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store pca scores results #5265

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bdbff75
add save pcs btn
isaak Nov 12, 2024
dc4ba1d
Merge branch 'master' into topic/solgs/store-pca-results
isaak Nov 18, 2024
5125aa5
save pca scores
isaak Nov 22, 2024
7e7554c
make analysis save methods generic
isaak Nov 22, 2024
f42a5f6
reuse analysisSave methods
isaak Nov 29, 2024
09fa87c
use solGS.save.storeAnalysisResults
isaak Nov 29, 2024
765d663
load analysisSave js lib
isaak Nov 29, 2024
18388c6
add include_rownames param
isaak Nov 29, 2024
43674d8
refactor pca analysis args structuring and parsing
isaak Dec 2, 2024
25ce791
move gebvs saving code into gebvsSave.js
isaak Dec 2, 2024
48bc51f
use getPcaAnalysisArgs method
isaak Dec 3, 2024
c797ff0
add functions for getting breeding prog id
isaak Dec 9, 2024
9295872
add get_trial_id_by_accession
isaak Dec 9, 2024
89898cc
tweak pca args structuring
isaak Dec 9, 2024
3ad03c3
clean up
isaak Dec 9, 2024
516cab4
save top 10 principal components
isaak Dec 13, 2024
a579819
add PCA score terms
isaak Dec 13, 2024
ef3ee1d
fix style
isaak Dec 13, 2024
2efd1ba
add prcomp protocol type
isaak Dec 13, 2024
a36b3b4
import gebvsSave js
isaak Dec 13, 2024
74b176f
add prcomp protocol_type entry
isaak Dec 13, 2024
65f97aa
pca result save controller
isaak Dec 13, 2024
ff17fbb
gbvs save controller
isaak Dec 13, 2024
df58e67
clean up modules, fix indentations
isaak Dec 13, 2024
4889372
add pca results detail ajax req
isaak Dec 13, 2024
0ca8334
update get analysis results method names
isaak Dec 13, 2024
3efada4
move gebvs save logic to gebvsSave controller
isaak Dec 13, 2024
dd5210e
tweak convert_arrayref_to_hashref fun to make it wrok with multi trai…
isaak Dec 16, 2024
e613889
update div elem names
isaak Dec 16, 2024
f42e009
make selenium tests work with private lists
isaak Dec 17, 2024
7d2f3ff
update fixture dump with db patches and cxgn_statistics.obo (PCA) terms
isaak Dec 17, 2024
fb0954d
tweak pca args parsing
isaak Dec 18, 2024
19ea1cf
make pcs saving work for different data types from trial detail page
isaak Dec 18, 2024
c6348a6
add analysis_page to args
isaak Dec 18, 2024
3aaebc4
organize code
isaak Dec 18, 2024
3208d9e
delete double variable_of cvterm in fixture
isaak Dec 19, 2024
8ea228c
update parsing list or dataset ids
isaak Dec 23, 2024
5e5c492
clean up redundant code for pca and clustering file id
isaak Dec 23, 2024
624b89a
remove selection pop id...
isaak Dec 24, 2024
6fc027f
make loading pca result from selection predition page load in standal…
isaak Dec 24, 2024
e358bfa
ad pca resuls saving selenium tests
isaak Dec 24, 2024
5c3bb7e
show save pcs on analysis with submitted job names only
isaak Dec 31, 2024
9329d8e
fix conflict and merge master
isaak Jan 2, 2025
bcc68c5
fix logged analysis name check and pass selenium tests
isaak Jan 2, 2025
5ef4147
update expected recordsTotal and recordsFiltered and pass unit_mech/A…
isaak Jan 6, 2025
fe4163c
update BrAPI_v1 mech tests to reflect changes to new cvterm entries i…
isaak Jan 8, 2025
7a259a9
update BrAPIV2 phenotying mech test to reflect new cvterm entries in …
isaak Jan 8, 2025
d264b95
fix lint test failures
isaak Jan 8, 2025
9506d26
Merge branch 'master' into topic/solgs/store-pca-results
isaak Jan 13, 2025
7e74097
limit loading pca results to once, regardless of how many times a use…
isaak Jan 20, 2025
ee1cdb3
retrieve the latest analysis job details
isaak Jan 27, 2025
364b59b
apply Prettier formatting
isaak Jan 27, 2025
a870075
apply formatting
isaak Jan 27, 2025
d887c3d
show Run PCA again, if data type changes
isaak Feb 3, 2025
2a563b8
apply Prettier formatting
isaak Feb 3, 2025
2a4c13f
undo Prettier formatting
isaak Feb 3, 2025
c34f811
strip string chars from dataset and list ids
isaak Feb 3, 2025
63406d0
add _trial__ to germplasm suffix
isaak Feb 4, 2025
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update BrAPIV2 phenotying mech test to reflect new cvterm entries in …
…the fixture db
isaak committed Jan 8, 2025
commit 7a259a94d51853a54a19c68f0f735b9a047cb9f6
6 changes: 3 additions & 3 deletions t/unit_mech/AJAX/_BrAPIv2_phenotyping.t
Original file line number Diff line number Diff line change
@@ -184,7 +184,7 @@ is_deeply($response, { 'result' => {'data' => [ { 'collector' => 'John Doe', 'ob
$mech->get_ok('http://localhost:3010/brapi/v2/variables?pageSize=2');
$response = decode_json $mech->content;
#print STDERR "\n\n" . Dumper$response;
is_deeply($response, {'metadata' => {'status' => [{'messageType' => 'INFO','message' => 'BrAPI base call found with page=0, pageSize=2'},{'message' => 'Loading CXGN::BrAPI::v2::ObservationVariables','messageType' => 'INFO'},{'message' => 'Observationvariable search result constructed','messageType' => 'INFO'}],'pagination' => {'totalCount' => 257,'pageSize' => 2,'totalPages' => 129,'currentPage' => 0},'datafiles' => []},'result' => {'data' => [ { 'documentationURL' => '', 'growthStage' => undef, 'institution' => undef, 'observationVariableDbId' => '70692', 'additionalInfo' => {}, 'observationVariableName' => 'abscisic acid content of leaf ug/g|CO_334:0000047', 'synonyms' => [ 'abscon', 'AbsCt_Meas_ugg' ], 'language' => 'eng', 'ontologyReference' => { 'ontologyName' => 'CO_334', 'documentationLinks' => undef, 'ontologyDbId' => '186', 'version' => undef }, 'commonCropName' => 'Cassava', 'contextOfUse' => undef, 'observationVariablePUI' => 'CO_334:0000047', 'method' => {}, 'scientist' => undef, 'trait' => { 'attribute' => undef, 'synonyms' => [ 'abscon', 'AbsCt_Meas_ugg' ], 'additionalInfo' => {}, 'alternativeAbbreviations' => undef, 'entity' => undef, 'traitDescription' => 'Abscisic acid content of leaf sample.', 'attributePUI' => undef, 'externalReferences' => [ { 'referenceId' => 'CO_334:0000047', 'referenceSource' => 'Crop Ontology' } ], 'entityPUI' => undef, 'status' => 'active', 'mainAbbreviation' => undef, 'traitPUI' => undef, 'traitClass' => undef, 'traitDbId' => '70692', 'traitName' => 'abscisic acid content of leaf ug/g', 'ontologyReference' => { 'documentationLinks' => undef, 'ontologyName' => 'CO_334', 'version' => undef, 'ontologyDbId' => '186' } }, 'defaultValue' => '', 'status' => 'active', 'externalReferences' => [ { 'referenceId' => 'CO_334:0000047', 'referenceSource' => 'Crop Ontology' } ], 'scale' => { 'dataType' => 'Text', 'decimalPlaces' => undef, 'scalePUI' => undef, 'ontologyReference' => undef, 'scaleDbId' => undef, 'scaleName' => undef, 'externalReferences' => undef, 'validValues' => { 'categories' => undef, 'maximumValue' => undef, 'minimumValue' => undef }, 'units' => undef, 'additionalInfo' => undef }, 'submissionTimestamp' => undef }, { 'defaultValue' => '', 'status' => 'active', 'scale' => { 'externalReferences' => undef, 'scaleDbId' => undef, 'scaleName' => undef, 'additionalInfo' => undef, 'units' => undef, 'validValues' => { 'categories' => undef, 'maximumValue' => undef, 'minimumValue' => undef }, 'dataType' => 'Text', 'ontologyReference' => undef, 'decimalPlaces' => undef, 'scalePUI' => undef }, 'externalReferences' => [ { 'referenceId' => 'CO_334:0000121', 'referenceSource' => 'Crop Ontology' } ], 'submissionTimestamp' => undef, 'ontologyReference' => { 'documentationLinks' => undef, 'ontologyName' => 'CO_334', 'version' => undef, 'ontologyDbId' => '186' }, 'commonCropName' => 'Cassava', 'observationVariablePUI' => 'CO_334:0000121', 'contextOfUse' => undef, 'method' => {}, 'scientist' => undef, 'trait' => { 'ontologyReference' => { 'documentationLinks' => undef, 'ontologyName' => 'CO_334', 'version' => undef, 'ontologyDbId' => '186' }, 'traitName' => 'amylopectin content ug/g in percentage', 'traitDbId' => '70761', 'traitClass' => undef, 'status' => 'active', 'traitPUI' => undef, 'mainAbbreviation' => undef, 'entityPUI' => undef, 'externalReferences' => [ { 'referenceSource' => 'Crop Ontology', 'referenceId' => 'CO_334:0000121' } ], 'entity' => undef, 'traitDescription' => 'Estimation of amylopectin content of cassava roots in percentage(%).', 'attributePUI' => undef, 'alternativeAbbreviations' => undef, 'additionalInfo' => {}, 'attribute' => undef, 'synonyms' => [ 'amylp', 'AmylPCt_Meas_pct' ] }, 'additionalInfo' => {}, 'observationVariableName' => 'amylopectin content ug/g in percentage|CO_334:0000121', 'synonyms' => [ 'amylp', 'AmylPCt_Meas_pct' ], 'language' => 'eng', 'documentationURL' => '', 'growthStage' => undef, 'institution' => undef, 'observationVariableDbId' => '70761'} ] }});
is_deeply($response, {'metadata' => {'status' => [{'messageType' => 'INFO','message' => 'BrAPI base call found with page=0, pageSize=2'},{'message' => 'Loading CXGN::BrAPI::v2::ObservationVariables','messageType' => 'INFO'},{'message' => 'Observationvariable search result constructed','messageType' => 'INFO'}],'pagination' => {'totalCount' => 267,'pageSize' => 2,'totalPages' => 134,'currentPage' => 0},'datafiles' => []},'result' => {'data' => [ { 'documentationURL' => '', 'growthStage' => undef, 'institution' => undef, 'observationVariableDbId' => '70692', 'additionalInfo' => {}, 'observationVariableName' => 'abscisic acid content of leaf ug/g|CO_334:0000047', 'synonyms' => [ 'abscon', 'AbsCt_Meas_ugg' ], 'language' => 'eng', 'ontologyReference' => { 'ontologyName' => 'CO_334', 'documentationLinks' => undef, 'ontologyDbId' => '186', 'version' => undef }, 'commonCropName' => 'Cassava', 'contextOfUse' => undef, 'observationVariablePUI' => 'CO_334:0000047', 'method' => {}, 'scientist' => undef, 'trait' => { 'attribute' => undef, 'synonyms' => [ 'abscon', 'AbsCt_Meas_ugg' ], 'additionalInfo' => {}, 'alternativeAbbreviations' => undef, 'entity' => undef, 'traitDescription' => 'Abscisic acid content of leaf sample.', 'attributePUI' => undef, 'externalReferences' => [ { 'referenceId' => 'CO_334:0000047', 'referenceSource' => 'Crop Ontology' } ], 'entityPUI' => undef, 'status' => 'active', 'mainAbbreviation' => undef, 'traitPUI' => undef, 'traitClass' => undef, 'traitDbId' => '70692', 'traitName' => 'abscisic acid content of leaf ug/g', 'ontologyReference' => { 'documentationLinks' => undef, 'ontologyName' => 'CO_334', 'version' => undef, 'ontologyDbId' => '186' } }, 'defaultValue' => '', 'status' => 'active', 'externalReferences' => [ { 'referenceId' => 'CO_334:0000047', 'referenceSource' => 'Crop Ontology' } ], 'scale' => { 'dataType' => 'Text', 'decimalPlaces' => undef, 'scalePUI' => undef, 'ontologyReference' => undef, 'scaleDbId' => undef, 'scaleName' => undef, 'externalReferences' => undef, 'validValues' => { 'categories' => undef, 'maximumValue' => undef, 'minimumValue' => undef }, 'units' => undef, 'additionalInfo' => undef }, 'submissionTimestamp' => undef }, { 'defaultValue' => '', 'status' => 'active', 'scale' => { 'externalReferences' => undef, 'scaleDbId' => undef, 'scaleName' => undef, 'additionalInfo' => undef, 'units' => undef, 'validValues' => { 'categories' => undef, 'maximumValue' => undef, 'minimumValue' => undef }, 'dataType' => 'Text', 'ontologyReference' => undef, 'decimalPlaces' => undef, 'scalePUI' => undef }, 'externalReferences' => [ { 'referenceId' => 'CO_334:0000121', 'referenceSource' => 'Crop Ontology' } ], 'submissionTimestamp' => undef, 'ontologyReference' => { 'documentationLinks' => undef, 'ontologyName' => 'CO_334', 'version' => undef, 'ontologyDbId' => '186' }, 'commonCropName' => 'Cassava', 'observationVariablePUI' => 'CO_334:0000121', 'contextOfUse' => undef, 'method' => {}, 'scientist' => undef, 'trait' => { 'ontologyReference' => { 'documentationLinks' => undef, 'ontologyName' => 'CO_334', 'version' => undef, 'ontologyDbId' => '186' }, 'traitName' => 'amylopectin content ug/g in percentage', 'traitDbId' => '70761', 'traitClass' => undef, 'status' => 'active', 'traitPUI' => undef, 'mainAbbreviation' => undef, 'entityPUI' => undef, 'externalReferences' => [ { 'referenceSource' => 'Crop Ontology', 'referenceId' => 'CO_334:0000121' } ], 'entity' => undef, 'traitDescription' => 'Estimation of amylopectin content of cassava roots in percentage(%).', 'attributePUI' => undef, 'alternativeAbbreviations' => undef, 'additionalInfo' => {}, 'attribute' => undef, 'synonyms' => [ 'amylp', 'AmylPCt_Meas_pct' ] }, 'additionalInfo' => {}, 'observationVariableName' => 'amylopectin content ug/g in percentage|CO_334:0000121', 'synonyms' => [ 'amylp', 'AmylPCt_Meas_pct' ], 'language' => 'eng', 'documentationURL' => '', 'growthStage' => undef, 'institution' => undef, 'observationVariableDbId' => '70761'} ] }});

$mech->get_ok('http://localhost:3010/brapi/v2/variables/70752');
$response = decode_json $mech->content;
@@ -226,8 +226,8 @@ is_deeply($response, {
'pagination' => {
'pageSize' => 1,
'currentPage' => 1,
'totalPages' => 7024,
'totalCount' => 7024
'totalPages' => 7035,
'totalCount' => 7035
}
},
'result' => {