tests/test_data_delivery.py
def create_fake_fastq_fastqc_md5_from_commands(instance):
    """
    This function replaces run_aggregate_commands and take an instance of DataDelivery.
    It will create the output as if the command were run.
    It only supports fastqc and command that redirects there outputs
    """
    for commands in instance.all_commands_for_cluster:
        for command in commands.split(';'):
            if len(command.split('>')) > 1:
                output = command.split('>')[1].strip()
                if output.endswith('.md5'):
                    touch(output, 'd41d8cd98f00b204e9800998ecf8427e  ' + os.path.basename(output))
                else:
                    touch(output)
            elif command.strip().startswith('fastqc'):
                touch(command.split()[-1].split('.fastq')[0] + '_fastqc.zip')
                touch(command.split()[-1].split('.fastq')[0] + '_fastqc.html')

    This function replaces run_aggregate_commands and take an instance of DataDelivery.
    It will create the output as if the command were run.
    It only supports fastqc and command that redirects there outputs
    
This function replaces run_aggregate_commands and take an instance of DataDelivery.
It will create the output as if the command were run.
It only supports fastqc and command that redirects there outputs
This function replaces run_aggregate_commands and take an instance of DataDelivery . It will create the output as if the command were run . It only supports fastqc and command that redirects there outputs
def create_fake_fastq_fastqc_md5_from_commands(instance):
    for commands in instance.all_commands_for_cluster:
        for command in commands.split(';'):
            if len(command.split('>')) > 1:
                output = command.split('>')[1].strip()
                if output.endswith('.md5'):
                    touch(output, 'd41d8cd98f00b204e9800998ecf8427e  ' + os.path.basename(output))
                else:
                    touch(output)
            elif command.strip().startswith('fastqc'):
                touch(command.split()[-1].split('.fastq')[0] + '_fastqc.zip')
                touch(command.split()[-1].split('.fastq')[0] + '_fastqc.html')
def create_fake_fastq_fastqc_md5_from_commands ( instance ) : for commands in instance . all_commands_for_cluster : for command in commands . split ( ';' ) : if len ( command . split ( '>' ) ) > 1 : output = command . split ( '>' ) [ 1 ] . strip ( ) if output . endswith ( '.md5' ) : touch ( output , 'd41d8cd98f00b204e9800998ecf8427e  ' + os . path . basename ( output ) ) else : touch ( output ) elif command . strip ( ) . startswith ( 'fastqc' ) : touch ( command . split ( ) [ - 1 ] . split ( '.fastq' ) [ 0 ] + '_fastqc.zip' ) touch ( command . split ( ) [ - 1 ] . split ( '.fastq' ) [ 0 ] + '_fastqc.html' )
This function replaces run_aggregate_commands and take an instance of DataDelivery.
This function replaces run_aggregate_commands and take an instance of DataDelivery .
"""
    This function replaces run_aggregate_commands and take an instance of DataDelivery.
    It will create the output as if the command were run.
    It only supports fastqc and command that redirects there outputs
    """
instance