7d8ba1aa1c0512bed1
      
https://github.com/PathwayCommons/factoid/commit/1773d9a50281efa3ac149a7d8ba1aa1c0512bed1
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-12 (Mon, 12 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  add specific copy for biologists and journals


  Commit: b19a9ab5538b0985b3cb615c977906fbbaee4eaa
      
https://github.com/PathwayCommons/factoid/commit/b19a9ab5538b0985b3cb615c977906fbbaee4eaa
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M .travis.yml

  Log Message:
  -----------
  Turn off node@6 and node@7 for travis


  Commit: ea6b2479ffbd9edebae3b3b6c5d1e702507e2411
      
https://github.com/PathwayCommons/factoid/commit/ea6b2479ffbd9edebae3b3b6c5d1e702507e2411
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  EntityInfo : Limit the number of displayed synonyms to 10 in the entity 
wizard popovers

This is a simple solution to #202.  A more sophisticated solution may be 
necessary if Pubchem's sorting is not adequate.


  Commit: af25d5fb84da0041f773c74843727749487eed1d
      
https://github.com/PathwayCommons/factoid/commit/af25d5fb84da0041f773c74843727749487eed1d
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M src/config.js

  Log Message:
  -----------
  Change the default reach instance to point to localhost


  Commit: 37fbe07dff5e7d1029eea34b569cee8421cf5e08
      
https://github.com/PathwayCommons/factoid/commit/37fbe07dff5e7d1029eea34b569cee8421cf5e08
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  Allow a user to click the "Unmodified" radio directly even when the state is 
already unmodified.

Users tend to click it rather than the next button.


  Commit: a5ea4a3171d3f3b1108dde237000873c210bf624
      
https://github.com/PathwayCommons/factoid/commit/a5ea4a3171d3f3b1108dde237000873c210bf624
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M src/client/components/editor/cy/stylesheet.js

  Log Message:
  -----------
  Reduce the extra hit area for the edgehandles.

Users tend to accidentally get into the draw-an-edge state.


  Commit: bc71467c53875d723e904305d681bf65b14fced1
      
https://github.com/PathwayCommons/factoid/commit/bc71467c53875d723e904305d681bf65b14fced1
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M src/client/components/editor/cy/tippy.js

  Log Message:
  -----------
  Allow double clicking nodes to open them

Some users double click for whatever reason, so now we allow both regular 
clicking and double clicking to open nodes.


  Commit: 4b24d0b934a59f1f4339dfd7890eb85409dfc6f1
      
https://github.com/PathwayCommons/factoid/commit/4b24d0b934a59f1f4339dfd7890eb85409dfc6f1
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M src/client/components/editor/cy/edgehandles.js

  Log Message:
  -----------
  Allow tap-tap to create edge in draw mode.

Some users try to do this rather than drag.


  Commit: 96ac816e3d292c2f7a2a7ced0a9f5305ffa8248c
      
https://github.com/PathwayCommons/factoid/commit/96ac816e3d292c2f7a2a7ced0a9f5305ffa8248c
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M src/client/components/editor/cy/edgehandles.js

  Log Message:
  -----------
  Tapping the background allows the user to cancel interaction drawing

Users try to do this to cancel rather than toggling the button.


  Commit: 86e077512cc90ba8472654c49067fac169d627db
      
https://github.com/PathwayCommons/factoid/commit/86e077512cc90ba8472654c49067fac169d627db
  Author: Dylan Fong <dylanfong...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M src/server/routes/api/document/index.js
    M src/server/routes/api/document/reach.js

  Log Message:
  -----------
  log error message when the reach provider fails (#205)

* log error message when the reach provider fails
- clean up require statements

* Set response status to 500 on reach doc error
- log error in the main http post function instead of the fill doc function

* rethrow reach erros after logging them

* log timeouts for reach service
- logs error when reach takes too long to respond
- adds reach response time limit to config
- todo still need to change server response to 504

* send 504 when REACH times out

* Log when reach gives back no recognized entities

* General error logging for reach
- remove timeout specific reach error logging
- log successful doc creation
- log error messages on separate log error lines


  Commit: af3b9a81bf22ba0fe1eb538c1bc1d42376937dd6
      
https://github.com/PathwayCommons/factoid/commit/af3b9a81bf22ba0fe1eb538c1bc1d42376937dd6
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-13 (Tue, 13 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/server/routes/api/element-association/uniprot.js

  Log Message:
  -----------
  Improve quality of Uniprot results

- Show the typed name as the main name on the end of the entity wizard.  Show 
the Uniprot name underneath if it's different than what's typed.
- Do not use the "main" Uniprot name.  Even though it's supposed to be a 
human-readable name (according to Uniprot), it looks like an ID.  Instead use 
the first protein name.  Users react better to the first protein name.
- Only allow reviewed:true results.  This removes "garbage" entries.


  Commit: b6349dba2dcaf70afc9d2df038d5713d2a76c209
      
https://github.com/PathwayCommons/factoid/commit/b6349dba2dcaf70afc9d2df038d5713d2a76c209
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    M package-lock.json
    M package.json
    M src/client/components/home.js

  Log Message:
  -----------
  Smooth scroll when clicking anchor links in the landing-page


  Commit: 165b40b79ed0293c1596588d5af137a300b794c2
      
https://github.com/PathwayCommons/factoid/commit/165b40b79ed0293c1596588d5af137a300b794c2
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    M package-lock.json
    M package.json
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  Merge pull request #212 from PathwayCommons/landing-page

more placeholder sections for the landing page, smooth scroll when clicking 
anchor links in the landing page


  Commit: 4258b1ce48ac958139c59e1b71b04f9544259687
      
https://github.com/PathwayCommons/factoid/commit/4258b1ce48ac958139c59e1b71b04f9544259687
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css
    A src/styles/image/infographic-factoid.svg

  Log Message:
  -----------
  Landing page copy, infographic
- use updated copy for authors, journals
- add the factoid infographic


  Commit: d430d487825360824c057d62c446a0cd155fca6d
      
https://github.com/PathwayCommons/factoid/commit/d430d487825360824c057d62c446a0cd155fca6d
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    M README.md
    M src/config.js

  Log Message:
  -----------
  Improve default reach url and improve env var docs in readme


  Commit: c68f06eb307a8f46e2891e1976592ca4e27bc27e
      
https://github.com/PathwayCommons/factoid/commit/c68f06eb307a8f46e2891e1976592ca4e27bc27e
  Author: metincansiper <metincansi...@gmail.com>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/client/components/highlighter.js

  Log Message:
  -----------
  Allow the Highligher component to highlight multiple terms (#210)

* Allow the Highligher component to highlight multiple terms #206

* Remove the mistakenly introduced new lines.

* Handle unexpected spaces in tooltip search string #206


  Commit: 0b1da900e567d6585e50449d964d2244861a08cc
      
https://github.com/PathwayCommons/factoid/commit/0b1da900e567d6585e50449d964d2244861a08cc
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    M src/client/components/home.js

  Log Message:
  -----------
  Minor copy changes


  Commit: 5732828ca17376daceecc249b64542d46a6de586
      
https://github.com/PathwayCommons/factoid/commit/5732828ca17376daceecc249b64542d46a6de586
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    M src/styles/home.css

  Log Message:
  -----------
  consistent p tag font size for landing page


  Commit: 76d75bd5dbf0fbfc8780cabadead7f6c2c09ec91
      
https://github.com/PathwayCommons/factoid/commit/76d75bd5dbf0fbfc8780cabadead7f6c2c09ec91
  Author: metincansiper <metincansi...@gmail.com>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    M package.json
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  Use a special shortening method for displaying synonyms in context of #202


  Commit: 496d5a422bcca4f0239a205c212a93ae87eac479
      
https://github.com/PathwayCommons/factoid/commit/496d5a422bcca4f0239a205c212a93ae87eac479
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    A src/client/components/debug-document-seeder.js
    M src/client/components/debug.js
    R src/client/components/document-filler.js
    A src/client/components/document-seeder.js
    A src/client/components/document-view-chooser.js
    A src/client/components/document-wizard-stepper.js
    A src/client/components/form-editor/index.js
    A src/client/components/page-not-found.js
    M src/client/router.js
    A src/styles/debug-document-seeder.css
    R src/styles/document-filler.css
    A src/styles/document-seeder.css
    A src/styles/document-view-chooser.css
    A src/styles/document-wizard-stepper.css
    M src/styles/index.css

  Log Message:
  -----------
  Initial stubbed pages (including data flow) for

- 404
- /new/seed
- /new/choice
- /form

Each component then just needs to be filled in more.  This filling in should be 
driven by wireframes.

Ref : Separation of pages to accommodate workflow of separate views #200


  Commit: 002e20b0b1990a47bd51c92a7da4519f2e396c54
      
https://github.com/PathwayCommons/factoid/commit/002e20b0b1990a47bd51c92a7da4519f2e396c54
  Author: metincansiper <metincansi...@gmail.com>
  Date:   2018-03-14 (Wed, 14 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  Memoize distances rather than memoizing results of cmp() #202


  Commit: 25bf289b0fa6c61976bb0dafe099d5f480ef67e9
      
https://github.com/PathwayCommons/factoid/commit/25bf289b0fa6c61976bb0dafe099d5f480ef67e9
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  Update factoid help email, change text to be smaller


  Commit: 73701bdbed813289fea6443f56f82273570be088
      
https://github.com/PathwayCommons/factoid/commit/73701bdbed813289fea6443f56f82273570be088
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/styles/home.css
    A src/styles/image/hero-splash-0.png

  Log Message:
  -----------
  use cytoscape generated network image


  Commit: 472ee8b6a4698e76fa301946bdf84a1f333d6e36
      
https://github.com/PathwayCommons/factoid/commit/472ee8b6a4698e76fa301946bdf84a1f333d6e36
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/styles/image/hero-splash-0.png

  Log Message:
  -----------
  update hero splash


  Commit: 3c15ef97fbcbc5e19972ae1cb86ff394582efe53
      
https://github.com/PathwayCommons/factoid/commit/3c15ef97fbcbc5e19972ae1cb86ff394582efe53
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css
    A src/styles/image/hero-splash-0.png
    A src/styles/image/infographic-factoid.svg

  Log Message:
  -----------
  Merge pull request #214 from PathwayCommons/landing-page

Landing page


  Commit: 6e569bf1bde83d73541ed1aa0941c92408449470
      
https://github.com/PathwayCommons/factoid/commit/6e569bf1bde83d73541ed1aa0941c92408449470
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  Fix for #210 breaking completed entity display


  Commit: bf8e8f9f7e048f5126f51bd6fd73951b9bd0be57
      
https://github.com/PathwayCommons/factoid/commit/bf8e8f9f7e048f5126f51bd6fd73951b9bd0be57
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  Only generate Highlighter components when necessary


  Commit: 256313f12c57abfb09c1ecbe0e1b995f3f789e2e
      
https://github.com/PathwayCommons/factoid/commit/256313f12c57abfb09c1ecbe0e1b995f3f789e2e
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/client/components/editor/cy/stylesheet.js

  Log Message:
  -----------
  Disable the edgehandles blue dot for now.

It needs to be redesigned if we want to use it in future:

- Users do not use the blue dot.
- The blue dot should be redesigned (maybe as a green outlined circle).  It 
looks too much like selection with the blue colour.
- Edgehandles should probably have a snapping feature (snap to nearest node), 
but this doesn't exist yet.  It would have to consider the cancel case 
carefully.


  Commit: d8c9551bf413abe6d125386805d57feae84ea5e5
      
https://github.com/PathwayCommons/factoid/commit/d8c9551bf413abe6d125386805d57feae84ea5e5
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/client/components/notification/base.js

  Log Message:
  -----------
  Change the notification dismiss button to "dismiss" text rather than an x

Users misinterpret the x to mean "close the popover" rather than dismiss the 
notification, probably because it's an x in the corner of the popover.


  Commit: 1df33fdde20e9d36e80728a30b6d088f15341a90
      
https://github.com/PathwayCommons/factoid/commit/1df33fdde20e9d36e80728a30b6d088f15341a90
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/client/components/editor/cy/stylesheet.js

  Log Message:
  -----------
  Disable interactivity on interaction nodes


  Commit: ceda2b31aaeaefdf655a76e7861f06636cfb91a1
      
https://github.com/PathwayCommons/factoid/commit/ceda2b31aaeaefdf655a76e7861f06636cfb91a1
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/styles/element-info/entity-info.css

  Log Message:
  -----------
  Add an edit button to edit modification for a completed entity (just goes 
back one step)


  Commit: 9d4897a404b0eedef09517b3ecb3333f59c06a74
      
https://github.com/PathwayCommons/factoid/commit/9d4897a404b0eedef09517b3ecb3333f59c06a74
  Author: metincansiper <metincansi...@gmail.com>
  Date:   2018-03-15 (Thu, 15 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  Get short synonyms list inside updateMatches() #202


  Commit: 469cfef9ab70b369cbdeeecfa46bbb3ca68b287b
      
https://github.com/PathwayCommons/factoid/commit/469cfef9ab70b369cbdeeecfa46bbb3ca68b287b
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-19 (Mon, 19 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js

  Log Message:
  -----------
  Intiial form MVP work
- change title from 'form editor' -> 'Insert Pathway Information As Text'
- add new interaction button works now
- create dummy model to show how one can enter information
- add select option for two new interactions -- enzyme reaction and 
phosphorylation

refs #208


  Commit: 7a194a3f5ab72c617d1308f23a747edb1b08041f
      
https://github.com/PathwayCommons/factoid/commit/7a194a3f5ab72c617d1308f23a747edb1b08041f
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-19 (Mon, 19 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js

  Log Message:
  -----------
  Hook up the doc model to the form component


  Commit: d9d842162ba52a4c9543921f4b8e3265811f1b75
      
https://github.com/PathwayCommons/factoid/commit/d9d842162ba52a4c9543921f4b8e3265811f1b75
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-19 (Mon, 19 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js

  Log Message:
  -----------
  Add methods for adding elements in the form editor


  Commit: 18b896eb8deba246091c688b420da6fc95bc1680
      
https://github.com/PathwayCommons/factoid/commit/18b896eb8deba246091c688b420da6fc95bc1680
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-19 (Mon, 19 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js

  Log Message:
  -----------
  fix errors for form editor dummy model
- added elements are just blank and don't reflect the current doc state
- interactions are empty, containing no source/target
- still need to know how to introduce the wizard for each entity


  Commit: 11607c8a81f5521a4e6c8b220f9742d10564913d
      
https://github.com/PathwayCommons/factoid/commit/11607c8a81f5521a4e6c8b220f9742d10564913d
  Author: metincansiper <metincansi...@gmail.com>
  Date:   2018-03-19 (Mon, 19 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/server/routes/api/element-association/aggregate.js
    M src/util/index.js
    A src/util/strings.js

  Log Message:
  -----------
  introduce util.stringDistanceMetric() and use it from both server and client 
#202


  Commit: 02179fd281db1798384f602d6d093a1b75d5e8d6
      
https://github.com/PathwayCommons/factoid/commit/02179fd281db1798384f602d6d093a1b75d5e8d6
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-20 (Tue, 20 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js

  Log Message:
  -----------
  Sync doc with form ui


  Commit: 17c357cf79aae5c858fb06e4d26c77695af1cf7a
      
https://github.com/PathwayCommons/factoid/commit/17c357cf79aae5c858fb06e4d26c77695af1cf7a
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-20 (Tue, 20 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js

  Log Message:
  -----------
  fix react warning for the form interaction select


  Commit: c81f2ebdd61028dd436847ba555b052ab80aa814
      
https://github.com/PathwayCommons/factoid/commit/c81f2ebdd61028dd436847ba555b052ab80aa814
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-20 (Tue, 20 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js

  Log Message:
  -----------
  persist interaction type in the form editor


  Commit: 27eee562ba7035e6e87ee226b9607e82d262780b
      
https://github.com/PathwayCommons/factoid/commit/27eee562ba7035e6e87ee226b9607e82d262780b
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-20 (Tue, 20 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js

  Log Message:
  -----------
  entity name persists in form ui
- todo: fancy/demoable form ui


  Commit: 496ca9aa9b522565e908e572203276798b156f1a
      
https://github.com/PathwayCommons/factoid/commit/496ca9aa9b522565e908e572203276798b156f1a
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-21 (Wed, 21 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js
    A src/styles/form-editor/form-editor.css
    A src/styles/form-editor/index.css
    M src/styles/index.css

  Log Message:
  -----------
  Form UI visual styling


  Commit: b9aa988f66d4effdb9b4fadffb082c4b1b5c5394
      
https://github.com/PathwayCommons/factoid/commit/b9aa988f66d4effdb9b4fadffb082c4b1b5c5394
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-21 (Wed, 21 Mar 2018)

  Changed paths:
    M src/server/routes/api/document/reach.js

  Log Message:
  -----------
  Reach fails on "Since our results demonstrated that Hzf binds to p53 and 
differentially modulates expression levels of the p53" #222
- Ignore all argument frames that do not specify an ID.
- Stricter check for arg types.


  Commit: d9f63db6a068762b343cea3288603ff290604446
      
https://github.com/PathwayCommons/factoid/commit/d9f63db6a068762b343cea3288603ff290604446
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-03-21 (Wed, 21 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js
    M src/styles/form-editor/form-editor.css

  Log Message:
  -----------
  Dummy delete interaction button


  Commit: 95da01cd547dd7f8b13f84a72b947b6b33ad7960
      
https://github.com/PathwayCommons/factoid/commit/95da01cd547dd7f8b13f84a72b947b6b33ad7960
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M src/client/components/editor/cy/stylesheet.js

  Log Message:
  -----------
  Fix edgehandle events in stylesheet


  Commit: 5648712970972314ac4b0a520fd8b10e1301cdae
      
https://github.com/PathwayCommons/factoid/commit/5648712970972314ac4b0a520fd8b10e1301cdae
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M src/server/routes/api/element-association/search-string-conversion.js

  Log Message:
  -----------
  Add aluminium alias


  Commit: e086bb604f36f0dfb778716a20c3964ce2f9222f
      
https://github.com/PathwayCommons/factoid/commit/e086bb604f36f0dfb778716a20c3964ce2f9222f
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M src/server/routes/api/element-association/pubchem.js

  Log Message:
  -----------
  Fix aliasing in pubchem service and better detect pubchem errors so they are 
non-blocking


  Commit: 76a07ed0ae4470caa2aa6c5fb71ed062787db85f
      
https://github.com/PathwayCommons/factoid/commit/76a07ed0ae4470caa2aa6c5fb71ed062787db85f
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M package-lock.json
    M package.json

  Log Message:
  -----------
  Update form-data and node-fetch for improved request support to external
services


  Commit: 55fd78553f8ab344b40835471f83b27a33a37437
      
https://github.com/PathwayCommons/factoid/commit/55fd78553f8ab344b40835471f83b27a33a37437
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M src/server/routes/api/document/reach.js

  Log Message:
  -----------
  Change reach to use the upload file route


  Commit: a89cdd8cafdc7c35e05346247c1307e0069817f1
      
https://github.com/PathwayCommons/factoid/commit/a89cdd8cafdc7c35e05346247c1307e0069817f1
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M package.json
    M src/client/components/element-info/entity-info.js
    M src/server/routes/api/element-association/aggregate.js
    M src/util/index.js
    A src/util/strings.js

  Log Message:
  -----------
  Merge pull request #213 from metincansiper/cut-synonyms

Use a special shortening method for displaying synonyms


  Commit: e750faf4f068d55954a937d23958376a3fc72f15
      
https://github.com/PathwayCommons/factoid/commit/e750faf4f068d55954a937d23958376a3fc72f15
  Author: Dylan Fong <dylanfong...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M src/client/components/form-editor/index.js
    A src/styles/form-editor/form-editor.css
    A src/styles/form-editor/index.css
    M src/styles/index.css

  Log Message:
  -----------
  Merge pull request #223 from PathwayCommons/form-editor-mvp

Form editor mvp cont.


  Commit: c1969e57466467e5fd23e3d23831aadfc1157a99
      
https://github.com/PathwayCommons/factoid/commit/c1969e57466467e5fd23e3d23831aadfc1157a99
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M src/server/routes/api/element-association/pubchem.js

  Log Message:
  -----------
  Always use first synonym for Pubchem results


  Commit: a220b17d2a46eb95cdeb9f58cabc239fe162d700
      
https://github.com/PathwayCommons/factoid/commit/a220b17d2a46eb95cdeb9f58cabc239fe162d700
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/image/infographic-factoid.svg

  Log Message:
  -----------
  Improve the landing page with Dylan and Jeff


  Commit: 1d5db90e0a3b8a60f71f82eac2244b47df8c6f5b
      
https://github.com/PathwayCommons/factoid/commit/1d5db90e0a3b8a60f71f82eac2244b47df8c6f5b
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-22 (Thu, 22 Mar 2018)

  Changed paths:
    M src/server/routes/api/element-association/uniprot.js

  Log Message:
  -----------
  Fix reviewed:yes filter on Uniprot searches -- move out of inner OR, put in 
outer AND


  Commit: 1b430b768d2360758293221d80ee4fe656701672
      
https://github.com/PathwayCommons/factoid/commit/1b430b768d2360758293221d80ee4fe656701672
  Author: metincansiper <metincansi...@gmail.com>
  Date:   2018-03-23 (Fri, 23 Mar 2018)

  Changed paths:
    M src/client/components/document-seeder.js
    A src/client/components/interval-highlighter.js
    M src/server/routes/api/document/index.js
    M src/server/routes/api/document/reach.js
    M src/styles/document-seeder.css

  Log Message:
  -----------
  Reach text highlighting #167


  Commit: 47a67dfcf8427344e04c97f4c7f0107854665caf
      
https://github.com/PathwayCommons/factoid/commit/47a67dfcf8427344e04c97f4c7f0107854665caf
  Author: metincansiper <metincansi...@gmail.com>
  Date:   2018-03-23 (Fri, 23 Mar 2018)

  Changed paths:
    M src/client/components/document-seeder.js

  Log Message:
  -----------
  Fix weird indentation in mergeIntervals()


  Commit: f195f078189be3b914feddb5470a7e2ba1b0df0b
      
https://github.com/PathwayCommons/factoid/commit/f195f078189be3b914feddb5470a7e2ba1b0df0b
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-26 (Mon, 26 Mar 2018)

  Changed paths:
    M src/model/document/document.js
    M src/util/obj.js
    M test/document.js

  Log Message:
  -----------
  Add a count for organism mentions
- An explicit mention counts as 1.
- Each entity associated with the organism counts as 1.
- This gives a total for the number of implicit and explicit organism mentions.
- Add tests.
- There is no caching, so you probably shouldn't call `doc.organismCount()` 
over and over.


  Commit: e5a6be9de1469bb398c00477be7822617f0c708c
      
https://github.com/PathwayCommons/factoid/commit/e5a6be9de1469bb398c00477be7822617f0c708c
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-26 (Mon, 26 Mar 2018)

  Changed paths:
    M src/util/memoize.js

  Log Message:
  -----------
  Allow `util.memoize()` to specify the key function args more naturally


  Commit: bd52ef6f748b83fd66c46c559dae243aee209cc6
      
https://github.com/PathwayCommons/factoid/commit/bd52ef6f748b83fd66c46c559dae243aee209cc6
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-26 (Mon, 26 Mar 2018)

  Changed paths:
    M src/server/routes/api/element-association/aggregate.js

  Log Message:
  -----------
  Decorate the entities returned by the aggregate search service with distance


  Commit: 12196ad74a29845cbd9126947ca733f7731750c1
      
https://github.com/PathwayCommons/factoid/commit/12196ad74a29845cbd9126947ca733f7731750c1
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-26 (Mon, 26 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  Do not filter by organism in the entity association UI


  Commit: 326f3aa0ac58f7d1bea920a57469224e9c35d280
      
https://github.com/PathwayCommons/factoid/commit/326f3aa0ac58f7d1bea920a57469224e9c35d280
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-26 (Mon, 26 Mar 2018)

  Changed paths:
    M src/util/memoize.js

  Log Message:
  -----------
  Use a map by default for memoize


  Commit: f6a4cfc930f937ed83eb713c5f8127da1430a310
      
https://github.com/PathwayCommons/factoid/commit/f6a4cfc930f937ed83eb713c5f8127da1430a310
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-26 (Mon, 26 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/model/document/document.js
    M src/server/routes/api/element-association/aggregate.js
    M src/server/routes/api/element-association/index.js

  Log Message:
  -----------
  Search takes into account organism counts


  Commit: 5c705bc4dbbcbcfae31c097a0f6a759dc21e6160
      
https://github.com/PathwayCommons/factoid/commit/5c705bc4dbbcbcfae31c097a0f6a759dc21e6160
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-26 (Mon, 26 Mar 2018)

  Changed paths:
    M src/config.js

  Log Message:
  -----------
  Use `'http://reach.baderlab.org/api/textBody'` by default for `REACH_URL`

Ref : Expose the Reach Docker service as reach.baderlab.org #233


  Commit: 5ad5506f6755cd6bcd4cd9d4156c8a9a5c330c2f
      
https://github.com/PathwayCommons/factoid/commit/5ad5506f6755cd6bcd4cd9d4156c8a9a5c330c2f
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-26 (Mon, 26 Mar 2018)

  Changed paths:
    M src/config.js

  Log Message:
  -----------
  Do not let empty strings (e.g. `export REACH_URL=''`) override defaults


  Commit: be6492f165c2c446f30cfe8cf4da0beeca521e68
      
https://github.com/PathwayCommons/factoid/commit/be6492f165c2c446f30cfe8cf4da0beeca521e68
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-27 (Tue, 27 Mar 2018)

  Changed paths:
    M src/model/organism.js
    M src/server/routes/api/element-association/aggregate.js

  Log Message:
  -----------
  Add a default organism ordering for unseeded, empty documents


  Commit: f0f4a7bd5077702de158b6b39a380ab9f76e8837
      
https://github.com/PathwayCommons/factoid/commit/f0f4a7bd5077702de158b6b39a380ab9f76e8837
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-27 (Tue, 27 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/model/document/document.js
    M src/model/organism.js
    M src/server/routes/api/element-association/aggregate.js
    M src/server/routes/api/element-association/index.js
    M src/util/memoize.js
    M src/util/obj.js
    M test/document.js

  Log Message:
  -----------
  Automate organism input #169


  Commit: d7c465a213d37f4b9f0bd39587ed32dbd2f41b5c
      
https://github.com/PathwayCommons/factoid/commit/d7c465a213d37f4b9f0bd39587ed32dbd2f41b5c
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-27 (Tue, 27 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js

  Log Message:
  -----------
  Even the selected modification may be clicked to go to the next stage.

This is useful in the case where a user cancels modification when he goes back.


  Commit: 526745883ea74c194d413c2da450d597c5cac874
      
https://github.com/PathwayCommons/factoid/commit/526745883ea74c194d413c2da450d597c5cac874
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-27 (Tue, 27 Mar 2018)

  Changed paths:
    M src/server/routes/api/document/reach.js

  Log Message:
  -----------
  Use the uploadFile endpoint for REACH docker instance. #231

Merge reach-upload into unstable


  Commit: 1b7cb381723ed706336040581a1f2ac5e3e6f201
      
https://github.com/PathwayCommons/factoid/commit/1b7cb381723ed706336040581a1f2ac5e3e6f201
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-28 (Wed, 28 Mar 2018)

  Changed paths:
    M src/config.js

  Log Message:
  -----------
  Change default reach ref on baderlab.org to use uploadFIle


  Commit: 7811a1c1382cdb6fc5a9b661d18748e2f7e9353e
      
https://github.com/PathwayCommons/factoid/commit/7811a1c1382cdb6fc5a9b661d18748e2f7e9353e
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-03-29 (Thu, 29 Mar 2018)

  Changed paths:
    M src/client/components/element-info/entity-info.js
    M src/styles/notification.css

  Log Message:
  -----------
  Tweaks to the notifications #238

- Make the notifications have shorter text.
- Increase the font size of the notifications.
- Resolve a minor alignment issue for inline notifications on large screens.


  Commit: 81f3fea90df4e49b24b18202bb0dd13ea252bcf4
      
https://github.com/PathwayCommons/factoid/commit/81f3fea90df4e49b24b18202bb0dd13ea252bcf4
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-04-04 (Wed, 04 Apr 2018)

  Changed paths:
    M src/client/components/home.js

  Log Message:
  -----------
  landing page try factoid button goes to the sample doc route


  Commit: 5175930d72493d3e3b278e9e064d6719be068fd1
      
https://github.com/PathwayCommons/factoid/commit/5175930d72493d3e3b278e9e064d6719be068fd1
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-04 (Wed, 04 Apr 2018)

  Changed paths:
    M src/client/components/home.js

  Log Message:
  -----------
  Merge pull request #240 from PathwayCommons/lp-changes

landing page try factoid button goes to the sample doc route


  Commit: ae0fb37f0f8b28aaa53427e5b80872850e8f984d
      
https://github.com/PathwayCommons/factoid/commit/ae0fb37f0f8b28aaa53427e5b80872850e8f984d
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-09 (Mon, 09 Apr 2018)

  Changed paths:
    M .travis.yml
    M package.json

  Log Message:
  -----------
  Add stricter Travis tests : To pass, a PR must pass all automated tests *and* 
linting.

Ref : Add stricter CI checks for PRs #243


  Commit: e5234ca6ab144d0d14f933a4d7ba8602f22bfc6f
      
https://github.com/PathwayCommons/factoid/commit/e5234ca6ab144d0d14f933a4d7ba8602f22bfc6f
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-09 (Mon, 09 Apr 2018)

  Changed paths:
    M src/client/components/document-view-chooser.js
    M src/client/components/editor/cy/cxtmenu.js
    M src/client/components/editor/cy/doc.js
    M src/client/components/element-info/entity-info.js
    M src/client/components/element-info/participant-info.js
    M src/client/components/form-editor/index.js
    M src/server/routes/api/document/index.js
    M src/server/routes/api/document/reach.js
    M src/server/routes/api/element-association/pubchem.js
    M src/server/routes/api/element-association/uniprot.js
    R src/server/routes/users.js
    M src/styles/base.css
    M src/styles/deps.css
    M src/styles/home.css
    M src/styles/react-tabs.css
    M src/util/obj.js
    M src/util/strings.js

  Log Message:
  -----------
  Clean up re. linting

Ref : Add stricter CI checks for PRs #243


  Commit: 13b7497091f58f35de98828feee402feb8e41601
      
https://github.com/PathwayCommons/factoid/commit/13b7497091f58f35de98828feee402feb8e41601
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-09 (Mon, 09 Apr 2018)

  Changed paths:
    M README.md

  Log Message:
  -----------
  Add fix target to the readme

Ref : Add stricter CI checks for PRs #243


  Commit: 00e6d6f54d406c612dc22eb5edc16c5faccc230a
      
https://github.com/PathwayCommons/factoid/commit/00e6d6f54d406c612dc22eb5edc16c5faccc230a
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-09 (Mon, 09 Apr 2018)

  Changed paths:
    M src/client/components/editor/cy/doc.js
    M src/client/components/element-info/entity-info.js
    M src/client/components/element-info/interaction-info.js
    A src/model/element/element-type.js
    M src/model/element/element.js
    A src/model/element/entity-mods.js
    M src/model/element/entity.js
    M src/model/element/factory.js
    A src/model/element/interaction-type/chemical-affects-protein.js
    A src/model/element/interaction-type/enum.js
    A src/model/element/interaction-type/expression.js
    A src/model/element/interaction-type/general.js
    A src/model/element/interaction-type/interaction-type.js
    A src/model/element/interaction-type/modification.js
    A src/model/element/interaction-type/protein-affects-chemical.js
    M src/model/element/interaction.js
    A src/model/element/participant-type.js
    M src/styles/element-info/interaction-info.css
    M test/interaction.js

  Log Message:
  -----------
  Add initial interaction subtype support #244

- Types: ChemicalAffectsProtein, Expression, Modification, 
ProteinAffectsChemical
- Interaction subtypes are indicated with an association, just like entities.
- Add tests for interaction type.
- Add basic UI for interaction type (not yet wizard) -- hidden for now as it's 
just for testing.
- Move many enum-like objects to separate files.


  Commit: d4bf5e42a9cf1d55c88cd71012d04bf2b86a5a38
      
https://github.com/PathwayCommons/factoid/commit/d4bf5e42a9cf1d55c88cd71012d04bf2b86a5a38
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-09 (Mon, 09 Apr 2018)

  Changed paths:
    M src/server/routes/api/document/reach.js
    M src/server/routes/api/element-association/aggregate.js

  Log Message:
  -----------
  Back to Chebi for now

- Replace pubchem with chebi as the chemical service used in the aggregate 
search service.
- Disable chemical grounding from Reach.

Ref : Pubchem is unreliable #228


  Commit: 6b29ed787b656756759e4797edc743e3b0fefa10
      
https://github.com/PathwayCommons/factoid/commit/6b29ed787b656756759e4797edc743e3b0fefa10
  Author: Dylan Fong <d2f...@uwaterloo.ca>
  Date:   2018-04-09 (Mon, 09 Apr 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css
    A src/styles/image/how-it-works-detailed.png
    A src/styles/image/how-it-works.png

  Log Message:
  -----------
  add how it works figures to the landing page

refs #242


  Commit: 811ac853f480400678ba23fe206de521b566ac2a
      
https://github.com/PathwayCommons/factoid/commit/811ac853f480400678ba23fe206de521b566ac2a
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-10 (Tue, 10 Apr 2018)

  Changed paths:
    A private/res/infographic-factoid.idraw

  Log Message:
  -----------
  Add landing page infographic to repo


  Commit: 18846a7d52aaf4bbb21040a22a2e2ef3f7e65008
      
https://github.com/PathwayCommons/factoid/commit/18846a7d52aaf4bbb21040a22a2e2ef3f7e65008
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-10 (Tue, 10 Apr 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css
    A src/styles/image/how-it-works-detailed.png
    A src/styles/image/how-it-works.png

  Log Message:
  -----------
  Merge pull request #246 from d2fong/unstable

add how it works figures to the landing page


  Commit: 12b8a0bb92d9ef605b49f14836a1f7252b3cc6e8
      
https://github.com/PathwayCommons/factoid/commit/12b8a0bb92d9ef605b49f14836a1f7252b3cc6e8
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-10 (Tue, 10 Apr 2018)

  Changed paths:
    M src/styles/home.css
    A src/styles/image/author-workflow.svg
    M src/styles/image/infographic-factoid.svg
    A src/styles/image/workflow-detailed.svg

  Log Message:
  -----------
  Tweaks to the landing page re. figures

- Maintain aspect ratio of figures so they don't have lots of extra padding at 
the bottom on small screens.
- Update to use SVGs for new figures.
- Better spacing between white and grey sections.

Ref #246


  Commit: 8269de81c798ef71c955171da04c0dfa7c59b7a5
      
https://github.com/PathwayCommons/factoid/commit/8269de81c798ef71c955171da04c0dfa7c59b7a5
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-10 (Tue, 10 Apr 2018)

  Changed paths:
    M src/client/components/document-seeder.js
    A src/client/components/interval-highlighter.js
    M src/server/routes/api/document/index.js
    M src/server/routes/api/document/reach.js
    M src/styles/document-seeder.css

  Log Message:
  -----------
  Merge branch 'reach-text-highlighting' of 
https://github.com/metincansiper/factoid into 
metincansiper-reach-text-highlighting


  Commit: b41ac18117e4ec15872b52542f957bbf6b06f631
      
https://github.com/PathwayCommons/factoid/commit/b41ac18117e4ec15872b52542f957bbf6b06f631
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-10 (Tue, 10 Apr 2018)

  Changed paths:
    M src/client/components/document-seeder.js
    M src/server/routes/api/document/index.js
    M src/server/routes/api/document/reach.js

  Log Message:
  -----------
  Fix query-reach casing and todos re. exposing reach


  Commit: 1fb4fb1fdf7d8cc270af8a0171edced3c91edc84
      
https://github.com/PathwayCommons/factoid/commit/1fb4fb1fdf7d8cc270af8a0171edced3c91edc84
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-10 (Tue, 10 Apr 2018)

  Changed paths:
    M src/client/components/home.js
    M src/styles/home.css

  Log Message:
  -----------
  Landing page tweaks

- Comment out the infographic for now (until we come up with a better design)
- Tweaks to spacing
- Remove alternative grey sections colour
- Centre 'how it works' figure
- More section spacing


  Commit: e202cb9d119712c3eeb048ee5388fb4bc59f1fc3
      
https://github.com/PathwayCommons/factoid/commit/e202cb9d119712c3eeb048ee5388fb4bc59f1fc3
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-10 (Tue, 10 Apr 2018)

  Changed paths:
    M postcss.config.js

  Log Message:
  -----------
  Fixes minification issues of css with embedded svg


  Commit: f9bb31fa86fa9a1cdd243e748675b5a681245573
      
https://github.com/PathwayCommons/factoid/commit/f9bb31fa86fa9a1cdd243e748675b5a681245573
  Author: Max Franz <maxkfr...@gmail.com>
  Date:   2018-04-10 (Tue, 10 Apr 2018)

  Changed paths:
    M .travis.yml
    M README.md
    M package-lock.json
    M package.json
    M postcss.config.js
    A private/res/infographic-factoid.idraw
    A src/client/components/debug-document-seeder.js
    M src/client/components/debug.js
    R src/client/components/document-filler.js
    A src/client/components/document-seeder.js
    A src/client/components/document-view-chooser.js
    A src/client/components/document-wizard-stepper.js
    M src/client/components/editor/cy/cxtmenu.js
    M src/client/components/editor/cy/doc.js
    M src/client/components/editor/cy/edgehandles.js
    M src/client/components/editor/cy/stylesheet.js
    M src/client/components/editor/cy/tippy.js
    M src/client/components/element-info/entity-info.js
    M src/client/components/element-info/interaction-info.js
    M src/client/components/element-info/participant-info.js
    A src/client/components/form-editor/index.js
    M src/client/components/highlighter.js
    M src/client/components/home.js
    A src/client/components/interval-highlighter.js
    M src/client/components/notification/base.js
    A src/client/components/page-not-found.js
    M src/client/components/popover/tooltip.js
    M src/client/router.js
    M src/config.js
    M src/model/document/document.js
    A src/model/element/element-type.js
    M src/model/element/element.js
    A src/model/element/entity-mods.js
    M src/model/element/entity.js
    M src/model/element/factory.js
    A src/model/element/interaction-type/chemical-affects-protein.js
    A src/model/element/interaction-type/enum.js
    A src/model/element/interaction-type/expression.js
    A src/model/element/interaction-type/general.js
    A src/model/element/interaction-type/interaction-type.js
    A src/model/element/interaction-type/modification.js
    A src/model/element/interaction-type/protein-affects-chemical.js
    M src/model/element/interaction.js
    A src/model/element/participant-type.js
    M src/model/organism.js
    M src/server/routes/api/document/index.js
    M src/server/routes/api/document/reach.js
    M src/server/routes/api/element-association/aggregate.js
    M src/server/routes/api/element-association/index.js
    M src/server/routes/api/element-association/pubchem.js
    M src/server/routes/api/element-association/search-string-conversion.js
    M src/server/routes/api/element-association/uniprot.js
    R src/server/routes/users.js
    M src/styles/base.css
    A src/styles/debug-document-seeder.css
    M src/styles/deps.css
    R src/styles/document-filler.css
    A src/styles/document-seeder.css
    A src/styles/document-view-chooser.css
    A src/styles/document-wizard-stepper.css
    M src/styles/element-info/entity-info.css
    M src/styles/element-info/interaction-info.css
    A src/styles/form-editor/form-editor.css
    A src/styles/form-editor/index.css
    M src/styles/home.css
    A src/styles/image/author-workflow.svg
    A src/styles/image/hero-splash-0.png
    A src/styles/image/hero-splash.jpg
    A src/styles/image/how-it-works-detailed.png
    A src/styles/image/how-it-works.png
    A src/styles/image/infographic-factoid.svg
    A src/styles/image/workflow-detailed.svg
    M src/styles/index.css
    M src/styles/notification.css
    M src/styles/react-tabs.css
    M src/styles/vars.css
    M src/util/index.js
    M src/util/memoize.js
    M src/util/obj.js
    A src/util/strings.js
    M test/document.js
    M test/interaction.js

  Log Message:
  -----------
  Iteration complete

- Fixes and changes motivated by the last round of user testing
- Initial 'demoable' version of the landing page
- Merge unstable into master
- N.b. contains wip brainstorming changes but these are not normally visible


Compare: 
https://github.com/PathwayCommons/factoid/compare/dd96d32d791b...f9bb31fa86fa

-- 
You received this message because you are subscribed to the Google Groups 
"cytoscape-cvs" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to cytoscape-cvs+unsubscr...@googlegroups.com.
To post to this group, send email to cytoscape-cvs@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-cvs.
For more options, visit https://groups.google.com/d/optout.

Reply via email to