dropbox script to import antibodies from BOXIT into openBIS

SVN: 32862

plasmid/source/drop-boxes/BOXIT-integration/import_antibody.py

+#!/usr/bin/env python
+
+
+import sys, csv, os, re
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
+from datetime import datetime
+
+print "########################################################"
+
+SPACE_CODE = "INVENTORY"
+PROJECT_CODE = "MATERIALS"
+PROJECT_ID = "/%(SPACE_CODE)s/%(PROJECT_CODE)s" % vars()
+EXPERIMENT_CODE = "ANTIBODY"
+EXPERIMENT_ID = "/%(SPACE_CODE)s/%(PROJECT_CODE)s/%(EXPERIMENT_CODE)s" % vars()
+
+# A map that has the sample property codes as the key and the CSV header as the value
+CSV_TO_PROPERTY_MAPPING = {
+  # PROPERTY_CODE : (CSV_HEADER, FORMAT)
+  'NAME'  : ('Antibody ID', DataType.VARCHAR),
+  'ANTIBODY_ID_NR': ('antibody_id_nr', DataType.VARCHAR),  
+  'ANTIGEN ': ('antigen', DataType.VARCHAR),
+  'BARCODE' : ('barcode', DataType.VARCHAR),
+  'BARCODE_LABEL' : ('barcode', DataType.VARCHAR),
+  'ANTIBODY_FACS_BLOCK' : ('block facs', DataType.VARCHAR),
+  'ANTIBODY_IF_BLOCK' : ('block IFF', DataType.VARCHAR),
+  'ANTIBODY_WB_BLOCK' : ('block western', DataType.VARCHAR),
+  'BOX' : ('box', DataType.VARCHAR),
+  'CATALOGUE_NUMBER' : ('catalog id #', DataType.VARCHAR),
+  'CLASS' : ('class', DataType.VARCHAR),
+  'CLONE' : ('clone', DataType.VARCHAR),
+  'ANTIBODY_FACS_CONC' : ('conc facs', DataType.VARCHAR), 
+  'ANTIBODY_IF_CONC'  : ('conc IFF', DataType.VARCHAR),
+  'ANTIBODY_IP_CONC' : ('conc ip', DataType.VARCHAR),
+  'ANTIBODY_WB_CONC' : ('ANTIBODY_WB_CONC', DataType.VARCHAR), 
+  'ANTIBODY_CONCENTRATION' : ('concentration', DataType.VARCHAR),   
+  'ANTIBODY_CROSSREACTIVITY'  : ('crossreactivity', DataType.VARCHAR),  
+  'ANTIBODY_FACS_FIX' : ('fix facs', DataType.VARCHAR),
+  'ANTIBODY_IF_FIX' : ('fix IFF', DataType.VARCHAR),
+  'ANTIBODY_WB_FIX' : ('fix western', DataType.VARCHAR),
+  'COMMENTS'  : ('info', DataType.VARCHAR),
+  'LOTNUMBER' : ('lotnumber', DataType.VARCHAR),
+  'MODIFIED_BY': ('modified by', DataType.VARCHAR), 
+  'ANTIBODY_FACS_NOTES' : ('notes FACS', DataType.VARCHAR),
+  'ANTIBODY_IF_NOTES' : ('notes IFF', DataType.VARCHAR),
+  'ANTIBODY_IP_NOTES': ('notes IP', DataType.VARCHAR),
+  'ANTIBODY_WB_NOTES' : ('notes western', DataType.VARCHAR),
+  'RACK' : ('rack', DataType.VARCHAR),
+  'PUBLISHED' : ('reference', DataType.VARCHAR),
+  'SERIAL_NUMBER' : ('serial number', DataType.INTEGER),
+  'ANTIGEN_SIZE'  : ('size', DataType.VARCHAR),
+  'BOX_NUMBER' : ('antibody ID data box::box label', DataType.VARCHAR),
+  'FROZEN_BY' : ('antibody ID data box::frozen by', DataType.VARCHAR),
+  'FREEZER_NAME'  : ('antibody ID data box::location', DataType.CONTROLLEDVOCABULARY),
+  'BOX_POSITION': ('antibody ID data box::position', DataType.VARCHAR),
+
+}
+
+#create a space if it does not exist
+def create_space_if_needed(tr):
+  space = tr.getSpace(SPACE_CODE)
+  if None == space:
+    space = tr.createNewSpace(SPACE_CODE, None)
+    space.setDescription("Inventory space")
+
+#create a project if it does not exist
+def create_project_if_needed(tr):
+  project = tr.getProject(PROJECT_ID)
+  if None == project:
+    create_space_if_needed(tr)
+    project = tr.createNewProject(PROJECT_ID)
+    project.setDescription("Materials purchased or produced in the lab")
+
+#create an experiment if it does not exist
+def create_experiment_if_needed(tr):
+  """ Get the specified experiment or register it if necessary """
+  exp = tr.getExperiment(EXPERIMENT_ID)
+  if None == exp:
+    create_project_if_needed(tr)
+    exp = tr.createNewExperiment(EXPERIMENT_ID, 'DEFAULT_EXPERIMENT')
+    
+  return exp
+
+#parse the csv file exported form Filemaker
+def parse_incoming(tr,exp): 
+  data_rows = []
+  f = open(tr.getIncoming().getAbsolutePath(), 'rU')
+  dialect = csv.Sniffer().sniff(f.read())
+  f.seek(0)
+  reader = csv.DictReader(f,  dialect = dialect)
+  
+  ##
+  ## 0. Current sample and storage properties being used
+  ##
+  storageProperties = [{
+    "FREEZER_NAME" : "FREEZER_NAME",
+    "ROW" : "ROW",
+    "COLUMN" : "COLUMN",
+    "BOX_NUMBER" : "BOX_NUMBER",
+    "BOX_POSITION" : "BOX_POSITION",
+    "USER_ID" : "USER_PROPERTY"
+  }, {
+    "FREEZER_NAME" : "FREEZER_NAME_2",
+    "ROW" : "ROW_2",
+    "COLUMN" : "COLUMN_2",
+    "BOX_NUMBER" : "BOX_NUMBER_2",
+    "BOX_POSITION" : "BOX_POSITION_2",
+    "USER_ID" : "USER_PROPERTY_2"
+  }, {
+    "FREEZER_NAME" : "FREEZER_NAME_3",
+    "ROW" : "ROW_3",
+    "COLUMN" : "COLUMN_3",
+    "BOX_NUMBER" : "BOX_NUMBER_3",
+    "BOX_POSITION" : "BOX_POSITION_3",
+    "USER_ID" : "USER_PROPERTY_3"
+  }, {
+    "FREEZER_NAME" : "FREEZER_NAME_4",
+    "ROW" : "ROW_4",
+    "COLUMN" : "COLUMN_4",
+    "BOX_NUMBER" : "BOX_NUMBER_4",
+    "BOX_POSITION" : "BOX_POSITION_4",
+    "USER_ID" : "USER_PROPERTY_4"
+  }, {
+    "FREEZER_NAME" : "FREEZER_NAME_5",
+    "ROW" : "ROW_5",
+    "COLUMN" : "COLUMN_5",
+    "BOX_NUMBER" : "BOX_NUMBER_5",
+    "BOX_POSITION" : "BOX_POSITION_5",
+    "USER_ID" : "USER_PROPERTY_5"
+  }, {
+    "FREEZER_NAME" : "FREEZER_NAME_6",
+    "ROW" : "ROW_6",
+    "COLUMN" : "COLUMN_6",
+    "BOX_NUMBER" : "BOX_NUMBER_6",
+    "BOX_POSITION" : "BOX_POSITION_6",
+    "USER_ID" : "USER_PROPERTY_6"
+  }, {
+    "FREEZER_NAME" : "FREEZER_NAME_7",
+    "ROW" : "ROW_7",
+    "COLUMN" : "COLUMN_7",
+    "BOX_NUMBER" : "BOX_NUMBER_7",
+    "BOX_POSITION" : "BOX_POSITION_7",
+    "USER_ID" : "USER_PROPERTY_7"
+  }, {
+    "FREEZER_NAME" : "FREEZER_NAME_8",
+    "ROW" : "ROW_8",
+    "COLUMN" : "COLUMN_8",
+    "BOX_NUMBER" : "BOX_NUMBER_8",
+    "BOX_POSITION" : "BOX_POSITION_8",
+    "USER_ID" : "USER_PROPERTY_8"
+  }, {
+    "FREEZER_NAME" : "FREEZER_NAME_9",
+    "ROW" : "ROW_9",
+    "COLUMN" : "COLUMN_9",
+    "BOX_NUMBER" : "BOX_NUMBER_9",
+    "BOX_POSITION" : "BOX_POSITION_9",
+    "USER_ID" : "USER_PROPERTY_9"
+  }, {
+    "FREEZER_NAME" : "FREEZER_NAME_10",
+    "ROW" : "ROW_10",
+    "COLUMN" : "COLUMN_10",
+    "BOX_NUMBER" : "BOX_NUMBER_10",
+    "BOX_POSITION" : "BOX_POSITION_10",
+    "USER_ID" : "USER_PROPERTY_10"
+  }
+  ];
+
+  
+  currentSample = None
+  storagePropertiesIndex = 0
+
+  for row in reader:
+    ##
+    ## 1. Check if there is an entity with all information or only new storage data
+    ##
+    onlyStorage = None
+    
+    space_code = SPACE_CODE
+    sample_code = row.get('ANTIBODY_ID_NR')
+    sample_id = "/%(space_code)s/%(sample_code)s" % vars()
+    
+    if sample_code != None and sample_code != '':
+      storagePropertiesIndex = 0
+      onlyStorage = False
+    else:
+      onlyStorage = True
+      storagePropertiesIndex += 1
+
+     
+    ##
+    ## 2. Depending on the outcome you set all fields or only new storage fields
+    ##
+    if not onlyStorage:
+      # 1. Set all properties
+
+      currentSample = tr.getSample(sample_id)
+      if not currentSample:
+        currentSample = tr.createNewSample(sample_id, 'ANTIBODY')
+      currentSample.setExperiment(exp)
+      
+      for key in CSV_TO_PROPERTY_MAPPING:
+        prop_value = row[CSV_TO_PROPERTY_MAPPING[key][0]]
+        if prop_value == '' or prop_value == None:
+          prop_value = 'n.a.'
+        currentSample.setPropertyValue(CSV_TO_PROPERTY_MAPPING[key][0],prop_value)
+    
+    else:
+      # 2. Set always the storage properties
+    
+
+      freezer_name_label =storageProperties[storagePropertiesIndex]['FREEZER_NAME']
+      freezer_name_value =row[CSV_TO_PROPERTY_MAPPING['FREEZER_NAME'][0]]
+      box_number_label =storageProperties[storagePropertiesIndex]['BOX_NUMBER']
+      box_number_value =row[CSV_TO_PROPERTY_MAPPING['BOX_NUMBER'][0]]
+      box_position_label = storageProperties[storagePropertiesIndex]['BOX_POSITION']
+      box_position_value = row[CSV_TO_PROPERTY_MAPPING['BOX_POSITION'][0]]
+  
+     # row_label =storageProperties[storagePropertiesIndex]['ROW']
+     # row_value =row[CSV_TO_PROPERTY_MAPPING['ROW'][0]]
+    #  column_label =storageProperties[storagePropertiesIndex]['COLUMN']
+     # column_value =row[CSV_TO_PROPERTY_MAPPING['COLUMN'][0]]
+     # user_id_label =storageProperties[storagePropertiesIndex]['USER_ID']
+    #  user_id_value = row[CSV_TO_PROPERTY_MAPPING['USER_ID'][0]]
+
+
+      currentSample.setPropertyValue(freezer_name_label, freezer_name_value)      
+      currentSample.setPropertyValue(box_number_label, box_number_value)      
+      currentSample.setPropertyValue(box_position_label, box_position_value)      
+      #currentSample.setPropertyValue(row_label, row_value)      
+     # currentSample.setPropertyValue(column_label, column_value)     
+     # currentSample.setPropertyValue(user_id_label, user_id_value)    
+   
+
+  f.close()
+  return data_rows
+
+
+def process(tr):
+  exp = create_experiment_if_needed(tr)
+  data_rows = parse_incoming(tr,exp)
+
+
+  
+ 
+