From 096d64bddd1458b7625bc2bc982096507ebd5ac0 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 16 May 2012 14:41:51 +0000
Subject: [PATCH] SP-31 BIS-28 : Have the metabolomics2 data set handler use
the METABOLITE_INTENSITIES data set type
SVN: 25288
---
eu_basynthec/dist/etc/data-set-validator.py | 4 +---
.../etc/metabolomics2/data-set-handler.py | 4 ++--
eu_basynthec/etc/service.properties | 24 +++++++++----------
3 files changed, 15 insertions(+), 17 deletions(-)
diff --git a/eu_basynthec/dist/etc/data-set-validator.py b/eu_basynthec/dist/etc/data-set-validator.py
index 8af662eac42..567cb2e9fad 100644
--- a/eu_basynthec/dist/etc/data-set-validator.py
+++ b/eu_basynthec/dist/etc/data-set-validator.py
@@ -1,6 +1,4 @@
-import os
-import re
-
+
def validate_data_set_file(file):
errors = []
return errors
diff --git a/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py b/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
index 1cb69b52a57..30a4a053675 100644
--- a/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
+++ b/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
@@ -157,7 +157,7 @@ timeSeriesData = TimeSeriesDataExcel.createTimeSeriesDataExcel(incoming.getAbsol
dataStart = getInitialDataRowAndCol(timeSeriesData.getMetadataMap())
# create the data set and assign the metadata from the file
-dataset = tr.createNewDataSet("METABOLITE_INTENSITIES_GROUPED")
+dataset = tr.createNewDataSet("METABOLITE_INTENSITIES")
metadata = timeSeriesData.getMetadataMap()
metadata["STRAIN_NAMES"] = extract_strains(dataStart[0], dataStart[1])
assign_properties(dataset, metadata)
@@ -167,7 +167,7 @@ original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
set_data_type(original_dataset)
store_original_data(tr, original_dataset, "xls")
-tsv_dataset = tr.createNewDataSet("TSV_EXPORT")
+tsv_dataset = tr.createNewDataSet("TSV_MULTISTRAIN_EXPORT")
set_data_type(tsv_dataset)
convert_data_to_tsv(tr, tsv_dataset, "tsv")
diff --git a/eu_basynthec/etc/service.properties b/eu_basynthec/etc/service.properties
index a513c2e2f64..2bd62a7a9ae 100644
--- a/eu_basynthec/etc/service.properties
+++ b/eu_basynthec/etc/service.properties
@@ -1,7 +1,7 @@
# Unique code of this Data Store Server. Not more than 40 characters.
-data-store-server-code = BASYNTHEC
+data-store-server-code = DSS1
-data-folder = targets/playground/data
+data-folder = ../eu_basynthec/targets/data
# The root directory of the data store
storeroot-dir = ${data-folder}/store
@@ -127,8 +127,8 @@ main-thread.delete-unidentified = true
main-thread.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-main-thread.script-path = dist/etc/data-set-handler.py
-main-thread.validation-script-path = dist/etc/data-set-validator.py
+main-thread.script-path = ../eu_basynthec/dist/etc/data-set-handler.py
+main-thread.validation-script-path = ../eu_basynthec/dist/etc/data-set-validator.py
# ---------------------------------------------------------------------------
# metabolomics thread configuration
@@ -138,8 +138,8 @@ metabolomics.incoming-data-completeness-condition = auto-detection
metabolomics.delete-unidentified = true
metabolomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
metabolomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-metabolomics.script-path = dist/etc/metabolomics2/data-set-handler.py
-metabolomics.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/metabolomics2/data-set-validator.py
+metabolomics.script-path = ../eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
+metabolomics.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/metabolomics2/data-set-validator.py
# ---------------------------------------------------------------------------
# growth-profiles thread configuration
@@ -149,8 +149,8 @@ growth-profiles.incoming-data-completeness-condition = auto-detection
growth-profiles.delete-unidentified = true
growth-profiles.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
growth-profiles.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-growth-profiles.script-path = dist/etc/growth-profiles/data-set-handler.py
-growth-profiles.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/growth-profiles/data-set-validator.py
+growth-profiles.script-path = ../eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
+growth-profiles.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/growth-profiles/data-set-validator.py
# ---------------------------------------------------------------------------
# transcriptomics thread configuration
@@ -160,8 +160,8 @@ transcriptomics.incoming-data-completeness-condition = auto-detection
transcriptomics.delete-unidentified = true
transcriptomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
transcriptomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-transcriptomics.script-path = dist/etc/transcriptomics/data-set-handler.py
-transcriptomics.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/transcriptomics/data-set-validator.py
+transcriptomics.script-path = ../eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
+transcriptomics.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/transcriptomics/data-set-validator.py
# ---------------------------------------------------------------------------
# proteomics thread configuration
@@ -171,8 +171,8 @@ proteomics.incoming-data-completeness-condition = auto-detection
proteomics.delete-unidentified = true
proteomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
proteomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-proteomics.script-path = dist/etc/proteomics/data-set-handler.py
-proteomics.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/proteomics/data-set-validator.py
+proteomics.script-path = ../eu_basynthec/dist/etc/proteomics/data-set-handler.py
+proteomics.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/proteomics/data-set-validator.py
#
--
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