def get_datasetdata_cursor(dataset_id):
dataset = DataSet.objects.get(id=dataset_id)
timepoint_columns = (
DataColumn.objects.all()
.filter(dataset_id=dataset_id)
.filter(unit__in=['day','hour','minute','second']) )
reagent_columns = ( DataColumn.objects.filter(dataset_id=dataset_id)
.filter(data_type__in=[
'small_molecule','cell','primary_cell','protein','antibody',
'otherreagent']).order_by('display_order') )
dc_ids_to_exclude = [dc.id for dc in timepoint_columns]
dc_ids_to_exclude.extend([dc.id for dc in reagent_columns])
col_query_string = (
', (SELECT '
' {column_to_select} '
' FROM db_datapoint as {alias} '
' WHERE {alias}.datacolumn_id={dc_id} '
' AND {alias}.datarecord_id=datarecord.id ) as "{column_name}" '
)
timepoint_unit_string = ',$${dc_unit}$$ as "{dc_name}_timepointUnit" '
timepoint_description_string = (
',$${dc_description}$$ as "{dc_name}_timepointDescription" ')
query_string = (
'WITH drs as ('
' SELECT '
' datarecord.id as "datarecordID"'
', dataset.facility_id as "hmsDatasetID"'
', datarecord.plate as "recordedPlate"'
', datarecord.well as "recordedWell"'
', datarecord.control_type as "controlType"'
)
alias_count = 0
for dc in timepoint_columns:
column_to_select = None
alias_count += 1
alias = 'dp_%d'%alias_count
column_name = '%s_timepoint' % camel_case_dwg(dc.name)
if(dc.data_type == 'Numeric' or dc.data_type == 'omero_image'):
if dc.precision == 0 or dc.data_type == 'omero_image':
column_to_select = "int_value"
else:
column_to_select = "round( float_value::numeric, 2 )"
else:
column_to_select = "text_value"
query_string += col_query_string.format(
column_to_select=column_to_select,
alias=alias,dc_id=dc.id,column_name=column_name)
query_string += timepoint_unit_string.format(
dc_unit=dc.unit, dc_name=camel_case_dwg(dc.name))
if dc.description:
query_string += timepoint_description_string.format(
dc_description=dc.description,
dc_name=camel_case_dwg(dc.name))
reagent_id_query = (
', (SELECT r.facility_id '
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
sm_salt_query = (
', (SELECT r.salt_id'
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
reagent_lincs_id_query = (
', (SELECT r.lincs_id'
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
reagent_batch_id_query = (
', (SELECT '
" CASE WHEN rb.batch_id = '0' THEN '' ELSE rb.batch_id END"
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
reagent_name_query = (
', ( SELECT r.name '
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
prefixes = { 'small_molecule': 'sm', 'protein': 'pp', 'antibody': 'ab',
'otherreagent': 'or', 'cell': 'cl', 'primary_cell': 'pc'}
for dc in reagent_columns:
prefix = prefixes[dc.data_type]
if dc.data_type == 'small_molecule':
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += sm_salt_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'Salt'))
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += reagent_id_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'CenterCompoundID'))
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += reagent_lincs_id_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'LincsID'))
else:
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += reagent_id_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'CenterCanonicalID'))
alias_count += 1
alias = 'dp_%d' % alias_count
# Note: remove condition when new protein specification is released
if dc.data_type != 'protein':
query_string += reagent_lincs_id_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'LincsID'))
else:
query_string += (", '' as %s_%s%s"
% (camel_case_dwg(dc.name),prefix,'LincsID'))
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += reagent_batch_id_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'CenterBatchID'))
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += reagent_name_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'Name'))
query_string += """
from db_dataset dataset
join db_datarecord datarecord on(datarecord.dataset_id=dataset.id)
and dataset.id = %s )
"""
query_string += 'SELECT drs.* '
query_string += ', dc.name as "datapointName" '
query_string += ', dc.unit as "datapointUnit" '
query_string += (
', coalesce(dp.int_value::TEXT'
', dp.float_value::TEXT'
', dp.text_value) as "%s" '
% 'datapointValue' )
query_string += """
FROM drs
JOIN db_datapoint dp on dp.datarecord_id=drs."datarecordID"
join db_datacolumn dc on dp.datacolumn_id=dc.id
where dp.dataset_id = %s """
if dc_ids_to_exclude:
query_string += (
" and dp.datacolumn_id not in (%s)"
% ','.join([str(x) for x in dc_ids_to_exclude]))
query_string +=' order by "datarecordID",dc.id '
logger.info('query_string: %s' % query_string)
cursor = connection.cursor()
cursor.execute(query_string, [dataset_id,dataset_id])
return cursor
def get_datasetdata_cursor(dataset_id):
dataset = DataSet.objects.get(id=dataset_id)
timepoint_columns = (
DataColumn.objects.all()
.filter(dataset_id=dataset_id)
.filter(unit__in=['day','hour','minute','second']) )
reagent_columns = ( DataColumn.objects.filter(dataset_id=dataset_id)
.filter(data_type__in=[
'small_molecule','cell','protein','antibody','otherreagent']) )
dc_ids_to_exclude = [dc.id for dc in timepoint_columns]
dc_ids_to_exclude.extend([dc.id for dc in reagent_columns])
col_query_string = (
', (SELECT '
' {column_to_select} '
' FROM db_datapoint as {alias} '
' WHERE {alias}.datacolumn_id={dc_id} '
' AND {alias}.datarecord_id=datarecord.id ) as "{column_name}" '
)
timepoint_unit_string = ',$${dc_unit}$$ as "{dc_name}_timepointUnit" '
timepoint_description_string = (
',$${dc_description}$$ as "{dc_name}_timepointDescription" ')
query_string = (
'WITH drs as ('
' SELECT '
' datarecord.id as "datarecordID"'
', dataset.facility_id as "hmsDatasetID"'
', datarecord.plate as "recordedPlate"'
', datarecord.well as "recordedWell"'
', datarecord.control_type as "controlType"'
)
alias_count = 0
for dc in timepoint_columns:
column_to_select = None
alias_count += 1
alias = 'dp_%d'%alias_count
column_name = '%s_timepoint' % camel_case_dwg(dc.name)
if(dc.data_type == 'Numeric' or dc.data_type == 'omero_image'):
if dc.precision == 0 or dc.data_type == 'omero_image':
column_to_select = "int_value"
else:
column_to_select = "round( float_value::numeric, 2 )"
else:
column_to_select = "text_value"
query_string += col_query_string.format(
column_to_select=column_to_select,
alias=alias,dc_id=dc.id,column_name=column_name)
query_string += timepoint_unit_string.format(
dc_unit=dc.unit, dc_name=camel_case_dwg(dc.name))
if dc.description:
query_string += timepoint_description_string.format(
dc_description=dc.description,
dc_name=camel_case_dwg(dc.name))
reagent_id_query = (
', (SELECT r.facility_id '
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
sm_salt_query = (
', (SELECT r.salt_id'
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
sm_lincs_id_query = (
', (SELECT r.lincs_id'
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
reagent_batch_id_query = (
', (SELECT '
" CASE WHEN rb.batch_id = '0' THEN '' ELSE rb.batch_id END"
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
reagent_name_query = (
', ( SELECT r.name '
' FROM db_reagent r '
' JOIN db_reagentbatch rb on rb.reagent_id=r.id '
' JOIN db_datapoint {alias} on rb.id={alias}.reagent_batch_id '
' WHERE {alias}.datarecord_id=datarecord.id '
' AND {alias}.datacolumn_id={dc_id} ) as "{column_name}" '
)
prefixes = { 'small_molecule': 'sm', 'protein': 'pp', 'antibody': 'ab',
'otherreagent': 'or', 'cell': 'cl'}
for dc in reagent_columns:
prefix = prefixes[dc.data_type]
if dc.data_type == 'small_molecule':
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += sm_salt_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'Salt'))
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += reagent_id_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'CenterCompoundID'))
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += sm_lincs_id_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'LincsID'))
else:
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += reagent_id_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'CenterSpecificID'))
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += reagent_batch_id_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'CenterSampleID'))
alias_count += 1
alias = 'dp_%d' % alias_count
query_string += reagent_name_query.format(
alias=alias,
dc_id=dc.id,
column_name='%s_%s%s'
% (camel_case_dwg(dc.name),prefix,'Name'))
query_string += """
from db_dataset dataset
join db_datarecord datarecord on(datarecord.dataset_id=dataset.id)
and dataset.id = %s )
"""
query_string += 'SELECT drs.* '
query_string += ', dc.name as "datapointName" '
query_string += ', dc.unit as "datapointUnit" '
query_string += (
', coalesce(dp.int_value::TEXT, dp.float_value::TEXT, dp.text_value) as "%s" '
% 'datapointValue' )
query_string += """
FROM drs
JOIN db_datapoint dp on dp.datarecord_id=drs."datarecordID"
join db_datacolumn dc on dp.datacolumn_id=dc.id
where dp.dataset_id = %s """
if dc_ids_to_exclude:
query_string += (
" and dp.datacolumn_id not in (%s)"
% ','.join([str(x) for x in dc_ids_to_exclude]))
query_string +=' order by "datarecordID",dc.id '
logger.info('query_string: %s' % query_string)
cursor = connection.cursor()
cursor.execute(query_string, [dataset_id,dataset_id])
return cursor
final_val = util.convertdata(
val,type_lookup.get(recognized_label, None))
if final_val != None:
dc_dict[recognized_label] = final_val
if recognized_label == 'display_order':
# add 10 to the order, so default reagent cols can go first
dc_dict['display_order'] = (
dc_dict['display_order'] + 10)
if recognized_label == 'name':
# split on non-alphanumeric chars
temp = re.split(r'[^a-zA-Z0-9]+',dc_dict['name'])
# convert, if needed
if len(temp) > 1:
dc_dict['name'] = camel_case_dwg(dc_dict['name'])
else:
if recognized_label in required_labels:
raise Exception(
'Error, data column field is required: %s, col: %r'
% ( recognized_label, colname(j+1) ) )
else:
logger.debug(
'unrecognized label in "Data Columns" sheet %r' % label_read)
for dc_dict in dc_definitions:
for label in required_labels:
if label not in dc_dict:
raise Exception(
'required "Data Column" label not defined %r' % label)
def read_datacolumns(book):
'''
@return an array of data column definition dicts
'''
data_column_sheet = book.sheet_by_name('Data Columns')
labels = {
'Worksheet Column': 'worksheet_column',
'"Data" Worksheet Column': 'worksheet_column',
'Display Order': 'display_order',
'Display Name': 'display_name',
'Name': 'name',
'Data Type': 'data_type',
'Decimal Places': 'precision',
'Description': 'description',
'Replicate Number': 'replicate',
'Unit': 'unit',
'Assay readout type': 'readout_type',
'Comments': 'comments',
}
dc_definitions = []
datacolumn_fields = util.get_fields(DataColumn)
type_lookup = dict((f.name, iu.totype(f)) for f in datacolumn_fields)
logger.debug('datacolumn type lookups: %s' % type_lookup)
required_labels = ['name', 'data_type']
logger.info('read the data column definitions...')
for i in xrange(data_column_sheet.nrows):
row_values = data_column_sheet.row_values(i)
if i == 0:
for val in row_values[1:]:
dc_definitions.append({})
label_read = row_values[0]
recognized_label = next(
(field_name for label, field_name in labels.items()
if label_read and label.lower() == label_read.lower()), None)
if recognized_label:
logger.debug('label: %r, recognized_label: %r' %
(label_read, recognized_label))
for j, val in enumerate(row_values[1:]):
dc_dict = dc_definitions[j]
logger.debug('data column %s:%d:%d:%r' %
(recognized_label, i, j, val))
final_val = util.convertdata(
val, type_lookup.get(recognized_label, None))
if final_val != None:
dc_dict[recognized_label] = final_val
if recognized_label == 'display_order':
# add 10 to the order, so default reagent cols can go first
dc_dict['display_order'] = (dc_dict['display_order'] +
10)
if recognized_label == 'name':
# split on non-alphanumeric chars
temp = re.split(r'[^a-zA-Z0-9]+', dc_dict['name'])
# convert, if needed
if len(temp) > 1:
dc_dict['name'] = camel_case_dwg(dc_dict['name'])
else:
if recognized_label in required_labels:
raise Exception(
'Error, data column field is required: %s, col: %r'
% (recognized_label, colname(j + 1)))
else:
logger.debug('unrecognized label in "Data Columns" sheet %r' %
label_read)
for dc_dict in dc_definitions:
for label in required_labels:
if label not in dc_dict:
raise Exception('required "Data Column" label not defined %r' %
label)
logger.info('find the data columns on the "Data" sheet...')
data_sheet = book.sheet_by_name('Data')
data_sheet_labels = data_sheet.row_values(0)
dc_definitions_found = []
data_labels_found = []
for i, data_label in enumerate(data_sheet_labels):
if not data_label or not data_label.strip():
logger.info('break on data sheet col %d, blank' % i)
break
data_label = data_label.upper()
col_letter = colname(i)
for dc_dict in dc_definitions:
_dict = None
if 'worksheet_column' in dc_dict:
v = dc_dict['worksheet_column']
if v.upper() == col_letter:
data_labels_found.append(i)
dc_definitions_found.append(dc_dict)
_dict = dc_dict
elif 'name' in dc_dict or 'display_name' in dc_dict:
if (dc_dict.get('name', '').upper() == data_label or
dc_dict.get('display_name', '').upper() == data_label):
dc_dict['worksheet_column'] = col_letter
data_labels_found.append(i)
dc_definitions_found.append(dc_dict)
_dict = dc_dict
if _dict and 'display_order' not in _dict:
_dict['display_order'] = i + 10
logger.warn('auto assigning "display_order" for col %r as %d' %
(_dict['name'], i + 10))
if i not in data_labels_found:
logger.debug(('Data sheet label not found %r,'
' looking in default reagent definitions %s') %
(data_label, default_reagent_columns.keys()))
for key, dc_dict in default_reagent_columns.items():
if (key.upper() == data_label
or dc_dict.get('name', '').upper() == data_label or
dc_dict.get('display_name', '').upper() == data_label):
dc_dict['worksheet_column'] = col_letter
data_labels_found.append(i)
dc_definitions_found.append(dc_dict)
data_labels_not_found = [
data_label for i, data_label in enumerate(data_sheet_labels)
if data_label and data_label.strip() and i not in data_labels_found
and data_label not in meta_columns
]
if data_labels_not_found:
logger.warn('data sheet labels not recognized %s' %
data_labels_not_found)
# for legacy datasets: make sure the small molecule column 1 is always created
small_mol_col = None
for dc_dict in dc_definitions_found:
if dc_dict['data_type'] == 'small_molecule':
small_mol_col = dc_dict
break
if not small_mol_col:
dc_definitions_found.append(
default_reagent_columns['Small Molecule Batch'])
logger.info('data column definitions found: %s' %
[x['display_name'] for x in dc_definitions_found])
return dc_definitions_found
def read_datacolumns(book):
'''
@return an array of data column definition dicts
'''
data_column_sheet = book.sheet_by_name('Data Columns')
labels = {
'Worksheet Column':'worksheet_column',
'"Data" Worksheet Column':'worksheet_column',
'Display Order':'display_order',
'Display Name':'display_name',
'Name':'name',
'Data Type':'data_type',
'Decimal Places':'precision',
'Description':'description',
'Replicate Number':'replicate',
'Unit':'unit',
'Assay readout type':'readout_type',
'Comments':'comments',
}
dc_definitions = []
datacolumn_fields = util.get_fields(DataColumn)
type_lookup = dict((f.name, iu.totype(f)) for f in datacolumn_fields)
logger.debug('datacolumn type lookups: %s' % type_lookup)
required_labels = ['name', 'data_type']
logger.info('read the data column definitions...')
for i in xrange(data_column_sheet.nrows):
row_values = data_column_sheet.row_values(i)
if i == 0:
for val in row_values[1:]:
dc_definitions.append({})
label_read = row_values[0]
recognized_label = next(
(field_name for label, field_name in labels.items()
if label_read and label.lower() == label_read.lower() ), None)
if recognized_label:
logger.debug(
'label: %r, recognized_label: %r' % (label_read, recognized_label))
for j,val in enumerate(row_values[1:]):
dc_dict = dc_definitions[j]
logger.debug('data column %s:%d:%d:%r'
% ( recognized_label, i, j, val))
final_val = util.convertdata(
val,type_lookup.get(recognized_label, None))
if final_val != None:
dc_dict[recognized_label] = final_val
if recognized_label == 'display_order':
# add 10 to the order, so default reagent cols can go first
dc_dict['display_order'] = (
dc_dict['display_order'] + 10)
if recognized_label == 'name':
# split on non-alphanumeric chars
temp = re.split(r'[^a-zA-Z0-9]+',dc_dict['name'])
# convert, if needed
if len(temp) > 1:
dc_dict['name'] = camel_case_dwg(dc_dict['name'])
else:
if recognized_label in required_labels:
raise Exception(
'Error, data column field is required: %s, col: %r'
% ( recognized_label, colname(j+1) ) )
else:
logger.debug(
'unrecognized label in "Data Columns" sheet %r' % label_read)
for dc_dict in dc_definitions:
for label in required_labels:
if label not in dc_dict:
raise Exception(
'required "Data Column" label not defined %r' % label)
logger.info('find the data columns on the "Data" sheet...')
data_sheet = book.sheet_by_name('Data')
data_sheet_labels = data_sheet.row_values(0)
dc_definitions_found = []
data_labels_found = []
for i,data_label in enumerate(data_sheet_labels):
if not data_label or not data_label.strip():
logger.info('break on data sheet col %d, blank' % i)
break
data_label = data_label.upper()
col_letter = colname(i)
for dc_dict in dc_definitions:
_dict = None
if 'worksheet_column' in dc_dict:
v = dc_dict['worksheet_column']
if v.upper() == col_letter:
data_labels_found.append(i)
dc_definitions_found.append(dc_dict)
_dict = dc_dict
elif 'name' in dc_dict or 'display_name' in dc_dict:
if ( dc_dict.get('name', '').upper() == data_label
or dc_dict.get('display_name', '').upper() == data_label):
dc_dict['worksheet_column'] = col_letter
data_labels_found.append(i)
dc_definitions_found.append(dc_dict)
_dict = dc_dict
if _dict and 'display_order' not in _dict:
_dict['display_order'] = i+10
logger.warn(
'auto assigning "display_order" for col %r as %d'
% (_dict['name'], i+10))
if i not in data_labels_found:
logger.debug( (
'Data sheet label not found %r,'
' looking in default reagent definitions %s' )
% ( data_label, default_reagent_columns.keys() ) )
for key,dc_dict in default_reagent_columns.items():
if (key.upper() == data_label
or dc_dict.get('name', '').upper() == data_label
or dc_dict.get('display_name', '').upper() == data_label):
dc_dict['worksheet_column'] = col_letter
data_labels_found.append(i)
dc_definitions_found.append(dc_dict)
data_labels_not_found = [
data_label for i,data_label in enumerate(data_sheet_labels)
if data_label and data_label.strip()
and i not in data_labels_found and data_label not in meta_columns ]
if data_labels_not_found:
logger.warn(
'data sheet labels not recognized %s' % data_labels_not_found )
# for legacy datasets: make sure the small molecule column 1 is always created
small_mol_col = None
for dc_dict in dc_definitions_found:
if dc_dict['data_type'] == 'small_molecule':
small_mol_col = dc_dict
break
if not small_mol_col:
dc_definitions_found.append(default_reagent_columns['Small Molecule Batch'])
logger.info('data column definitions found: %s'
% [x['display_name'] for x in dc_definitions_found])
return dc_definitions_found