From 233d07ca6b65e1b2b9a7f44d7f442b71ff2fda13 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 19 Jun 2012 11:23:26 +0000
Subject: [PATCH] SP-130, CCS-11: improve performance
SVN: 25776
---
.../demo-proteomics-aggregation/script.py | 35 +++++++++++++------
1 file changed, 24 insertions(+), 11 deletions(-)
diff --git a/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/script.py b/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/script.py
index b0e5537147d..cc5503e87f5 100644
--- a/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/script.py
+++ b/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/script.py
@@ -1,3 +1,4 @@
+from java.util import ArrayList
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import MatchClause
@@ -63,14 +64,30 @@ def gatherExperimentsAndSamples(space):
searchExperiment2msInjectionSamplesDict[expId] = [msInjectionSample]
return bioSample2ExperimentDict, msInjectionSample2bioSamplesDict, \
searchExperiment2msInjectionSamplesDict, searchExperimentsByPermIdDict
+
+def createPermIdList(searchExperimentsByPermIdDict):
+ permIds = ""
+ for exp in searchExperimentsByPermIdDict.values():
+ if len(permIds) > 0:
+ permIds = permIds + ", "
+ permIds = permIds + "'" + exp.permId + "'"
+ return permIds
def aggregate(parameters, tableBuilder):
space = parameters.get('space').upper()
bioSample2ExperimentDict, msInjectionSample2bioSamplesDict, \
searchExperiment2msInjectionSamplesDict, searchExperimentsByPermIdDict \
= gatherExperimentsAndSamples(space)
-
- protein = parameters.get('protein')
+
+ tableBuilder.addHeader(BIO_EXPERIMENT)
+ tableBuilder.addHeader(BIO_SAMPLE)
+ tableBuilder.addHeader(MS_SAMPLE)
+ tableBuilder.addHeader(SEARCH_EXPERIMENT)
+ tableBuilder.addHeader(SEARCH_EXPERIMENT_PERM_ID)
+ tableBuilder.addHeader(ACCESION_NUMBER)
+ tableBuilder.addHeader(DESCRIPTION)
+ protein = '%' + parameters.get('protein') + '%'
+ permIds = createPermIdList(searchExperimentsByPermIdDict)
result = queryService.select("proteomics-db",
"""select e.perm_id, accession_number, description
from experiments as e join data_sets as d on d.expe_id = e.id
@@ -78,16 +95,11 @@ def aggregate(parameters, tableBuilder):
join identified_proteins as ip on ip.prot_id = p.id
join sequences as s on ip.sequ_id = s.id
join protein_references as pr on s.prre_id = pr.id
- where accession_number like ?{1} or description like ?{1}
+ where e.perm_id in ("""
+ + permIds +
+ """) and (accession_number like ?{1} or description like ?{1})
order by perm_id""",
- ['%' + protein + '%'])
- tableBuilder.addHeader(BIO_EXPERIMENT)
- tableBuilder.addHeader(BIO_SAMPLE)
- tableBuilder.addHeader(MS_SAMPLE)
- tableBuilder.addHeader(SEARCH_EXPERIMENT)
- tableBuilder.addHeader(SEARCH_EXPERIMENT_PERM_ID)
- tableBuilder.addHeader(ACCESION_NUMBER)
- tableBuilder.addHeader(DESCRIPTION)
+ [protein])
for resultRow in result:
permId = resultRow.get('perm_id')
if (permId in searchExperimentsByPermIdDict):
@@ -106,3 +118,4 @@ def aggregate(parameters, tableBuilder):
row.setCell(SEARCH_EXPERIMENT_PERM_ID, permId)
row.setCell(ACCESION_NUMBER, resultRow.get('accession_number'))
row.setCell(DESCRIPTION, resultRow.get('description'))
+ result.close()
--
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