SE-328 jython dropbox handler (example)

SVN: 19476

screening/etc/data-set-handler.py

+#! /usr/bin/env python
+# This is an example Jython dropbox for importing HCS image datasets
+
+import os
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier as identifier
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto as dto
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import ImageFileInfo, ImageDataSetInformation, Channel
+
+# ------------
+# You may want to modify this part.
+# ------------
+
+# type of the new dataset
+DATASET_TYPE = "HCS_IMAGE"
+# file format of files in a new dataset
+FILE_FORMAT = "TIFF"
+# space where the plate for which the dataset has been acquired exist
+SAMPLE_SPACE = "DEMO"
+# number of rile rows and columns on a well 
+TILE_ROWS_NUMBER = 2
+TILE_COLUMNS_NUMBER = 2
+# available channels, for each channel code and label have to be specified
+CHANNELS = [ Channel("DAPI", "DAPI"), Channel("FITC", "FITC"), Channel("CY5", "Cy5") ]
+
+
+# extracts code of the sample from the directory name
+def extract_sample_code(file_basename):
+    return file_basename.split(".")[0]
+
+# Creates ImageFileInfo for a given path to an image
+# Example file name: A - 1(fld 1 wv Cy5 - Cy5).tif
+def create_image_info(path):
+    basename = os.path.splitext(path)[0]
+
+    wellText = basename[0:find(basename, "(")] # A - 1
+    well = wellText.replace(" - ", "")
+    fieldText = basename[find(basename, "fld ")+4 : find(basename, " wv")]
+    try:
+        fieldNum = int(fieldText) - 1
+    except ValueError:
+        raise Exception("Cannot parse field number from '"+fieldText+"' in '"+basename+"' file name.")
+    channel = basename[rfind(basename, " - ") + 3 : -1]
+    
+    tileRow = (fieldNum / TILE_COLUMNS_NUMBER) + 1
+    tileCol = (fieldNum % TILE_COLUMNS_NUMBER) + 1
+    img = ImageFileInfo(channel, tileRow, tileCol, path)
+    img.setWell(well)
+    return img
+
+# ------------
+# You probably do not want to modify this part
+# ------------
+
+def rfind(text, pattern):
+    ix = text.rfind(pattern)
+    ensurePatternFound(ix, text, pattern)
+    return ix
+
+def find(text, pattern):
+    ix = text.find(pattern)
+    ensurePatternFound(ix, text, pattern)
+    return ix
+
+def ensurePatternFound(ix, file, pattern):
+    if ix == -1:
+        raise Exception("Cannot find '"+pattern+"' pattern in file name '"+file+"'")    
+
+def create_dataset():
+    basename = extract_file_basename(incoming.getName())
+    dataset = Dataset()
+    
+    dataset.dataset_type = DATASET_TYPE
+    dataset.file_format = FILE_FORMAT
+    dataset.sample_space = SAMPLE_SPACE
+    dataset.sample_code = extract_sample_code(basename)
+    
+    dataset.tile_rows_number = TILE_ROWS_NUMBER
+    dataset.tile_columns_number = TILE_COLUMNS_NUMBER
+    
+    return dataset
+
+def get_available_channels():
+    return CHANNELS
+
+class Dataset:
+    sample_code = None
+    sample_space = None
+    dataset_type = None
+    file_format = None
+    # -- imaging specific
+    tile_rows_number = -1
+    tile_columns_number = -1
+
+def create_image_infos(dir):
+    images = []
+    dir_path = dir.getPath()
+    for file in os.listdir(dir_path):
+        image = create_image_info(file)
+        images.append(image)
+    return images
+
+def set_dataset_info(registration_details, dataset):
+    data_set_info = registration_details.getDataSetInformation()
+    data_set_info.setSpaceCode(dataset.sample_space)
+    data_set_info.setSampleCode(dataset.sample_code)
+    registration_details.setFileFormatType(dto.FileFormatType(dataset.file_format));
+    registration_details.setDataSetType(dto.DataSetType(dataset.dataset_type));
+    registration_details.setMeasuredData(True);
+    # -- imaging specific
+    data_set_info.setTileGeometry(dataset.tile_rows_number, dataset.tile_columns_number)
+    images = create_image_infos(incoming)
+    data_set_info.setImages(images)
+    channels = get_available_channels()
+    data_set_info.setChannels(channels)
+    
+def extract_file_basename(filename):
+    lastDot = filename.rfind(".")
+    if lastDot != -1:
+        return filename[0:lastDot]
+    else:
+        return filename
+     
+dataset = create_dataset()
+registration_details = factory.createRegistrationDetails()
+set_dataset_info(registration_details, dataset)
+service.queueDataSetRegistration(incoming, registration_details)
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