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  • Dec 12 21:01
    susannasiebert commented #1255
  • Dec 12 21:00
    jmcmichael labeled #1260
  • Dec 12 21:00
    jmcmichael assigned #1260
  • Dec 12 21:00
    jmcmichael opened #1260
  • Dec 12 20:57
    susannasiebert commented #1255
  • Dec 12 20:44
    susannasiebert commented #1258
  • Dec 12 20:43
    susannasiebert commented #1258
  • Dec 10 18:42
    jmcmichael opened #1259
  • Dec 10 00:37

    jmcmichael on update-tagline

    updated header logo tagline updated text taglines updated presentation graphics l… (compare)

  • Dec 06 22:46
    malachig opened #1258
  • Dec 06 19:54

    jmcmichael on staging

    typeaheadWrapper modified to pa… add drug form now appends typea… fixed multiinput config on add … and 7 more (compare)

  • Dec 06 19:54
    jmcmichael closed #1257
  • Dec 06 19:46
    jmcmichael synchronize #1257
  • Dec 06 19:46

    jmcmichael on new-drug-multiinput

    improved add drug form instruct… fixed logged-out msg on add ass… multiinput notes that duplicate… and 1 more (compare)

  • Dec 05 21:18
    jmcmichael opened #1257
  • Dec 05 21:18
    jmcmichael review_requested #1257
  • Dec 05 21:15

    jmcmichael on new-drug-multiinput

    typeaheadWrapper modified to pa… add drug form now appends typea… fixed multiinput config on add … and 2 more (compare)

  • Dec 05 20:36
    kkrysiak assigned #1256
  • Dec 05 20:36
    kkrysiak unassigned #1256
  • Dec 05 20:36
    kkrysiak assigned #1256
Brian
@bwalsh
Hi. Brian from OHSU here. I was wondering how the refactoring is going to align with the latest civic-server?
Obi Griffith
@obigriffith
The civic-client refactor will work with the current/latest civic-server. I just fired up the latest civic-client (events-refactor branch) and the current master branch of civic-server and they seem to be working well together except for a few minor glitches. I believe @jmcmichael is planning to merge his branch back into master of civic-client and all will be as before.
Joshua McMichael
@jmcmichael
@bwalsh I merged the events-refactor branch into master late last last week, so civic-server and civic-client APIs are in sync. Let me know if you run into any API issues.
Joshua McMichael
@jmcmichael
Just pushed an update to civic-client master that fixes the quicksearch navigation (#90). Note that this requires updating your civic-server installation as well.
Malachi Griffith
@malachig
Hey Josh, when I try to edit anything right now I see "{{to.label}}" everywhere. Is this expected at the moment?
Joshua McMichael
@jmcmichael
checking...
I'm not seeing this - are you on the latest master?
I'm going some work in the edit-collections branch that might cause some form template issues like that but master should be OK
Joshua McMichael
@jmcmichael
just pushed an update to master that adds a /releases page containing links to all of the nightly and monthly generated TSV files
(the new Releases page is linked from the footer menu)
also to generate a release, fire up the rails console with 'rails c'
then enter
GenerateNightlyTsvs.new.perform
GenerateMonthlyTsvs.new.perform
Malachi Griffith
@malachig
I created a fresh install of the client by deleting my local repo and rebuilding. I encountered the same issue. I think it has to do with being on the wrong angular version.
If I do an bower update I get a warning about angular versions. If I pick 1.3.15 it seems to resolve the issue. But I still get warnings about dependencies resolving to the old version of Angular (1.2.28)...
Malachi Griffith
@malachig
I just finished what I hope was a fairly extensive tire kicking of editing and commenting on genes, variants, and to a less degree evidence items. Other than a few minor issue that I have submitted as github issues, it is really starting to work nicely!
Malachi Griffith
@malachig
I feel like this is in an issue somewhere but I could not immediately find it. I have been experimenting with applying edits to a series of variants with very similar variant summaries. I fixed the same typo in ~6 summaries. After Apply of each one I was wishing that I was automatically returned to either (1) the summary view for that variant if I did Apply OR (2) to the diff view in Variant Talk -> Revisions if I did Submit Revision for Review.
Joshua McMichael
@jmcmichael
@malachig I've created an issue (#100) to address this feature.
Joshua McMichael
@jmcmichael
A side note on the Releases page: the dev proxy will not redirect requests to the civic-server /downloads directory, so links on the Releases page will return a 404. However, the links will work in production where the civic-client distribution build is served from the same IP as the civic-server. I'm working on a fix but the proxy plugin I'm using doesn't seem to support proxy-ing two http paths and am looking for alternatives or a workaround.
Malachi Griffith
@malachig
I think as long as the releases links work on the live version this is certainly fine for now.
Joshua McMichael
@jmcmichael
just pushed an update to master that improves cache handling for entities and their comments, which results in fewer calls made to the server while changing states. The client’s responses to navigating within the events states should feel snappier, and the services code is a bit more elegant.
Joshua McMichael
@jmcmichael
just merged the collections-edit branch w/ master. civic-server doesn’t quite handle the collections arrays in edit/add interfaces but should shortly.
Joshua McMichael
@jmcmichael
just pushed an update to master that implements a couple of the active form features on the Add Evidence page (Evidence Type now influences the appearance of the Drug Names field, and changes the Clinical Significance options)
Joshua McMichael
@jmcmichael
FYI the latest civic-client master includes an update to a bower package for the active form features so be sure to do a ‘bower install’ in the client root directory after pulling the latest master updates.
Joshua McMichael
@jmcmichael
Pushed an update to master that adds a 'Updates' button to the right of the tabs. When clicked, it shows a list of all the updates, their timestamps, and the users responsible. Currently it only shows the last modified update but we'll be adding created-by, updated-by, etc. in the near future.
Note that this update requires a 'bower install' after pulling - I had to update the angular-bootstrap package.
Malachi Griffith
@malachig
Hi Josh. Minor question. When I click the button to show edit history for an entity I see I nice summary of who made modifications. To dismiss this summary I must also click the same button. Is that expected behavior? Should it disappear if the user clicks anywhere outside of the popup? That seems to be the behavior of the MyGeneInfo pop out and the user drop down menu.
Joshua McMichael
@jmcmichael
@malachig Yeah, that's currently expected behavior. I believe I can easily modify it to disappear when a click event occurs anywhere else, or fade out after a certain time. I'll switch it to disappear when anything else is clicked. BTW, I'm probably going to implement an different way of displaying that info very soon, so it's not hidden behind a button-click and instead displayed under the title or something like that.
General notice: I made quite a few updates to the master branch today that require a 'bower update' after pulling the latest. Also, be sure to check out the new comment form and display - you can now use markdown to add styling, links, etc. I'll add a notice to the instruction about this later but you can test out the feature now.
Joshua McMichael
@jmcmichael

I've just pushed another update to master that adds assistance features to the gene, variant, and disease fields in the add/edit evidence forms.

  • gene ID field now verifies the entered entrez id against the entrez DB, displaying its name below if found
  • variant name field shows a typeahead dropdown of matching names from the civic database. the user may also enter free text if the variant isn't known to civic
  • the diseases field checks the existence of a DOID, and displays it if found. Additionally the user may check the 'Could not locate DOID' checkbox, and a 'Disease Name' input will appear where they may enter a free-form disease name.

There are a few known server issues with submitting data from some of these updated fields which Adam and I should be able to get fixed in the next couple of days.

Malachi Griffith
@malachig
I currently get an error "500 - The CIViC server experienced an unrecoverable error, please check the console output for more information." if I try to change the PubMed ID associated with an evidence item. Is this a known issue waiting on a backend update maybe?
In general my tire kicking tonight has been way more smooth than previously! Everything is really coming together and looking amazing. Feels like we are sooo close to ditching the spreadsheets. :)
Malachi Griffith
@malachig
Josh, I was thinking about it last night and I think you are absolutely right. As we add more evidence items we are going to increasingly want a way to refer to them and EID is the way to do that.
Malachi Griffith
@malachig
Hey Josh, did you figure out what the deal was with this issue (I added on server side but it might be client related...): genome/civic-server#74
Malachi Griffith
@malachig
Hey josh, FYI, in my standalone civic instance with the latest commits the disease field in evidence items appears like this: "{"id":17,"name":"Acute Myeloid Leukemia","doid":"9119"}"