From 8dbcea2003cacb477219639c0f6b9c13fb04bfb6 Mon Sep 17 00:00:00 2001
From: barillac <barillac>
Date: Wed, 30 Oct 2013 09:54:07 +0000
Subject: [PATCH] dropbox script for importing movies of genes
SVN: 30059
---
screening/sinergia/import-genes.py | 75 ++++++++++++++++++++++++++++++
1 file changed, 75 insertions(+)
create mode 100644 screening/sinergia/import-genes.py
diff --git a/screening/sinergia/import-genes.py b/screening/sinergia/import-genes.py
new file mode 100644
index 00000000000..c111588e48e
--- /dev/null
+++ b/screening/sinergia/import-genes.py
@@ -0,0 +1,75 @@
+#! /usr/bin/env python
+"""
+ Script for uploading gene data. Data is organized in directories called as gene names. In each of these are:
+ two pdf files (gene and RNA); 10 mp4 gene files; 10 mp4 control files.
+ Samples with gene names must already exist in openBIS (created with import-clusters.py script). All data should go in the corresponding sample.
+"""
+
+import os, re, glob, shutil
+from time import *
+from datetime import *
+
+
+from java.io import File
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig, ImageMetadata, Location
+from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageContainerDataConfig, ChannelColor
+from loci.formats import ImageReader
+
+print "###################################################"
+tz=localtime()[3]-gmtime()[3]
+d=datetime.now()
+print d.strftime("%Y-%m-%d %H:%M:%S GMT"+"%+.2d" % tz+":00")
+
+
+def process(transaction):
+ incoming = transaction.getIncoming()
+ geneName = os.path.basename(incoming.getPath())
+
+#Set project/experiment/sample
+ project = transaction.getProject("/SINERGIA/CLUSTERS")
+ exp = transaction.getExperiment("/SINERGIA/CLUSTERS/CLUSTERS")
+ sample = transaction.getSample("/SINERGIA/" + geneName)
+
+#upload the gene pdf and the RNA pdf
+ for pdf in glob.glob(os.path.join(incoming.getPath(), '*.pdf')):
+ dataSetPDF = transaction.createNewDataSet()
+ dataSetPDF.setDataSetType("PDF")
+ dataSetPDF.setSample(sample)
+ transaction.moveFile(pdf, dataSetPDF)
+
+# upload the 10 tif images for each gene
+# tifDir = incoming.getPath() + "/tiffs"
+# if not os.path.exists(tifDir):
+# os.makedirs(tifDir)
+# for tif in glob.glob(os.path.join(incoming.getPath(), '*.tif')):
+# shutil.move(tif, tifDir)
+# dataSetTIF = transaction.createNewDataSet()
+# dataSetTIF.setDataSetType("TIF_IMAGES")
+# dataSetTIF.setSample(sample)
+# transaction.moveFile(tifDir, dataSetTIF)
+
+#upload the 10 control movies
+ videoControlDir = incoming.getPath() + "/controlVideos"
+ if not os.path.exists(videoControlDir):
+ os.makedirs(videoControlDir)
+ for mp4 in glob.glob(os.path.join(incoming.getPath(), 'control*.mp4')):
+ shutil.move(mp4, videoControlDir)
+ dataSetMP4Control = transaction.createNewDataSet()
+ dataSetMP4Control.setDataSetType("VIDEOS")
+ dataSetMP4Control.setSample(sample)
+ transaction.moveFile(videoControlDir, dataSetMP4Control)
+
+#upload the 10 gene synthetic movies
+ videoGeneDir = incoming.getPath() + "/geneVideos"
+ if not os.path.exists(videoGeneDir):
+ os.makedirs(videoGeneDir)
+ for mp4 in glob.glob(os.path.join(incoming.getPath(), '*.mp4')):
+ shutil.move(mp4, videoGeneDir)
+ dataSetMP4Gene = transaction.createNewDataSet()
+ dataSetMP4Gene.setDataSetType("VIDEOS")
+ dataSetMP4Gene.setSample(sample)
+ transaction.moveFile(videoGeneDir, dataSetMP4Gene)
+
+
+
--
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