https://github.com/ENCODE-DCC/encoded

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Revision Author Date Message Commit Date
efd4524 merged changes 09 August 2017, 21:21:39 UTC
48e73b1 merged changes 09 August 2017, 18:25:45 UTC
7b71428 condensed mapping of the array of dates 09 August 2017, 18:16:24 UTC
8a6793a created functions to limit duplicated code, added comments 09 August 2017, 18:14:55 UTC
817f216 added additional comments 09 August 2017, 01:07:42 UTC
518ab87 changed to NIH and refactored species list code to a function 08 August 2017, 21:31:51 UTC
32e8b1c fixed batch_download.py based on PR comments, cut down on number of parameters - converted to objects, simplified code for Status Stacked Bar Chart, added comments for chart.options.onClick.baseSearchUri 08 August 2017, 21:25:13 UTC
89266fe merged with remote 08 August 2017, 17:20:01 UTC
4ec0465 merged with master 08 August 2017, 17:12:06 UTC
096fff7 ENCD 3466 bot (#1951) * adding enbot ability to report results * updating requirements for checkfiles instance with enbot * modified to report the progress on bot-reporting channel * read_length to be 90% * fixing uninitialized data variable * adding handling 404 and IP address * fixing ip printout * adding checked instance URL in the printout 07 August 2017, 18:28:21 UTC
1ea6941 Merge pull request #1949 from ENCODE-DCC/ENCD-3459-safari-hang ENCD-3459 safari hang 07 August 2017, 18:26:59 UTC
210227f changed FetchGraphData 02 August 2017, 16:54:08 UTC
3802ec0 removed unnecessary code, added a few comments 02 August 2017, 16:43:14 UTC
0fc33b1 removed changes to item.js and schema.js 02 August 2017, 16:10:46 UTC
8b29c63 Merge remote-tracking branch 'origin/master' into ENCD-3439 02 August 2017, 16:03:25 UTC
5cda9ee Merge branch 'master' of https://github.com/ENCODE-DCC/encoded into ENCD-3459-safari-hang 01 August 2017, 23:22:25 UTC
6a82c32 ENCD 3460 audits (#1945) * removed control out of date audot and tests of it * modified the experiment out of date audit to not include file.dataset.file * commenting out the problematic audit in files * adding assay_term_name condition to file audits * fixing the condition of assay_name * Revert "fixing the condition of assay_name" This reverts commit 58829197e45c161a4c86d0dc99c33d7ca1a9a635. * Revert "adding assay_term_name condition to file audits" This reverts commit ab65dc733fd3ba0d1aa7f1b7aa05c7be64627253. * fixed the file audit with condition for ChIP-seq * adding back rfa conditions to File audits * fixing the audit rfa * commenting out file audit * Revert "commenting out file audit" This reverts commit 33b2ddb9e68083cfd89d20e65411b7a75d93896e. 01 August 2017, 18:04:05 UTC
f224e24 fixed Travis build errors 28 July 2017, 23:19:37 UTC
7c2c8e5 Merge remote-tracking branch 'origin/master' into ENCD-3439 28 July 2017, 22:06:30 UTC
54c83bf fixed status stacked bar chart, isogenic updateChart 28 July 2017, 22:00:44 UTC
e717985 ENCD-3416 pipeline assays (#1942) merged with some reluctance... * Idea of using $ref for list of assay_term_names * removing ref from mixins * adding assay_term_names to pipeline * Added pipeline_versiona and updated the inserts * updated chngelog * fixing tests * apdating boost, facets values * fixed the audit * fixed test and audit * assay_term_names are not required * updating image insert with email addresses correponding to the users emails * fixed the typo in the changelog of pipeline * removing unnecessary audit from pipeline 28 July 2017, 21:18:29 UTC
d1d75f3 fixed experiments donut links 28 July 2017, 18:04:01 UTC
252b07c Merge branch 'ENCD-3439' of github.com:ENCODE-DCC/encoded into ENCD-3439 27 July 2017, 22:44:35 UTC
f14ad1b fixed test file for batch_download.py 27 July 2017, 22:44:14 UTC
a765f90 fixed test data for batch_download.py 27 July 2017, 22:42:09 UTC
2e5d148 fixed antibody error, status bar chart specifies both replicate and status, reports responsive to genus buttons, donut sections all have genus associations 27 July 2017, 21:14:11 UTC
33f434e Merge remote-tracking branch 'origin/master' into ENCD-3439 26 July 2017, 20:29:36 UTC
4ef1461 Merge branch 'master' of https://github.com/ENCODE-DCC/encoded into ENCD-3459-safari-hang 25 July 2017, 21:38:08 UTC
f601764 fixed tsv link 25 July 2017, 20:24:53 UTC
d8d9df3 ENCD-2704 file filtering (#1943) * First implementation of tabbed file graph/tables File graphs and tables now appear tabbed, with either the graph or all the tables showing. The assembly/annotation now exists in its own section controlling both tabs. Next I need to introduce filtering for archived and revoked files. ENCD-2704 * Add additions and subtractions to url function Added ways to add or subtract statuses to the standard URL for unreleasedFilesUrl. This lets us more easily add a switch to show revoked and archived files in the file table. ENC-2704 * Have basic archive/revoked file filtering A basic checkbox now filters out/in archived and revoked files. Need to style the checkbox better, and work out what needs to be done for the graph — does it get filtered with this checkbox or not? ENCD-2704 * First demoable commit Abandoned the idea of using an iOS-style checkbox partly because that’s a very random decision to use, and it takes a *lot* of CSS to do. Ready to start a demo with this. ENCD-2704 * Update globals test for new properties Changed the property names in globals.unreleasedFilesUrl, so I had to update those property names in this test. ENCD-2704 * Add borders to browser result tabs The only other place in our code that uses the <TabPanel> component is the browser view. Changed the styling so that it adds a border and looks less weird with the new light gray background. ENCD-2704 25 July 2017, 19:18:18 UTC
cbf1eaa Sort <SortTable> only after mounting Safari and IE11 rendered before sorting, while Safari and IE11 render after sorting, causing a React invariant violation. Solved this by only sorting after the SortTable component is mounted. ENCD-3459 25 July 2017, 17:47:28 UTC
53eb18e fixed links for reagents, control, and status charts; removed PI from Affiliated Labs; created Milestones Panel 25 July 2017, 00:22:46 UTC
90b98d3 Merge remote-tracking branch 'origin/master' into ENCD-3439 24 July 2017, 22:55:02 UTC
df047a9 ENCD-3406: Mike Pazen would like to see milestones attached to awards (#1941) * Add milestones to awards and inserts * Remove the term_id calculation * Update the submitted_by user in image inserts so they can be loaded * Added assay_term_name enum list temporarily until snovault can be updated * Add import_items to award.milestones 24 July 2017, 14:47:17 UTC
7aac037 Use production version of React (#1940) Building with “npm run build” now uses the production version of React. “npm run dev” still uses the development version. ENCD-3351 (RM5148) 21 July 2017, 22:22:24 UTC
c9bd52b created dataset arrays with value 0, sorted legend using Array.some 21 July 2017, 18:49:50 UTC
0601f17 Merge remote-tracking branch 'origin/master' into ENCD-3439 21 July 2017, 17:33:29 UTC
382be8b fixed Assays Status bar chart 21 July 2017, 17:26:02 UTC
aab9685 ENCD-3174 (RM4900) missing biosample audit (#1926) * introduced dependency on biosample term id and type, simplified audit checking for inconsistency between them * fixing biosample term ids to fit types in tests * moving experiment biosample type and term_id into schema upgrading the schemas due to the dependencies we add * fixing missing biosample_type in test * fixing biosample)type test due to added dependency * another failing test due to the lack of bio sample type * removing audit (experiment missing biosample_type/term_id) removing the audit and the tests associated with it * making biosample_type required for experiment introducing dependency in experiment schema making biosample_term_id required for all cases except bio sample type “in vitro sample” * updating schema change log and fixing inserts * fixing tests fixtures to include bio sample type in experiments * fixing more data fixtures with experiment biosample_type * removed empty upgrades both bio sample and experiment updates removed, due to the aliases update happening in item * resolving the change log conflict * updating the versions of dataset to 12 adding the changelog in the correct version of dataset * fixing biosample_term audit in experiment excluding in vitro biosamples from the need to match term_id prefix with the type * bumping biosample and dataset versions adding change log to the relevant schemas * scaling down the changelog * updated change logs * resolving another conflict * updating all datasets with bio sample type/term_id dependency * Revert "Merge branch '4925-biosample-term' into 4900-missing-biosample" This reverts commit 5b2a4600465fbdeb6c9f6b6640225b4ea1b1b50a, reversing changes made to 80f4d9b11bfa604f3be49e6a9ed45f436f4a9f16. * adding dependency in antibody_characterization and modifying the experiment dependency the dependency in dataset is limited to only experiment - since all other datasets are calculating their values * fixing antibody audits and adding schema test for biosample dependency introduced in characterizations * fixing biosample properties in ab characterizations * scaling down the change log update and limiting the dependency to experiment only * adding bio sample dependency in annotation * fixing a test and removing conflict markup * fixing failing test * fixed changelogs * fixed project chagelog 21 July 2017, 14:56:33 UTC
de15b68 Merge pull request #1939 from ENCODE-DCC/ENCD-3464-user-timezone ENCD-3464 Remove timezone from local user test data 21 July 2017, 00:30:35 UTC
4a19f7c Remove timezone from local user test data Including timezone now causes server startup errors. ENCD-3464 20 July 2017, 23:54:11 UTC
8a6c984 ENCD-3194 4925 biosample term (#1924) * introduced dependency on biosample term id and type, simplified audit checking for inconsistency between them * fixing biosample term ids to fit types in tests * moving experiment biosample type and term_id into schema upgrading the schemas due to the dependencies we add * fixing missing biosample_type in test * fixing biosample)type test due to added dependency * another failing test due to the lack of bio sample type * removed empty upgrades both bio sample and experiment updates removed, due to the aliases update happening in item * bumping biosample and dataset versions adding change log to the relevant schemas * updating all datasets with bio sample type/term_id dependency * adding dependency in antibody_characterization and modifying the experiment dependency the dependency in dataset is limited to only experiment - since all other datasets are calculating their values * fixing antibody audits and adding schema test for biosample dependency introduced in characterizations * fixing biosample properties in ab characterizations * adding bio sample dependency in annotation * fixing failing test 20 July 2017, 22:15:31 UTC
aed79b7 ENCD-3409 simplify users (#1935) * Update user.json Removing phone, fax, timezone, google, skype from user * Update user.md Update change logs * Update user.json I need to get this to a real editor to get all the fax and googles out * removing unneeded fields from test data, inserts/user.json * adding user fields upgrade, tests, and merging in master * fixed upgrade to remove key rather than set value to None * Upgrade users from 5 to 6 and a test * fixed a typo * fixed another typo * I changed the schema version to 7 everywhere except the actual user.json schema. Adding it here * Updated user change log 6 to 7 description * fixing a few more conflicts with Cricket's changed email * found one fax number left in the test data 20 July 2017, 20:46:50 UTC
8ecbdb7 Merge pull request #1931 from ENCODE-DCC/ENCD-3419-assembly-order ENCD-3419 Update assembly order in graph drop-down 20 July 2017, 20:43:25 UTC
a4a69c2 Merge pull request #1932 from ENCODE-DCC/ENCD-3434-donor-id-regex ENCD-3434 donor id regex 20 July 2017, 20:42:10 UTC
1249114 Merge pull request #1937 from ENCODE-DCC/ENCD-3234-EFO-organ_slims ENCD-3234 EFO organ slims 20 July 2017, 19:57:53 UTC
a8f5f95 Merge pull request #1938 from ENCODE-DCC/ENCD-3463-travis-errors add dist: precise (12.02) 20 July 2017, 19:54:00 UTC
86d3b8d add dist: precise (12.02) 20 July 2017, 19:18:18 UTC
f67750a Merge pull request #1934 from ENCODE-DCC/ENCD-3433-version ENCD-3433 Show version number in pipeline graph modals 20 July 2017, 17:52:49 UTC
6de8da8 Merge pull request #1933 from ENCODE-DCC/ENCD-3437-truncate ENCD-3437 truncation incorrect 20 July 2017, 17:49:02 UTC
fa9dd15 Merge pull request #1936 from ENCODE-DCC/ENCD-3435-remove-2.7-from-travis do the thing 20 July 2017, 17:47:47 UTC
f2826e2 update ontology.json 19 July 2017, 19:26:10 UTC
467df93 added more EFO shims 19 July 2017, 19:24:41 UTC
5530796 add more organ slims, EFO shims, update ontology.json 18 July 2017, 23:45:04 UTC
05fd94f added control donut chart 18 July 2017, 22:32:53 UTC
4faed5c Merge branch 'master' into ENCD-3234-EFO-organ_slims 17 July 2017, 22:58:12 UTC
49d699c Fix default assembly for Reference datasets Reference datasets containing files with assemblies was displaying a blank assembly drop-down because it wasn’t setting “default” as the default assembly. Not related to this ticket, but found by testing this ticket. ENCD-3419 17 July 2017, 20:04:32 UTC
87cb592 merged in ENCD-5194-5195-5196-5197-5198 17 July 2017, 18:49:51 UTC
0abe624 Status stacked bar chart - displays status and replicate type - responsive to genus buttons 17 July 2017, 18:10:37 UTC
247ff1e update ontology.json at AWS and documentation 17 July 2017, 17:47:54 UTC
c8d65c6 remove muscle & embryonic structure 17 July 2017, 17:30:06 UTC
82481ac Update with NBRP URL ENCD-3434 17 July 2017, 16:44:43 UTC
7ac6fae Returned wrong string Part of AirBnB compliance is to stop mutating parameters. I had converted the truncation code to stop mutating its string parameter, but then returned the original string instead of the mutated one. ENCD-3437 17 July 2017, 16:01:36 UTC
a91c174 Display major version on pipeline graphs Pipeline graph modal now shows each step’s major_version. It does *not* display the minor version because the step_version isn’t available as it is with the file graphs — only an array of versions is available. ENCD-3433. 17 July 2017, 15:30:37 UTC
25a4f66 Add GRCh38-minimal to menu sorting priority I use an array of known assemblies to sort the array of assemblies in file graphs. Added GRCh38-minimal so that it sorts after GRCh38. ENCD-3419 17 July 2017, 14:02:33 UTC
e5ea217 Add JAX to dbxref URLs Still need to see if we need a separate one for NBRP:. ENCD-3434 17 July 2017, 13:50:01 UTC
0ab15ea Merge remote-tracking branch 'origin/new-users' into ENCD-3434-donor-id-regex 17 July 2017, 13:34:29 UTC
28a21f0 Merge remote-tracking branch 'origin/master' into ENCD-3434-donor-id-regex 17 July 2017, 13:34:12 UTC
16177a3 added comments and changed legend 14 July 2017, 18:27:18 UTC
018110e genus button appears when needed 13 July 2017, 22:07:20 UTC
4e4b178 genus buttons change 13 July 2017, 21:31:30 UTC
51df94b Added a uuid for Keenan Oops… Not associated with a ticket. 12 July 2017, 16:46:29 UTC
b0908b9 Added Keenan Graham to local users Not associated with a ticket. 12 July 2017, 15:02:45 UTC
650cbff graph only shows up when there's data, starting x-axis label corresponds to start date of assay 11 July 2017, 19:07:43 UTC
c1df94b Merge remote-tracking branch 'origin/ENCD-3435-remove-2.7-from-travis' into new-users 11 July 2017, 17:35:51 UTC
cb61fc4 Change Cricket's user email in images.json Cricket’s user account email changed from cricketsloan to crickets, so images.json had to be updated too. This isn’t associated with a ticket. 11 July 2017, 16:38:08 UTC
1d724b7 Add Kriti Jain to users.json Not part of a ticket 11 July 2017, 16:25:18 UTC
7ee00b7 Update user.json My email was never updated for local instances 11 July 2017, 16:07:37 UTC
4559c1c Merge pull request #1925 from ENCODE-DCC/ENCD-3237-step-upgrade-fix ENCD-3237: Tighten analysis_step.name regex and add calcprop analysis_step_version.name 11 July 2017, 00:12:32 UTC
7a540b7 put adding current date function within conditional 10 July 2017, 22:43:25 UTC
db68074 fixed in case of no date_submitted available 10 July 2017, 22:23:15 UTC
cd86196 Fix title for chromhmm state step 10 July 2017, 21:22:52 UTC
241509f Add upgrade data for new chromhmm steps 10 July 2017, 20:53:59 UTC
006d2ab cleaned up code, added comments 10 July 2017, 18:37:53 UTC
b51dbfc fixed key error for Affiliated Labs carriage return 10 July 2017, 16:58:34 UTC
2bbee4d added line for date submitted 09 July 2017, 20:51:28 UTC
1891087 Merge branch 'master' of github.com:ENCODE-DCC/encoded into ENCD-5194-5195-5196-5197-5198 07 July 2017, 21:08:25 UTC
41e7d23 Add JAX and NBRP to external_ids namespace list 07 July 2017, 20:42:16 UTC
634e182 do the thing 07 July 2017, 20:38:16 UTC
91d8d6b made report buttons conditional, formatted buttons, fixed antibody report link, added data label/legend for cumulative line graph 07 July 2017, 18:46:48 UTC
7700aed changed report.tsv file to have header with timestamp and link, filename to object and date accessed 07 July 2017, 17:44:54 UTC
76560a6 Merge pull request #1923 from ENCODE-DCC/ENCD-3431-construct-tags ENCD-3431 construct tags 06 July 2017, 23:13:03 UTC
edc2169 Merge pull request #1919 from ENCODE-DCC/ENCD-3427-view-more ENCD-3427 Fix changed property name 06 July 2017, 23:10:22 UTC
1e66f8c Merge pull request #1918 from ENCODE-DCC/ENCD-3426 ENCD-3426 Fix improper use of this.props 06 July 2017, 23:09:53 UTC
5092827 Merge pull request #1921 from ENCODE-DCC/ENCD-3420 ENCD-3420 Remove Download Elements button 06 July 2017, 23:09:07 UTC
b8c0e1f Merge pull request #1922 from ENCODE-DCC/ENCD-3411-date ENCD-3411: Experiments need a submission date 06 July 2017, 23:08:25 UTC
eb76b86 Revert "Fix display of construct documents" This reverts commit 372750295ade71a1be1f5a2db3577879e965e7d3. 06 July 2017, 22:04:40 UTC
3727502 Fix display of construct documents Biosample pages weren’t displaying construct documents because they used code that doesn’t apply anymore, so it never got executed. This fixes that for biosample pages. If you display a construct on its own page, no documents get rendered because we don’t really support that page. Experiment pages have already retrieved those documents properly, and still display them properly with this fix. 06 July 2017, 20:24:37 UTC
518f25c Update submission_date to date_submitted in schema, tests and inserts 06 July 2017, 19:51:56 UTC
714d73c returned to default report links 06 July 2017, 19:47:21 UTC
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