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Sample details refactor #1370

Merged
merged 428 commits into from
Oct 5, 2022
Merged

Sample details refactor #1370

merged 428 commits into from
Oct 5, 2022

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deepsidhu85
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@deepsidhu85 deepsidhu85 commented Sep 20, 2022 •
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Description of changes

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Checklist

Things for the developer to confirm they've done before the PR should be accepted:

  • CHANGELOG.md (and UPGRADING.md if necessary) updated with information for new change.
  • Tests added (or description of how to test) for any new features.
  • User documentation updated for UI or technical changes.

deepsidhu85 and others added 30 commits March 29, 2022 12:37
@deepsidhu85
Added missing classnames to sampleName causing project samples table,…
2b61502 
… and linelist UI tests to fail.
@deepsidhu85
Removed accidental typo
d2107de
@deepsidhu85
Added logging statement when getting user analysis output info. Updat…
22c9e20 
…ed test for getting analysis outputfile info for user
@deepsidhu85
Moved getting sample analyses into a new service
d3e0984
@deepsidhu85
Removed unused error catch
3cc32f0
@deepsidhu85
Created component to display state for a sample analysis
77a12d1
@deepsidhu85
Removed unused imports, added javadoc, fixed column sizes for sample …
84b01a2 
…analyses table
@deepsidhu85
Fixed logic which would allow a user to set as default an assembly wh…
180c7bd 
…ich has the same id as a sequence file pair
@deepsidhu85
Updated logic to get user from principal to fix broken test
3d416ef
@deepsidhu85
Removed unused import
6377251
@deepsidhu85
Merged in metadata field security and fixed merge conflicts
7d57284
@deepsidhu85
Fixed issue with projectmetadatarole being set to null when a new rol…
77ab1f4 
…e was passed but the field did not have a restriction before
@deepsidhu85
Merge branch 'sample-details-refactor' into sample_details_refactor/_…
432f926 
…sample_analyses
@deepsidhu85
Merged sample analyses and fixed merge conflicts
230bec1
@deepsidhu85
Removed padding around button
1441b74
@deepsidhu85
Removed unused variables and removed border from sample analyses table
02c490f
@joshsadam
Merge pull request #1207 from phac-nml/sample_details_refactor/_sampl…
6ca5e81 
…e_analyses
@deepsidhu85
Merge branch 'sample-details-refactor' into sample_details_refactor/_…
d78682a 
…metadata_and_details_fixes
@deepsidhu85
Updated fastqc results to be displayed in a modal when a file is clic…
088a287 
…ked on in the sample details viewer -> files tab
@deepsidhu85
Added constants, added missing @RequestParam for projectId, reverted …
cb3fd64 
…splitting of logic for getting a list of SampleMetadataFieldEntry
@joshsadam
Merge pull request #1227 from deepsidhu85/sample_details_refactor/_me…
22555b4 
…tadata_and_details_fixes

Sample details refactor/ metadata and details fixes
@deepsidhu85
merged metadata-field-security and fixed merge conflicts
6cd7a24
@deepsidhu85
Merge branch 'sample-details-refactor' into sample_details_refactor/_…
f71f28a 
…file_qc
@deepsidhu85
Merged metadata-field-security and fixed merge conflicts
c1d7b8e
@deepsidhu85
Merged sample-details-refactor and fixed merge conflicts
217d9a4
@deepsidhu85
Merge branch 'metadata-field-security' into sample-details-refactor
da7e918
@deepsidhu85
Merge branch 'sample-details-refactor' into sample_details_refactor/_…
6176385 
…file_qc
@deepsidhu85
Updated modal styling, refactored sample files page to only have a cl…
f8b8774 
…ickable link to fastqc results if fastqc finished sucessfully,
@deepsidhu85
Updated to allow setting of a default genome assembly object for a sa…
558c30c 
…mple
@deepsidhu85
Merged in metadata field security and fixed merge conflicts
b5ea74b
deepsidhu85 and others added 17 commits September 27, 2022 16:37
@deepsidhu85
Merge branch 'sample-details-refactor' into sample_details_refactor/_…
9b7b47e 
…documentation
@deepsidhu85
Merged dev and fixed merge conflicts
c3a4e0b
@deepsidhu85
Updated to use Duration.ofSeconds
69f4f89
@deepsidhu85
Merge branch 'development' into sample-details-refactor
4f8a44a
@deepsidhu85
Updated db file to include email pipeline result field for analysis s…
32608f8 
…ubmissions
@deepsidhu85
Increased size of reduction for height of sample files by 1 pixel to …
2b4e76b 
…account for fractional pixels
@deepsidhu85
Merge branch 'sample-details-refactor' into sample_details_refactor/_…
d665008 
…documentation
@deepsidhu85
Updated screenshots. Updated SampleInfo list item size
f0a1f42
@deepsidhu85
Merge branch 'sample_details_refactor/_documentation' into sample_det…
0423212 
…ails_refactor/_cleanup
@deepsidhu85
Removed files and translations no longer required
e2c9ff9
@deepsidhu85
Deleted test files no longer required
afe221f
@deepsidhu85
Removed translations and js/jsx files no longer required
08fa847
@deepsidhu85
Updated test db xml file and readded missing translation keys
44f2012
@joshsadam
Merge pull request #1366 from deepsidhu85/sample_details_refactor/_do…
62298e1 
…cumentation

Sample details refactor/ documentation
@deepsidhu85
Merge branch 'sample-details-refactor' into sample_details_refactor/_…
0a44362 
…cleanup
@deepsidhu85
Removed unused files and updated required data sql file
6988fec
@joshsadam
Merge pull request #1374 from deepsidhu85/sample_details_refactor/_cl…
d614c4d 
…eanup

Sample details refactor/ cleanup
ericenns
ericenns approved these changes Oct 4, 2022
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👍 I gave this a quick skim (since all the child pr's had already been reviewed and approved) and this looks good to me.

@deepsidhu85 deepsidhu85 marked this pull request as ready for review October 4, 2022 20:37
@deepsidhu85 deepsidhu85 requested a review from joshsadam October 4, 2022 20:46
@deepsidhu85 deepsidhu85 added the UI User Interface Issue label Oct 4, 2022
joshsadam
joshsadam approved these changes Oct 4, 2022
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Looks good to me.

@ericenns ericenns merged commit 81b4714 into development Oct 5, 2022
@ericenns ericenns deleted the sample-details-refactor branch October 5, 2022 12:16
@deepsidhu85 deepsidhu85 mentioned this pull request Oct 6, 2022
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@ericenns ericenns ericenns approved these changes

@joshsadam joshsadam joshsadam approved these changes

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@deepsidhu85 @ericenns @joshsadam