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Merged
bbimber merged 61 commits into from
Aug 8, 2023
Merged

Merge discvr-23.7 to develop #176

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cfa0442
Correct ExtendedFuncotator arguments
bbimber Jun 20, 2023
7b08af2
Correct ExtendedFuncotator arguments
bbimber Jun 20, 2023
7202897
Correct ExtendedFuncotator arguments
bbimber Jun 21, 2023
a2f2459
Allow ExtendedFuncotator to skip MT
bbimber Jun 22, 2023
09ded56
Add option to print missing fields for ExtendedFuncotator
bbimber Jun 23, 2023
d031a26
Specify the list of SnpSift fields to include
bbimber Jun 29, 2023
67abe4d
Basic support for GroupCompare tool
bbimber Jun 30, 2023
04f1245
Add more options for GroupCompareStep
bbimber Jun 30, 2023
0e7d3e4
Update variant filter panel
bbimber Jun 30, 2023
192c305
Correct arguments for GroupCompareStep
bbimber Jun 30, 2023
96cda11
Correct arguments for GroupCompareStep, missed with last commit
bbimber Jun 30, 2023
f567aeb
Correct arguments for GroupCompareStep
bbimber Jun 30, 2023
4f7e3c8
Try to avoid test timing issues
bbimber Jun 30, 2023
f7d146f
Add initial pipelne job to cleanup extraneous MHC typing results
bbimber Jul 3, 2023
6a413ab
Add stubs for IDR study
bbimber Jul 3, 2023
71aca34
Improved logging in MHC cleanup pipeline
bbimber Jul 3, 2023
e76425a
Allow more aspects of mGAP annotations to be driven using table (#113)
bbimber Jul 3, 2023
ce4dcc3
Update field case
bbimber Jul 3, 2023
e34b356
Add removal of low freq allele groups to MHC cleanup
bbimber Jul 3, 2023
b819d30
Add button to directly expose UpdateAnnotationsAction
bbimber Jul 3, 2023
01a410c
Fix button label
bbimber Jul 3, 2023
07cd1f0
UpdateAnnotationsAction: allow for source data with unequal line lengths
bbimber Jul 3, 2023
2215b80
Store annotation sourceField
bbimber Jul 4, 2023
8079599
Rely on funcotator for clinvar annotation
bbimber Jul 4, 2023
1b3c563
Update field case
bbimber Jul 4, 2023
a01eda2
Allow for more missing values in annotations
bbimber Jul 4, 2023
313d136
Update code to load variant annotations
bbimber Jul 4, 2023
5e45a28
Improve MhcCleanupPipeline logging
bbimber Jul 4, 2023
b6fe13d
Improve MhcCleanupPipeline logging
bbimber Jul 4, 2023
858b2ab
Switch MhcCleanupPipeline to use transaction
bbimber Jul 4, 2023
d39d0e9
Adjust logging thresholds for MhcCleanupPipeline
bbimber Jul 4, 2023
c20a471
Adjust logging thresholds for MhcCleanupPipeline
bbimber Jul 4, 2023
92caec5
Add additional MHC data collapse step
bbimber Jul 5, 2023
e87ebf6
Update location for MHC cleanup job
bbimber Jul 5, 2023
c2b66c3
Reduce logging for MHC cleanup job
bbimber Jul 5, 2023
735b8e2
Fix error in MCC import
bbimber Jul 6, 2023
f2f18c6
Improvements to MHC cleanup pipeline
bbimber Jul 6, 2023
ea8a83c
Fix longstanding bug in MhcMigrationPipelineJob
bbimber Jul 7, 2023
d00c595
Improve MhcCleanupPipelineJob and include group collapsing code in Se…
bbimber Jul 7, 2023
e7d4b6f
Improve MHC group collapsing code
bbimber Jul 7, 2023
ea43474
Allow ref VCF to be optional
bbimber Jul 7, 2023
52f894b
Misc improvements to variant annotation code
bbimber Jul 9, 2023
345e67e
Finalize implementation of fields/groups provider and add implementat…
bbimber Jul 19, 2023
bbd31c6
Make mGAP JBrowse fields data-driven (#116)
bbimber Jul 20, 2023
f434670
mGAP UI updates
bbimber Jul 20, 2023
bb4711c
Allow mGAP redirect to also use variant search
bbimber Jul 20, 2023
f3f8c25
Support both VCF and table selects for GroupCompare
bbimber Jul 21, 2023
35370a8
Misc improvements to JBrowse search
bbimber Jul 22, 2023
efd2488
Attempt to fix intermittent test failure
bbimber Jul 23, 2023
a72c769
Attempt to fix intermittent test failure
bbimber Jul 23, 2023
d5ad4f2
Allow JBrowse customizers to point toward parent, not workbook
bbimber Jul 25, 2023
bf17683
Bugfix to mGAP redirect links
bbimber Jul 25, 2023
28787f5
Improvements to the filter panel in JBrowse free-text search
bbimber Jul 25, 2023
acf560d
Bugfixes to filter panel
bbimber Jul 25, 2023
b12940e
Test fixes (#117)
bbimber Aug 3, 2023
130edf4
Correct study name in mGAP test
bbimber Aug 7, 2023
6490e55
Refactor mGAP study to folder export
bbimber Aug 7, 2023
12da49b
Refactor mGapReleaseGenerator to match new annotations
bbimber Aug 7, 2023
25dd791
Merge discvr-23.3 to discvr-23.7
bbimber Aug 8, 2023
c828500
Merge pull request #118 from bimberlabinternal/23.7_fb_merge
bbimber Aug 8, 2023
26eac1f
Merge discvr-23.7 to develop
bbimber Aug 8, 2023
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4 changes: 4 additions & 0 deletions IDR/resources/referenceStudy/folder.xml
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<?xml version="1.0" encoding="UTF-8"?>
<folder archiveVersion="22.0" xmlns="http://labkey.org/folder/xml">
<study dir="study"/>
</folder>
12 changes: 12 additions & 0 deletions IDR/resources/referenceStudy/study/README
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This folder contains the reference study for IDR data. It should be generated by performing
a folder export from the production server, then copying the datasets_manifest.xml, datasets_metadata.xml,
PrimateElectronicHealthRecord.dataset and study.xml files. After copying, the following can be used to find/replace
metadata in datasets_metadata.xml to remove unwanted information:

Replace the following regex expressions with empty string:

( )*<inputType>(.*)</inputType>\n
( )*<isHidden>(.*)</isHidden>\n|( )*<shownIn(.*)View>(.*)</shownIn(.*)View>\n
( )*<url>(.*)</url>\n|( )*<description>(.*)</description>\n|( )*<facetingBehavior>(.*)</facetingBehavior>\n|( )*<nullable>(.*)</nullable>\n
( )*<formatString>(.*)</formatString>\n|( )*<columnTitle>(.*)</columnTitle>\n|( )*<fk>(.)*\n( )*<fk(.)*\n( )*<fk(.)*\n( )*<fk(.)*\n( )*</fk>(.)*\n
( )*<dimension>(.*)</dimension>\n|( )*<measure>(.*)</measure>\n|( )*<isMvEnabled>(.*)</isMvEnabled>\n
0 ...ces/referenceStudy/datasets/mGAP.datasets → ...referenceStudy/study/datasets/IDR.dataset
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71 changes: 71 additions & 0 deletions IDR/resources/referenceStudy/study/datasets/datasets_manifest.xml
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<?xml version="1.0" encoding="UTF-8"?>
<datasets metaDataFile="datasets_metadata.xml" xmlns="http://labkey.org/study/xml">
<datasets>
<dataset name="flags" id="5019" category="Colony Management" type="Standard">
<tags/>
</dataset>
<dataset name="parentage" id="5025" showByDefault="true" category="Colony Management" type="Standard">
<tags/>
</dataset>
<dataset name="birth" id="1007" category="Colony Management" demographicData="true" type="Standard">
<tags/>
</dataset>
<dataset name="encounters" id="1067" showByDefault="false" category="Clinical" type="Standard">
<tags/>
</dataset>
<dataset name="medicationOrders" id="1037" showByDefault="false" category="Clinical" type="Standard">
<tags/>
</dataset>
<dataset name="treatment_order" id="5056" showByDefault="false" category="Clinical" type="Standard">
<tags/>
</dataset>
<dataset name="clinremarks" id="1047" showByDefault="false" category="Clinical" type="Standard">
<tags/>
</dataset>
<dataset name="medicationAdministration" id="1014" category="Clinical" type="Standard">
<tags/>
</dataset>
<dataset name="weight" id="1045" showByDefault="true" category="Clinical" type="Standard">
<tags/>
</dataset>
<dataset name="labwork" id="1073" showByDefault="false" category="ClinPath" type="Standard">
<tags/>
</dataset>
<dataset name="labworkResults" id="1074" showByDefault="false" category="ClinPath" type="Standard">
<tags/>
</dataset>
<dataset name="transfers" id="1001" category="Colony Management" type="Standard">
<tags/>
</dataset>
<dataset name="deaths" id="1048" showByDefault="true" category="Colony Management" demographicData="true" type="Standard">
<tags/>
</dataset>
<dataset name="demographics" id="1012" category="Colony Management" demographicData="true" type="Standard">
<tags/>
</dataset>
<dataset name="departure" id="1013" showByDefault="true" category="Colony Management" type="Standard">
<tags/>
</dataset>
<dataset name="assignment" id="1002" category="Colony Management" type="Standard">
<tags/>
</dataset>
<dataset name="problem" id="1030" showByDefault="false" category="Clinical" type="Standard">
<tags/>
</dataset>
<dataset name="housing" id="1018" category="Colony Management" type="Standard">
<tags/>
</dataset>
<dataset name="clinical_observations" id="5006" showByDefault="true" category="Clinical" type="Standard">
<tags/>
</dataset>
<dataset name="kinship" id="5007" showByDefault="true" category="Colony Management" type="Standard">
<tags/>
</dataset>
<dataset name="samples" id="1031" showByDefault="true" category="Research" type="Standard">
<tags/>
</dataset>
<dataset name="viralLoads" id="1032" showByDefault="true" category="Research" type="Standard">
<tags/>
</dataset>
</datasets>
</datasets>
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