Esempio n. 1
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 def build_schema(self):
     schema = super(CellResource,self).build_schema()
     schema['fields'] = get_detail_schema(Cell(),['cell'])
     return schema 
Esempio n. 2
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def main(path):
    """
    Read in the Cell
    """
    sheet_name = 'HMS-LINCS cell line metadata'
    sheet = iu.readtable([path, sheet_name, 1]) # Note, skipping the header row by default

    properties = ('model_field','required','default','converter')
    column_definitions = {
              'Facility ID':('facility_id',True,None, lambda x: x[x.index('HMSL')+4:]),
              'CL_Name':('name',True),
              'CL_LINCS_ID':'lincs_id',
              'CL_Alternate_Name':'alternative_names',
              'CL_Alternate_ID':'alternate_id',
              'CL_Center_Specific_ID':'center_specific_id',
              'MGH_ID':('mgh_id',False,None,lambda x:util.convertdata(x,int)),
              'Assay':'assay',
              'CL_Organism':'organism',
              'CL_Organ':'organ',
              'CL_Tissue':'tissue',
              'CL_Cell_Type':'cell_type',
              'CL_Cell_Type_Detail':'cell_type_detail',
              'CL_Donor_Sex': 'donor_sex',
              'CL_Donor_Age': ('donor_age_years',False,None,lambda x:util.convertdata(x,int)),
              'CL_Donor_Ethnicity': 'donor_ethnicity',
              'CL_Donor_Health_Status': 'donor_health_status',
              'CL_Disease':'disease',
              'CL_Disease_Detail':'disease_detail',
              'CL_Growth_Properties':'growth_properties',
              'CL_Genetic_Modification':'genetic_modification',
              'CL_Related_Projects':'related_projects',
              'CL_Recommended_Culture_Conditions':'recommended_culture_conditions',
              'CL_Verification_Reference_Profile':'verification_reference_profile',
              'CL_Known_Mutations':'mutations_known',
              'CL_Mutations_Citations':'mutations_citations',
              'CL_Molecular_Features': 'molecular_features',
              'CL_Relevant_Citations': 'relevant_citations',
              'CL_Reference_Source': 'reference_source',
              'CL_Reference_Source_ID': 'reference_source_id',
              'Reference Source URL': 'reference_source_url',
              'Usage Note': 'usage_note',
              
              'Date Data Received':('date_data_received',False,None,util.date_converter),
              'Date Loaded': ('date_loaded',False,None,util.date_converter),
              'Date Publicly Available': ('date_publicly_available',False,None,util.date_converter),
              'Most Recent Update': ('date_updated',False,None,util.date_converter),
              'Is Restricted':('is_restricted',False,False,util.bool_converter)}
    # convert the labels to fleshed out dict's, with strategies for optional, default and converter
    column_definitions = util.fill_in_column_definitions(properties,column_definitions)
    
    # create a dict mapping the column ordinal to the proper column definition dict
    cols = util.find_columns(column_definitions, sheet.labels, all_sheet_columns_required=False)
            
    rows = 0    
    logger.debug(str(('cols: ' , cols)))
    for row in sheet:
        r = util.make_row(row)
        initializer = {}
        for i,value in enumerate(r):
            if i not in cols: continue
            properties = cols[i]

            logger.debug(str(('read col: ', i, ', ', properties)))
            required = properties['required']
            default = properties['default']
            converter = properties['converter']
            model_field = properties['model_field']

            # Todo, refactor to a method
            logger.debug(str(('raw value', value)))
            if(converter != None):
                value = converter(value)
            if(value == None ):
                if( default != None ):
                    value = default
            if(value == None and  required == True):
                raise Exception('Field is required: %s, record: %d' % (properties['column_label'],rows))
            logger.debug(str(('model_field: ' , model_field, ', value: ', value)))
            initializer[model_field] = value

        try:
            logger.debug(str(('initializer: ', initializer)))
            cell = Cell(**initializer)
            cell.save()
            logger.info(str(('cell created:', cell)))
            rows += 1

            # create a default batch - 0
            CellBatch.objects.create(reagent=cell,batch_id=0)
            
        except Exception, e:
            print "Invalid Cell, name: ", r[0]
            raise e
Esempio n. 3
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def main(path):
    """
    Read in the Cell
    """
    sheet_name = 'HMS-LINCS cell line metadata'
    sheet = iu.readtable([path, sheet_name, 1]) # Note, skipping the header row by default

    properties = ('model_field','required','default','converter')
    column_definitions = {
              'Facility ID':('facility_id',True,None, lambda x: x[x.index('HMSL')+4:]),
              'CL_Name':('name',True),
              'CL_ID':'cl_id',
              'CL_Alternate_Name':'alternate_name',
              'CL_Alternate_ID':'alternate_id',
              'CL_Center_Name':'center_name',
              'CL_Center_Specific_ID':'center_specific_id',
              'MGH_ID':('mgh_id',False,None,lambda x:util.convertdata(x,int)),
              'Assay':'assay',
              'CL_Provider_Name':'provider_name',
              'CL_Provider_Catalog_ID':'provider_catalog_id',
              'CL_Batch_ID':'batch_id',
              'CL_Organism':'organism',
              'CL_Organ':'organ',
              'CL_Tissue':'tissue',
              'CL_Cell_Type':'cell_type',
              'CL_Cell_Type_Detail':'cell_type_detail',
              'CL_Disease':'disease',
              'CL_Disease_Detail':'disease_detail',
              'CL_Growth_Properties':'growth_properties',
              'CL_Genetic_Modification':'genetic_modification',
              'CL_Related_Projects':'related_projects',
              'CL_Recommended_Culture_Conditions':'recommended_culture_conditions',
              'CL_Verification_Profile':'verification_profile',
              'CL_Verification_Reference_Profile':'verification_reference_profile',
              'CL_Mutations_Reference':'mutations_reference',
              'CL_Mutations_Explicit':'mutations_explicit',
              'CL_Organism_Gender':'organism_gender',
              'Date Data Received':('date_data_received',False,None,util.date_converter),
              'Date Loaded': ('date_loaded',False,None,util.date_converter),
              'Date Publicly Available': ('date_publicly_available',False,None,util.date_converter),
              'Most Recent Update': ('date_updated',False,None,util.date_converter),
              'Is Restricted':('is_restricted',False,False,util.bool_converter)}
    # convert the labels to fleshed out dict's, with strategies for optional, default and converter
    column_definitions = util.fill_in_column_definitions(properties,column_definitions)
    
    # create a dict mapping the column ordinal to the proper column definition dict
    cols = util.find_columns(column_definitions, sheet.labels)
            
    rows = 0    
    logger.debug(str(('cols: ' , cols)))
    for row in sheet:
        r = util.make_row(row)
        initializer = {}
        for i,value in enumerate(r):
            if i not in cols: continue
            properties = cols[i]

            logger.debug(str(('read col: ', i, ', ', properties)))
            required = properties['required']
            default = properties['default']
            converter = properties['converter']
            model_field = properties['model_field']

            # Todo, refactor to a method
            logger.debug(str(('raw value', value)))
            if(converter != None):
                value = converter(value)
            if(value == None ):
                if( default != None ):
                    value = default
            if(value == None and  required == True):
                raise Exception('Field is required: %s, record: %d' % (properties['column_label'],rows))
            logger.debug(str(('model_field: ' , model_field, ', value: ', value)))
            initializer[model_field] = value

        try:
            logger.debug(str(('initializer: ', initializer)))
            cell = Cell(**initializer)
            cell.save()
            logger.info(str(('cell created:', cell)))
            rows += 1
        except Exception, e:
            print "Invalid Cell, name: ", r[0]
            raise e
Esempio n. 4
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def main(path, do_precursors_only):
    """
    Read in the Cell
    """
    sheet_name = 'HMS-LINCS cell line metadata'
    sheet = iu.readtable([path, sheet_name, 1]) # allow for informational header row

    properties = ('model_field','required','default','converter')
    column_definitions = {
        'Facility ID':('facility_id',True,None, lambda x: x[x.index('HMSL')+4:]),
        'CL_Name':('name',True),
        'CL_LINCS_ID':'lincs_id',
        'CL_Alternate_Name':'alternative_names',
        'CL_Alternate_ID':'alternative_id',
        'Precursor_Cell':'precursor_facility_batch_id',
        'CL_Organism':'organism',
        'CL_Organ':'organ',
        'CL_Tissue':'tissue',
        'CL_Cell_Type':'cell_type',
        'CL_Cell_Type_Detail':'cell_type_detail',
        'CL_Donor_Sex': 'donor_sex',
        'CL_Donor_Age': ('donor_age_years',False,None,lambda x:util.convertdata(x,int)),
        'CL_Donor_Ethnicity': 'donor_ethnicity',
        'CL_Donor_Health_Status': 'donor_health_status',
        'CL_Disease':'disease',
        'CL_Disease_Detail':'disease_detail',
        'CL_Production_Details': 'production_details',
        'CL_Genetic_Modification':'genetic_modification',
        'CL_Known_Mutations':'mutations_known',
        'CL_Mutation_Citations':'mutation_citations',
        'CL_Verification_Reference_Profile':'verification_reference_profile',
        'CL_Growth_Properties':'growth_properties',
        'CL_Recommended_Culture_Conditions':'recommended_culture_conditions',
        'CL_Relevant_Citations': 'relevant_citations',
        'Usage Note': 'usage_note',
        'CL_Reference_Source': 'reference_source',
        'Reference Source URL': 'reference_source_url',
        
        'Date Data Received':('date_data_received',False,None,util.date_converter),
        'Date Loaded': ('date_loaded',False,None,util.date_converter),
        'Date Publicly Available': ('date_publicly_available',False,None,util.date_converter),
        'Most Recent Update': ('date_updated',False,None,util.date_converter),
        'Is Restricted':('is_restricted',False,False,util.bool_converter)}
    # convert the labels to fleshed out dict's, with strategies for optional, default and converter
    column_definitions = util.fill_in_column_definitions(properties,column_definitions)
    
    # create a dict mapping the column ordinal to the proper column definition dict
    cols = util.find_columns(column_definitions, sheet.labels, all_sheet_columns_required=False)
            
    rows = 0    
    precursor_map = {}
    precursor_pattern = re.compile(r'HMSL(5\d{4})-(\d+)')
    for row in sheet:
        r = util.make_row(row)
        initializer = {}
        for i,value in enumerate(r):
            if i not in cols: continue
            properties = cols[i]
            required = properties['required']
            default = properties['default']
            converter = properties['converter']
            model_field = properties['model_field']
            
            value = convertdata(value)
            if value is not None:
                if converter:
                    try:
                        value = converter(value)
                    except Exception:
                        logger.error('field parse error: %r, value: %r, row: %d',
                            properties['column_label'],value,rows+2)
                        raise 
            if value is None:
                if default is not None:
                    value = default
            if value is None and required:
                raise Exception('Field is required: %s, record: %d' 
                    % (properties['column_label'],rows))

            logger.debug('model_field: %r, value: %r' , model_field, value)
            initializer[model_field] = value
            
        precursor_facility_batch_id = initializer.pop('precursor_facility_batch_id')
        if precursor_facility_batch_id:
            match = precursor_pattern.match(precursor_facility_batch_id)
            if not match:
                raise Exception('Invalid precursor pattern: needs: %s: %r, row: %d'
                    % (precursor_pattern, initializer, rows))
            precursor_map[initializer['facility_id']] = (match.group(1),match.group(2))
        
        if not do_precursors_only:
            try:
                logger.info('initializer: %r', initializer)
                cell = Cell(**initializer)
                cell.save()
                logger.info(str(('cell created:', cell)))
    
                # create a default batch - 0
                CellBatch.objects.create(reagent=cell,batch_id=0)
                
            except Exception, e:
                print "Invalid Cell, name: ", r[0]
                raise e
        
        rows += 1