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Commit a930a86a authored by barillac's avatar barillac
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script updated to import txt and images files correctly to database. 

SVN: 28615
parent 6c98f518
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screening/bsa_lab/czi-metadata-dropbox.py
+ 23
− 23
View file @ a930a86a
...@@ -155,37 +155,38 @@ def process(transaction): ...@@ -155,37 +155,38 @@ def process(transaction):
directoryName = os.path.basename(incoming.getPath()) directoryName = os.path.basename(incoming.getPath())
names = re.split(r"[-]",directoryName) names = re.split(r"[-]",directoryName)
projectName = names[0] + "-IMG" projectName = names[0] + "-IMG"
experimentName = names[1] experimentName = "-".join(names[1:])
experiment = "/PANTAZIS_GROUP/" + projectName + "/" + experimentName experiment = "/PANTAZIS_GROUP/" + projectName + "/" + experimentName
exp = transaction.getExperiment(experiment) exp = transaction.getExperiment(experiment)
if not exp: if not exp:
exp = transaction.createNewExperiment(experiment, 'IMAGING') exp = transaction.createNewExperiment(experiment, 'IMAGING')
for name in cziInfo.keys(): for name in cziInfo.keys():
sampleIdentifier = "/PANTAZIS_GROUP/" + name sampleIdentifier = "/PANTAZIS_GROUP/" + name
print "sample is", sampleIdentifier
sample = transaction.createNewSample(sampleIdentifier, "MICROSCOPY_IMG") sample = transaction.createNewSample(sampleIdentifier, "MICROSCOPY_IMG")
sample.setExperiment(exp) sample.setExperiment(exp)
sample.setPropertyValue("OBJECTIVE", cziInfo[name]["objective"]) sample.setPropertyValue("OBJECTIVE", cziInfo[name]["objective"])
sample.setPropertyValue("SCALING", cziInfo[name]["scaling"]) sample.setPropertyValue("SCALING", cziInfo[name]["scaling"])
# sample.setPropertyValue("Z_STEP_SIZE", cziInfo[name]["z_step_size"]) sample.setPropertyValue("Z_STEP_SIZE", cziInfo[name]["z_step_size"])
# sample.setPropertyValue("PIXEL_DWELL_TIME", cziInfo[name]["pixel_dwell_time"]) sample.setPropertyValue("PIXEL_DWELL_TIME", cziInfo[name]["pixel_dwell_time"])
# sample.setPropertyValue("CHANNEL_NAME_0", cziInfo[name]["channel_name_0"]) sample.setPropertyValue("CHANNEL_NAME_0", cziInfo[name]["channel_name_0"])
# sample.setPropertyValue("CHANNEL_NAME_1", cziInfo[name]["channel_name_1"]) sample.setPropertyValue("CHANNEL_NAME_1", cziInfo[name]["channel_name_1"])
# sample.setPropertyValue("CHANNEL_NAME_2", cziInfo[name]["channel_name_2"]) sample.setPropertyValue("CHANNEL_NAME_2", cziInfo[name]["channel_name_2"])
# sample.setPropertyValue("CHANNEL_NAME_3", cziInfo[name]["channel_name_3"]) sample.setPropertyValue("CHANNEL_NAME_3", cziInfo[name]["channel_name_3"])
# sample.setPropertyValue("CHANNEL_NAME_4", cziInfo[name]["channel_name_4"]) sample.setPropertyValue("CHANNEL_NAME_4", cziInfo[name]["channel_name_4"])
# sample.setPropertyValue("CHANNEL_NAME_5", cziInfo[name]["channel_name_5"]) sample.setPropertyValue("CHANNEL_NAME_5", cziInfo[name]["channel_name_5"])
# sample.setPropertyValue("CHANNEL_NAME_6", cziInfo[name]["channel_name_6"]) sample.setPropertyValue("CHANNEL_NAME_6", cziInfo[name]["channel_name_6"])
# sample.setPropertyValue("CHANNEL_NAME_7", cziInfo[name]["channel_name_7"]) sample.setPropertyValue("CHANNEL_NAME_7", cziInfo[name]["channel_name_7"])
# sample.setPropertyValue("DETECTOR_GAIN_0", cziInfo[name]["detector_gain_0"]) sample.setPropertyValue("DETECTOR_GAIN_0", cziInfo[name]["detector_gain_0"])
# sample.setPropertyValue("DETECTOR_GAIN_1", cziInfo[name]["detector_gain_1"]) sample.setPropertyValue("DETECTOR_GAIN_1", cziInfo[name]["detector_gain_1"])
# sample.setPropertyValue("DETECTOR_GAIN_2", cziInfo[name]["detector_gain_2"]) sample.setPropertyValue("DETECTOR_GAIN_2", cziInfo[name]["detector_gain_2"])
# sample.setPropertyValue("DETECTOR_GAIN_3", cziInfo[name]["detector_gain_3"]) sample.setPropertyValue("DETECTOR_GAIN_3", cziInfo[name]["detector_gain_3"])
# sample.setPropertyValue("DETECTOR_GAIN_4", cziInfo[name]["detector_gain_4"]) sample.setPropertyValue("DETECTOR_GAIN_4", cziInfo[name]["detector_gain_4"])
# sample.setPropertyValue("DETECTOR_GAIN_5", cziInfo[name]["detector_gain_5"]) sample.setPropertyValue("DETECTOR_GAIN_5", cziInfo[name]["detector_gain_5"])
# sample.setPropertyValue("DETECTOR_GAIN_6", cziInfo[name]["detector_gain_6"]) sample.setPropertyValue("DETECTOR_GAIN_6", cziInfo[name]["detector_gain_6"])
# sample.setPropertyValue("DETECTOR_GAIN_7", cziInfo[name]["detector_gain_7"]) sample.setPropertyValue("DETECTOR_GAIN_7", cziInfo[name]["detector_gain_7"])
imageDataset = SimpleImageContainerDataConfig() imageDataset = SimpleImageContainerDataConfig()
imageDataset.setPlate("PANTAZIS_GROUP", name) imageDataset.setPlate("PANTAZIS_GROUP", name)
...@@ -197,11 +198,10 @@ def process(transaction): ...@@ -197,11 +198,10 @@ def process(transaction):
sampleNamePath = incoming.getPath() + '/' + name + '.czi' sampleNamePath = incoming.getPath() + '/' + name + '.czi'
metadataPath = incoming.getPath() + '/' + name + '-metadata.txt' metadataPath = incoming.getPath() + '/' + name + '-metadata.txt'
dataSet = transaction.createNewImageDataSet(imageDataset, File(sampleNamePath)) dataSet = transaction.createNewImageDataSet(imageDataset, File(sampleNamePath))
transaction.moveFile(sampleNamePath, dataSet)
transaction.moveFile(metadataPath, dataSet) transaction.moveFile(metadataPath, dataSet)
transaction.moveFile(sampleNamePath, dataSet)
......
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