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f234fa6 Ulugbek Baymuradov 22 February 2018, 23:03:22 UTC lower embed_cache 22 February 2018, 23:03:22 UTC
2be43d6 caseylitton 20 February 2018, 23:39:54 UTC ENCD-3827 Fix ES5 version in README (#2141) 20 February 2018, 23:39:54 UTC
2c1f6e2 keenangraham 20 February 2018, 23:17:27 UTC ENCD-3698 Add Institutional certifications to biosample (#2140) 20 February 2018, 23:17:27 UTC
5fd266e Forrest Tanaka 20 February 2018, 22:09:24 UTC ENCD-1934 Format schema displays (#2115) 20 February 2018, 22:09:24 UTC
893728f caseylitton 20 February 2018, 22:03:37 UTC ENCD-3865 Update to snovault version 1.0.3 (#2139) 20 February 2018, 22:03:37 UTC
9b54526 Ben Hitz 20 February 2018, 21:51:43 UTC ENCD-3836 Small heap single machine (#2137) 20 February 2018, 21:51:43 UTC
35f426d estherc 20 February 2018, 21:35:02 UTC ENCD-3819 Add biosample preservation method (#2122) 20 February 2018, 21:35:02 UTC
70bce1f Idan Gabdank 20 February 2018, 20:25:23 UTC ENCD-3835 Fix inconsistent platforms audit HiSeq2K 2.5K (#2133) 20 February 2018, 20:25:23 UTC
65e246d Kathrina Casapao Onate 20 February 2018, 20:24:09 UTC ENCD-3341 Add new output_types to file json (#2132) 20 February 2018, 20:24:09 UTC
f9d3c43 Forrest Tanaka 20 February 2018, 20:21:35 UTC ENCD-3853 Remove UCSC logos (#2134) 20 February 2018, 20:21:35 UTC
61e223e Idan Gabdank 20 February 2018, 20:19:54 UTC ENCD-3757 Adjust histone broad peak read depth audit (#2125) 20 February 2018, 20:19:54 UTC
43fd2f4 Idan Gabdank 20 February 2018, 20:17:59 UTC ENCD-3831 Add exp audit to flag standards violations (#2124) 20 February 2018, 20:17:59 UTC
807fd58 Forrest Tanaka 20 February 2018, 20:15:43 UTC ENCD-3766 Add submitter comments to certain js pages (#2123) 20 February 2018, 20:15:43 UTC
563f262 estherc 16 February 2018, 01:20:11 UTC ENCD-3820 Biosample: PMI property (#2120) 16 February 2018, 01:20:11 UTC
2766100 jahilton 16 February 2018, 01:14:54 UTC ENCD-3798 Ontology Update Jan2018 (#2119) 16 February 2018, 01:14:54 UTC
e713f33 caseylitton 16 February 2018, 01:12:34 UTC ENCD-3816 Update selenium version to 3.8.1 (#2118) 16 February 2018, 01:12:34 UTC
cb676cd Idan Gabdank 16 February 2018, 01:07:20 UTC ENCD-3803 Allow fastq_sig to accept 3 in SRR headers (#2113) 16 February 2018, 01:07:20 UTC
3f0538c Forrest Tanaka 16 February 2018, 01:05:37 UTC ENCD-3456 Stringify array and object items in a cell (#2111) 16 February 2018, 01:05:37 UTC
c44a0e7 Forrest Tanaka 16 February 2018, 01:04:47 UTC ENCD-3762 Add RegulomeDB internal_tag and badge (#2110) 16 February 2018, 01:04:47 UTC
e06572d Forrest Tanaka 16 February 2018, 01:03:33 UTC ENCD-3421 Properly link home chart to matrix (#2108) 16 February 2018, 01:03:33 UTC
4145a2d Forrest Tanaka 16 February 2018, 01:00:15 UTC ENCD-2567 New report page column selector modal (#2105) 16 February 2018, 01:00:15 UTC
f457944 caseylitton 12 February 2018, 20:08:21 UTC Update to version 65.3 (#2131) 12 February 2018, 20:08:21 UTC
5551382 caseylitton 12 February 2018, 20:05:50 UTC ENCD-3851 Add max clause es5 updates (#2130) 12 February 2018, 20:05:50 UTC
9ff1b73 caseylitton 08 February 2018, 23:10:50 UTC Update to version 65.2 (#2129) 08 February 2018, 23:10:50 UTC
193ee1a caseylitton 08 February 2018, 22:50:06 UTC Update to snovault 1.0.2 (#2128) 08 February 2018, 22:50:06 UTC
f9dd5bc caseylitton 25 January 2018, 21:00:43 UTC ENCD-3813 Update to snovault 1.0.1 (#2116) 25 January 2018, 21:00:43 UTC
f5761a7 Ben Hitz 17 January 2018, 23:54:36 UTC ENCD-3815 Fix tests for facet aggregation set to 200 (#2109) 17 January 2018, 23:54:36 UTC
cd3dc73 estherc 17 January 2018, 01:13:24 UTC ENCD-3795 Fix spelling in histone and idr qm jsons (#2104) ENCD-3795 Fix spelling in histone and idr qm jsons 17 January 2018, 01:13:24 UTC
dbd4d29 Ulugbek Baymuradov 17 January 2018, 01:10:23 UTC ENCD-3810 Set facet aggregation to 200 in search (#2107) 17 January 2018, 01:10:23 UTC
0ffe153 Karthik Kalyanaraman 09 January 2018, 17:50:56 UTC ENCD 3749: Update README for ES5 and dependency requirements (#2087) 09 January 2018, 17:50:56 UTC
c51f970 caseylitton 09 January 2018, 17:44:33 UTC Merge pull request #2102 from ENCODE-DCC/es5-update-three-tickets 09 January 2018, 17:44:33 UTC
25f5497 Forrest Tanaka 09 January 2018, 00:54:43 UTC ENCD-3741 Search for objects based on associated grant number (#2103) 09 January 2018, 00:54:43 UTC
718a0c0 J. Seth Strattan 09 January 2018, 00:50:01 UTC ENCD-3792 Add histone_chip_quality_metric PIP-198 (#2101) 09 January 2018, 00:50:01 UTC
4673c93 caseylitton 08 January 2018, 23:08:44 UTC Update to snovault v1.0.0 08 January 2018, 23:08:44 UTC
6802683 Idan Gabdank 08 January 2018, 23:05:52 UTC ENCD-3745 Add platform to file and exp facets (#2088) 08 January 2018, 23:05:52 UTC
ffa11cf Ulugbek Baymuradov 14 December 2017, 18:08:04 UTC ENCD-3765 Set max_result_window for annotations index (#2083) max_result_window was set to 99999 08 January 2018, 22:39:40 UTC
e1c1489 Ulugbek Baymuradov 01 December 2017, 22:27:31 UTC ENCD-2488 ES5 Update aka RM3910 08 January 2018, 22:39:11 UTC
136bdc8 David Glick 08 January 2018, 19:09:30 UTC ENCD-3546 Create 'save and add' button to add forms (#2100) 08 January 2018, 19:09:30 UTC
ca1208f caseylitton 08 January 2018, 19:05:19 UTC Merge pull request #2094 from ENCODE-DCC/ENCD-3579-Batch-download-is-broken 08 January 2018, 19:05:19 UTC
a63edea jahilton 08 January 2018, 18:59:59 UTC ENCD-3700 Remove unreplicated exp audit for genetic mod DNase (#2096) 08 January 2018, 18:59:59 UTC
7a53a6d Idan Gabdank 08 January 2018, 18:54:50 UTC ENCD-3781 Resolve WGBS lambda audit error (#2095) 08 January 2018, 18:54:50 UTC
aa712c3 Idan Gabdank 08 January 2018, 18:43:11 UTC ENCD 3759 Fix WGBS coverage audit (#2093) 08 January 2018, 18:43:11 UTC
da42912 Idan Gabdank 08 January 2018, 18:38:55 UTC ENCD-3743 Fix read depth audits for DNase and ChIP (#2091) 08 January 2018, 18:38:55 UTC
1d500e3 Idan Gabdank 08 January 2018, 18:34:52 UTC ENCD-3760 Remove the NTR assay audit (#2089) 08 January 2018, 18:34:52 UTC
fa35bcb Forrest Tanaka 08 January 2018, 18:31:49 UTC ENCD-3724 Adjust facet term display check (#2086) 08 January 2018, 18:31:49 UTC
3c22d56 keenangraham 08 January 2018, 18:29:48 UTC ENCD-3755 Remove schemas for RNAi and construct characterizations (#2085) 08 January 2018, 18:29:48 UTC
9983b4b Idan Gabdank 08 January 2018, 18:27:27 UTC ENCD-3737 Add M14 gencode annotations to file enums (#2084) ENCD-3737 Add M14 gencode annotations to file enums 08 January 2018, 18:27:27 UTC
638bea2 estherc 08 January 2018, 18:19:40 UTC ENCD-3708 Update publication states (#2077) 08 January 2018, 18:19:40 UTC
7e8649e Idan Gabdank 08 January 2018, 18:17:04 UTC ENCD-3699 Remove mixed run type audit from DNase (#2065) 08 January 2018, 18:17:03 UTC
9c730cd Forrest Tanaka 08 January 2018, 18:13:57 UTC ENCD-3661 Update drawing file graphs and JS Tests (#2080) 08 January 2018, 18:13:57 UTC
e318096 Idan Gabdank 08 January 2018, 18:13:32 UTC ENCD-3764 Fix message typo in Assay audit (#2081) 08 January 2018, 18:13:32 UTC
deb2ba9 kakaly 21 December 2017, 19:54:09 UTC ENCD-3473 Fix for unknown error in batch_download pep8 fixes 21 December 2017, 23:17:40 UTC
f9cb6d6 kakaly 18 December 2017, 22:24:44 UTC ENCD-3579 Fix for batch download error Replace if block with .get() 21 December 2017, 23:13:20 UTC
97afad2 David Glick 21 December 2017, 18:23:49 UTC ENCD-3566 Fix JS FileInput add document (#2076) 21 December 2017, 18:23:49 UTC
0e54f47 David Glick 21 December 2017, 18:13:18 UTC ENCD-3597 Use obj picker for user impersonation (#2068) 21 December 2017, 18:13:18 UTC
62282d4 estherc 21 December 2017, 18:10:02 UTC ENCD-3721 Allow 'in vitro sample' to have biosample_term_name (#2067) 21 December 2017, 18:10:02 UTC
45809f1 Idan Gabdank 21 December 2017, 18:06:15 UTC ENCD-3734 file audit escalation (#2066) 21 December 2017, 18:06:15 UTC
d7aa9e2 caseylitton 20 December 2017, 17:57:56 UTC ENCD-3785 Add user to deploy auth keys (#2097) 20 December 2017, 17:57:56 UTC
e211b3f caseylitton 20 December 2017, 17:56:30 UTC [hotfix] ENCD-3736 Fix pop error (#2099) 20 December 2017, 17:56:30 UTC
f767ec5 caseylitton 19 December 2017, 00:57:15 UTC Merge pull request #2052 from ENCODE-DCC/ENCD-3656-include-ssh-keys-in-deploy ENCD-3656 include ssh keys in deploy and fix pep8 in deploy script 19 December 2017, 00:57:15 UTC
549fd65 Casey Litton 14 November 2017, 19:30:03 UTC ENCD-3656 Include ssh keys in deploy 18 December 2017, 23:19:55 UTC
e876301 Casey Litton 14 November 2017, 23:26:20 UTC Fix pylint issues in deploy script 18 December 2017, 23:19:55 UTC
d143961 Idan Gabdank 05 December 2017, 15:01:47 UTC ENCD-3710 Remove unused code from audits of Experiment (#2059) removing pipeline_structures.py from audit code 05 December 2017, 15:01:47 UTC
9f8e14d keenangraham 30 November 2017, 19:19:28 UTC ENCD-3707-scrub-proposed-preliminary (#2054) 30 November 2017, 19:19:28 UTC
f2b4fcb keenangraham 30 November 2017, 19:11:43 UTC ENCD-3740-duplicate-quality-metric-audit (#2058) 30 November 2017, 19:11:43 UTC
9ab6e10 caseylitton 28 November 2017, 17:54:07 UTC ENCD-3722 Pre Install setuptools with pip for travis (#2056) 28 November 2017, 17:54:07 UTC
22377dc caseylitton 20 November 2017, 23:42:32 UTC ENCD-3702 Update to snovault 0.32 (#2053) 20 November 2017, 23:42:32 UTC
ea4fd5f estherc 20 November 2017, 23:40:52 UTC ENCD-3683 Add new redacted output_types (#2049) 20 November 2017, 23:40:52 UTC
465fcb8 estherc 20 November 2017, 23:39:35 UTC ENCD-3469 Update software purpose assay list (#2051) * Add assays to software.purpose * Add back community resource enum to software.purpose 20 November 2017, 23:39:35 UTC
c106edd Forrest Tanaka 20 November 2017, 18:43:52 UTC ENCD-1972(update) Add status facet for analysis-step (#2047) * Add status facet for analysis-steps for its collections page donut 20 November 2017, 18:43:52 UTC
9947a84 Forrest Tanaka 20 November 2017, 18:39:45 UTC ENCD-1972(partial revert) Return Lab facet in Human Donor (#2048) * Due to bug found when testing ENCD-3581 20 November 2017, 18:39:45 UTC
02cdd7a David Glick 20 November 2017, 18:18:30 UTC ENCD-3691 Restore select button and audits to file listing view (#2050) * Restore select button (for object picker) and audits to file listing view 20 November 2017, 18:18:30 UTC
0bf52ef David Glick 14 November 2017, 18:45:42 UTC Specify reverse link properties which should not be submittable (#2045) this got left out of v64rc1 14 November 2017, 18:45:42 UTC
2b48eb6 caseylitton 12 November 2017, 18:19:03 UTC ENCD-3687 Update to snovault 0.31 (#2044) 12 November 2017, 18:19:03 UTC
15a49a7 Forrest Tanaka 11 November 2017, 00:06:16 UTC ENCD-1972 Collections page replacement (#2043) RM3130 Replace collections pages 11 November 2017, 00:06:16 UTC
a3c2dcf caseylitton 10 November 2017, 21:46:29 UTC ENCD 3659 assemblies key not in result set items (#2042) tdreszer code, PR by caseylitton in order so split ticket. Same for ENCD-3625 10 November 2017, 21:46:29 UTC
a45b7f4 caseylitton 10 November 2017, 20:56:58 UTC ENCD-3625 Add missing visualiztion button (#2041) 10 November 2017, 20:56:58 UTC
4d5bf21 Ben Hitz 08 November 2017, 19:07:03 UTC Encd 3647 schema docs (#2034) * ENCD-3647 add schema upgrade checks to docs * Update schema-changes.md add \n * Update schema-changes.md 08 November 2017, 19:07:03 UTC
c94b0aa Ben Hitz 07 November 2017, 23:16:49 UTC fix buildout-version reference 2.4.1 -> 2.9.5 wasn't done in all places. 07 November 2017, 23:16:49 UTC
fc11d7e jahilton 07 November 2017, 18:12:42 UTC encd 3495 remove 'mRNA ' (#2038) 07 November 2017, 18:12:42 UTC
648c63e jahilton 07 November 2017, 18:09:40 UTC Encd 3632 reshim methylations (#2037) * shim 4 assays to DNAme, update ontology.json ENCD-3632 * shim 3 brain tissues (ntr-469), update ontology.json * Remove NTR biosample shim 07 November 2017, 18:09:40 UTC
c6a714e Forrest Tanaka 07 November 2017, 18:06:48 UTC ENCD-3637 Change alternate accessions display (#2036) * Update displays for alternate accession Modified all existing “Replaces” displays to instead show “Alternate accessions:” for the alternate_accession property. ENCD-3637 * Handle plural/singular alternate accessions Creates a new component to display alternate_accessions that all components that have them can use. Displays singlar/plural as appropriate. ENCD-3637 * Fix code indenting ENCD-3637 07 November 2017, 18:06:48 UTC
386e491 Idan Gabdank 07 November 2017, 18:05:03 UTC ENCD-3609 updating file.json dependency (#2035) * fixing file dependencies to exclude assembly in raw data files * fixing file schema version * rewriting the dependency * fixes of indentation according to PR review 07 November 2017, 18:05:03 UTC
3dbff0f David Glick 07 November 2017, 18:03:00 UTC ENCD-3607 fix binding of remove method (#2033) 07 November 2017, 18:03:00 UTC
79255f8 David Glick 07 November 2017, 18:01:52 UTC ENCD-3655 Move file assemblies calculation into ResultTable #2032 07 November 2017, 18:01:52 UTC
ae14a38 Idan Gabdank 07 November 2017, 18:00:47 UTC ENCD 3631 summary treatment (#2031) * making experiment biosample summary to include treatment details * fixing treatment phrase typo * fixing code according to PR review * typo in variable name correction 07 November 2017, 18:00:47 UTC
159771e Forrest Tanaka 07 November 2017, 17:58:17 UTC ENCD-3581 Donor UI cleanup (#2029) * Fill out donor facets Added to fly, worm, and mouse facets. ENCD-3581 * Clean up donor facets and search results Also have donor pages do a GET request to show a table of genetic modificastions. ENCD-3581 * GM search temporary implmentation I misunderstood GMs in donors. I’ll commit this for now in case the code becomes useful some time, but I’ll remove a lot of it for now. ENCD-3581 * Redo GM display for donor.genetic_modifications Removed the GET request that was never needed in the first place. ENCD-3581 * Trying zc.buildout 2.9.5 Based on a suggestion from David Glick to work around our demo launching failures. ENCD-3581 * More changes to get demos to work ENCD-3581 * More to get demos working ENCD-3581 * Handle “unknown” properties of donors better Now show “unknown strain background,” “unknown sex,” “unknown life stage,” and “unknown age” if any of those have the value “unknown.” This also fixes a bug where human donors show “unknown undefined” in the title of search results. ENCD-3581 * Revert bootstrap.py change While debugging a demo startup failure, I brought in a new version of bootstrap.py, but it only changed some help text over what we already hand. This commit reverts that. ENCD-3581 * Removed unused component I had put in a component that did a GET request of genetic modification objects, only to find I didn’t need that. This commit removes that unused component. ENCD-3581 * Removed unused imports from donor.js ENCD-3581 07 November 2017, 17:58:17 UTC
045bc46 Idan Gabdank 07 November 2017, 17:56:45 UTC ENCD-3576 Fixing the DNase out of date analysis audit (#2028) * fixing the audit message for "assembly-less" outdated experiments * splitting out of date analysis to support DNase * fixing dnase out of date analysis audit to work properly with PE data * optimized the code bby removal of unnecessary loops * fixing out of date audit * Allow java install by version in cloud config * Add public key for dev[REVERT] * point to snovault tag 0.30 * removing print out statements * adding bams belonging to multipl ereplicates as possible cause for out of date analysis * started to fix the code according to PR review * done fixing the code according to PR review * reverting the change in cloud-config.yml * fixing varable name typo * fixing according to PR review some of the if statements * fixing the format and long line in audit detail 07 November 2017, 17:56:45 UTC
6ab7d51 keenangraham 28 October 2017, 18:19:09 UTC Only try to upgrade if object has annotation_type field (#2027) 28 October 2017, 18:19:09 UTC
6f238d3 keenangraham 28 October 2017, 18:18:00 UTC ENCD-3646-fix-publication-upgrade (#2026) * Add publication upgrade * Add publication fixture and test for status upgrade 28 October 2017, 18:18:00 UTC
975d70a Forrest Tanaka 28 October 2017, 00:18:19 UTC ENCD-3615 Fly TRiP (#2024) * Add TRiP to donor.external_ids namespace regex * Add TRiP dbxref URL pattern Also added a TRiP test to dbxref Jest tests. * Update a feailing forms test Also add command-line option to get more information about failing Travis CI test. * Fix oddly faliing browser tests ENCD-3615 * Try mr.developer 1.38 To try to get demos to come up. ENCD-3615 * Revert earlier test change ENCD-3615 28 October 2017, 00:18:19 UTC
6ef298f caseylitton 28 October 2017, 00:17:16 UTC Merge pull request #2025 from ENCODE-DCC/ENCD-3648-fix-buildout-setuptool-versions ENCD 3648 fix buildout setuptool versions 28 October 2017, 00:17:16 UTC
d1a54e2 Casey Litton 27 October 2017, 23:07:21 UTC ENCD-3648-fix-buildout-setuptool-versions 27 October 2017, 23:07:21 UTC
fdd92c3 keenangraham 27 October 2017, 18:02:09 UTC ENCD-3616-donor-parents (#2022) * adding parent_strains in fly and worm donors * fixing loadxl and adding insert * adding test for dependency * removing default empty list for parent_strains * Revert "removing default empty list for parent_strains" This reverts commit cbfc460ffabea7a5ecd1b5d78dd99dbdd809b2a2. * resolving mapping errors * embedding GM in mouse and adding GM to mouse boost values * fixing parent_strains dependency and removing mutagen dependency * adding test for donor schema dependencies * adding upgrade and schema tests * remove return * adding missing "@" * fixing mouse donor upgrade * Pep8 fixes 27 October 2017, 18:02:09 UTC
0cfeea4 keenangraham 26 October 2017, 23:41:52 UTC ENCD-3595-missing-derived-from-audit-refactor (#2007) * Add csfasta and csqual to detected files * Add tests for fastq/csfasta/csqual not triggering missing derived_from * Ignore replaced BAMs in missing derived_from audit * Test that replaced BAMs ignored by missing derived_from audit * Test released derived_from revoked triggers missing derived_from audit * Add more tests for inverse status relationships * Rely on STATUS_LEVEL dict to determine if parent should count * Add content error status to STATUS_LEVEL dict * Test that statuses in file schema are also in STATUS_LEVEL dict * Test file with status not in STATUS_LEVEL dict * Return if status not in STATUS_LEVEL * Add item test that all statuses in schema are in STATUS_LEVEL dict * Add virtual to STATUS_LEVEL dict * Add in preparation to STATUS_LEVEL dict * Remove in press, in revision, planned, replaced from Publication schema without upgrade (ENCD-3627) * Update Publication changelog * Add preliminary to STATUS_LEVEL dict to get test to pass * Add active to STATUS_LEVEL dict * Remove print statement from test * Update missing derived_from with unknown status test in test_audit_file * Remove schema check from test_audit_file 26 October 2017, 23:41:52 UTC
fc152bd keenangraham 26 October 2017, 22:54:36 UTC ENCD-3578-content-eror-audit (#2021) * separating the files in uploading from upload failed and content error states for the audit * Test file in uploading state audit * Add elif statement to uploading files audit * Refactor detail string * Only build detail string if audit triggers 26 October 2017, 22:54:36 UTC
7d5cf80 Forrest Tanaka 26 October 2017, 22:40:36 UTC ENCD-3510 graph refactor (#2020) * Initial commit Only changes what the inclusion status button controls (added deleted-status files), for feedback. ENCD-3517 * Initial demo of colorized ENCD-3510 * Add coloring for deleted and replaced Deleted now red, and replaced now gray. ENCD-3517 * Fix crash when drawing no graph after drawing one ENCD-3517 * Remove file search URL-generation code As we no longer ask for specific statuses, this code isn’t useful anymore. ENCD-3517 * Set colors to the same as table statuses ENCD-3510 * Fix contributing file bug Was simpliy caused by an uninitialized state variable. ENCD-3510 * Marking this spot: drawing graphs First step of refactoring: Moving all the graphing code out of filegallery.js into graph.js. Now it draw the graph again, but nothing’s clickable yet. ENCD-3510 * In progress * Revert "In progress" This reverts commit 04f89761b0e223efde32f60be3b088ab317b0c08. * Redo modal display control Modal displays for clicks on graph nodes now handled in the <Graph> component — the first step towards separating the graph modal displays from <FileGalleryRenderer>. ENCD-3510 * Working table modals Needs lots of cleanup, but it seems to work. ENCD-3510 * Fix empty-graph bug Graphs that had no files in it were still displaying as empty graphs. ENCD-3510 * Get audit displays working Well, for the most part. They work when clicking files (and presumably steps) from the graph. QC doesn’t work because it does things differently, but I’ll next see if I can make those consistent. ENCD-3510 * FIles, QC, QC from files works in modals But now the info buttons on the table cause a JS crash. ENCD-3510 * File modals from table again work Also the QC buttons in file modals from the file tables work. ENCD-3510 * A little cleanup before tackling contributing ENCD-3510 * Contributing and coalesced modals work Needed to update to having the node click handler in graph.js instead of filegallery.js. ENCD-3510 * Fix graph jest tests assembleGraph parameters changed completely, so the Jest tests had to be rewritten for this. ENCD-3510 * Resort functions/components for pipeline graphs To prepare for pipeline graphs, had to reshuffle the functions and components to be more consistent to their role in their files. ENCD-3510 * One small eslint cleanup ENCD-3510 * Get analysis step modals working ENCD-3510 * Get graph Jest test working ENCD-3510 * Fix graph panels File graphs had a panel within a panel. Changed this to not use a Panel component, and changed pipeline graphs to compensate. ENCD-3510 * Clicked graph nodes now highlight They always did, but they stopped with this branch until now. ENCD-3510 * Add file graph color legend The inclusion checkbox not only adds deprecated files to the graph, and not only colors each node, it also makes a legend appear while the checkbox is checked. ENCD-3510 * Default to include deprecated files for admins Also fixed a missing React key warning for the file status legend. ENCD-3510 * Redo the file statuses in the file tables File table statuses used the standard status routines which don’t work with file status colors. Redid the file table statuses. Thinking I should redo status displays completely so that different objects can have their own status colors more reliably. Also removed the pink color for restricted files. ENCD-3510 * Add data items to file modals ENCD-3510 * Color modal title bars Lost this in refactor, but it’s back now. ENCD_3510 * Update file page status colors It’s a mess; it’ll have to do for now. ENCD-3510 * Add Restricted File indicator Adds line to File page header to indicate a restricted file. ENCD-3510 * Update file status colors Change uploading and replaced statuses to new colors. Also update at what lightness level you get white text on the color as opposed to black text. ENCD-3510 * Add legend item for unknown files in the file graph ENCD-3510 * Add Status column to coalesce file modal tables ENCD-3510 * Change file graph legend order https://encodedcc.atlassian.net/browse/ENCD-3510?focusedCommentId=68909&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#comment-68909 26 October 2017, 22:40:36 UTC
fdb1abc Forrest Tanaka 26 October 2017, 22:15:41 UTC ENCD-3584 submitter comments (#2023) * Mix submitter_comment into donor, library, file, pipeline, and genetic_modification * Rename comment to submitter_comment in characterizations in upgrade * Update test data for submitter_comments * Update antibody lot types test with submitter_comment * AB characterizations display submitter_comment Changed from displaying anitbody_characterization.comment to anitbody_characterization.submitter_comment. This gets displayed in the drop-down characterization panel. ENCD-3584 * Trigger 26 October 2017, 22:15:41 UTC
424cc86 Ulugbek Baymuradov 23 October 2017, 20:58:39 UTC point to snovault tag 0.30 (#2019) 23 October 2017, 20:58:39 UTC
340c7d9 Forrest Tanaka 23 October 2017, 20:09:45 UTC ENCD-3606 Cellosaurus (#2013) * Change Cellosaurus URL pattern to https Also removed a completely unrelated now-unused reference to a GeneticModification import. VSCode gave a warning on that. ENCD-3606 * Fix dbxref Jest test For the Cellosaurus protocol change. ENCD-3606 * Remove dbxrefPrefixMap mapping object Using a completely different mechanism for mapping dbxref prefixes to URLs with ENCD-3489. That left this object unused, but I forgot to remove it. ENCD-3606 * Restore two dbxrefPrefixMap entries Turns out target.js still uses the dbxrefPrefixMap, and I’d forgotten. I think it can probably get rid of all that and just use the default dbxref code, but it was put there fore some reason to begin with, and it’s surprisingly complicated and has no comments. So I think leave it for now, and if we really feel like it, we can tackle deciphering that later. ENCD-3606 23 October 2017, 20:09:45 UTC
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