Adjust transmart-batch to load high-dim data in the new way #122
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Fix NOS-4 - loading of gene expression data Make tm-batch load high-dim data with the new observations/modifiers that this data needs in 17.1: - High dim observations having textual value with sample name (subject sample mapping). - Modifier on it specifying high dim data type and as value assay ID.
| sourcesystem_cd: STUDY_ID | ||
| assert count == 45 | ||
| } | ||
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it would be nice to add a test for the column values of the HD observation rows.
...art-batch/src/main/groovy/org/transmartproject/batch/facts/ObservationFactStepsConfig.groovy
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| // add modifier for each assay_id | ||
| String modifier = 'TRANSMART:HIGHDIM:' + platform.markerType.toUpperCase() | ||
| for (int i=0; i<result.size(); i++){ | ||
| rowSet.instanceNum = i+1 |
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it does not look right. instance_id should be unique for each row. Pass it maybe to addValue method?
| """, [study_num: study.studyNum] | ||
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| if (trialVisit) { | ||
| def t = trialVisit?.first() |
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Would it work for the data people to bind row with a first trial visit from the study? If so you should do it once per job.
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I wasn't sure how to get a trial visit there and what to do, if there is more than one visit or none (for now there is a function to add a default visit then)
transmart-batch/src/main/groovy/org/transmartproject/batch/facts/DummyFactGenerator.groovy
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| @@ -72,4 +110,30 @@ class DummyFactGenerator extends AbstractItemCountingItemStreamItemReader<Clinic | |||
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| @Override | |||
| protected void doClose() throws Exception {} | |||
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| private List<Map<String, Object>> getAssayIds(String sample_id) { | |||
| List result = jdbcTemplate.queryForList """ | |||
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What about making the result of the query the main data source, instead of reading from subjectConceptMappingFileRows?
Added conditional before destroying analysis dialog
Added conditional before destroying analysis dialog
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Fix NOS-4 - loading of gene expression data
Make tm-batch load high-dim data with the new observations/modifiers in 17.1:
sample mapping).