assignqcflags.py

import argparse
from lxml import etree
import pycurl
from StringIO import StringIO

import glsapiutil

__author__ = "CTMR, Kim Wong"
__date__ = "2018"
__doc__ = """
Assign the QC flags to samples based on the uploaded concentration.
Written as a learning exercise and to replace the in-built Assign QC Flags
script which does not work in LIMS version 5.0.4.
Note that this script is fairly restricted in that it can only take
one mandatory condition and one optional condition; more than that will have
to be manually programmed in."""

HOSTNAME = "https://ctmr-lims.scilifelab.se"
VERSION = "v2"

def less_equal(a, b):
   return a <= b

def greater_equal(a, b):
   return a >= b

def equal(a, b):
   return a == b

def not_equal(a, b):
   return a != b

operator_map = {
   '<=': less_equal,
   '>=': greater_equal,
   '=': equal,
   '==': equal,
   '!=': not_equal,
}

def check_qc_pass(value, operator, threshold):
    return operator_map[operator](value, threshold)

def determine_qc_flag(concentration, operator, threshold):
    flag = check_qc_pass(concentration, operator, threshold)
    return 'PASSED' if flag else 'FAILED'

def extract_xml(username, password, artifactsURI, outputFileLuid):
    """Extracts the individual XML structures from the given
    artifact outputFileLuid.
    """
    url = artifactsURI + outputFileLuid

    c = pycurl.Curl()
    c.setopt(c.USERPWD, "%s:%s" % (username, password))
    c.setopt(c.URL, url)
    curl_buffer = StringIO()
    c.setopt(c.WRITEFUNCTION, curl_buffer.write)
    c.perform()
    c.close()
    xml = etree.fromstring(curl_buffer.getvalue())
    return xml

def extract_udf_from_xml(xml, udf_name):
    """Extracts a UDF from an XML element.
    TODO: implement different type handling
    """
    # a bit hacky, but xml.findall('udf:field', xml.nsmap) as in this
    # link doesn't seem to work, so...
    #https://stackoverflow.com/questions/14853243/parsing-xml-with-namespace-in-python-via-elementtree
    tags = xml.findall('{' + xml.nsmap['udf'] + '}field')
    if len(tags) == 0:
        return None
    for tag in tags:
        tag_attribs = tag.attrib
        udf_type = tag_attribs['type']
        udf_name_ = tag_attribs['name']
        if udf_name_ == udf_name:
            return tag.text

def update_qc_flag(input_xml, qc_flag):
    tag = input_xml.find('qc-flag')
    if tag is not None:
        tag.text = qc_flag
        input_xml
    else:
        raise AttributeError("The given XML does not have a qc-flag!")

    return input_xml

def run_put_request(username, password, artifactsURI, outputFileLuid, xml_data):
    curl_buffer = StringIO()

    url = artifactsURI + outputFileLuid
    post_data = etree.tostring(xml_data)

    c = pycurl.Curl()
    c.setopt(c.USERPWD, "%s:%s" % (username, password))
    c.setopt(c.URL, url)
    c.setopt(c.WRITEFUNCTION, curl_buffer.write)
    header = [
        'Content-Type: application/xml',
        'Accept: application/xml'
    ]
    c.setopt(c.HTTPHEADER, header)
    c.setopt(c.CUSTOMREQUEST, "PUT")
    c.setopt(c.POSTFIELDS, post_data)
    c.perform()
    c.close()
    
    return curl_buffer.getvalue()

def determine_and_set_qc_flags_2(username, password, artifactsURI, outputFileLuids, source_field, operator, threshold, source_field_2, operator_2, threshold_2):
    threshold = float(threshold)
    threshold_2 = float(threshold_2)

    for luid in outputFileLuids:
        xml = extract_xml(username, password, artifactsURI, luid)
        concentration = extract_udf_from_xml(xml, source_field)
        concentration_2 = extract_udf_from_xml(xml, source_field_2)
        if concentration:
            concentration = float(concentration)
        qc_flag = determine_qc_flag(concentration, operator, threshold)
        qc_flag_final = 'PASSED'
        if concentration_2:
            concentration_2 = float(concentration_2)
            qc_flag_2 = determine_qc_flag(concentration_2, operator_2, threshold_2)
            if not (qc_flag=='PASSED' and qc_flag_2=='PASSED'):
                qc_flag_final = 'FAILED'
        modified_xml = update_qc_flag(xml, qc_flag_final)
        run_put_request(username, password, artifactsURI, luid, modified_xml)

def determine_and_set_qc_flags(username, password, artifactsURI, outputFileLuids, source_field, operator, threshold):
    threshold = float(threshold)
    for luid in outputFileLuids:
        xml = extract_xml(username, password, artifactsURI, luid)
        concentration = extract_udf_from_xml(xml, source_field)
        if concentration:
            concentration = float(concentration)
        qc_flag = determine_qc_flag(concentration, operator, threshold)
        modified_xml = update_qc_flag(xml, qc_flag)
        run_put_request(username, password, artifactsURI, luid, modified_xml)

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='Parse concentrations and modify QC flags')
    parser.add_argument('-u', '--username', required=True, help='username')
    parser.add_argument('-p', '--password', required=True, help='password')
    parser.add_argument('-o', '--operator', required=True, help='comparison operator')
    parser.add_argument('-t', '--threshold', required=True, help='concentration threshold')
    parser.add_argument('-s', '--sourceField', required=True, help='source data field')
    parser.add_argument('-o2', '--operator2', help='optional, second comparison operator')
    parser.add_argument('-t2', '--threshold2', help='optional, second concentration threshold')
    parser.add_argument('-s2', '--sourceField2', help='optional, second source data field')
    parser.add_argument('-a', '--artifactsURI', required=True, help='artifacts uri')
    parser.add_argument('-x', '--outputFileLuids', required=True, help='output file luids')

    args = parser.parse_args()

    api = glsapiutil.glsapiutil()
    api.setHostname(HOSTNAME)
    api.setVersion(VERSION)
    api.setup(args.username, args.password)

    outputFileLuids = args.outputFileLuids.split(' ')

    if args.sourceField2 and args.operator2 and args.threshold2:
        determine_and_set_qc_flags_2(args.username, args.password, args.artifactsURI, outputFileLuids, args.sourceField, args.operator, args.threshold, args.sourceField2, args.operator2, args.threshold2)
    else:
        determine_and_set_qc_flags(args.username, args.password, args.artifactsURI, outputFileLuids, args.sourceField, args.operator, args.threshold)

""" Example XML of a relevant artifact:
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<art:artifact xmlns:udf="http://genologics.com/ri/userdefined" xmlns:file="http://genologics.com/ri/file" xmlns:art="http://genologics.com/ri/artifact" uri="http://localhost:9080/api/v2/artifacts/92-37152?state=22418" limsid="92-37152">
    <name>DHR003_working</name>
    <type>ResultFile</type>
    <output-type>ResultFile</output-type>
    <parent-process uri="http://localhost:9080/api/v2/processes/24-8222" limsid="24-8222"/>
    <qc-flag>UNKNOWN</qc-flag>
    <sample uri="http://localhost:9080/api/v2/samples/WON301A292" limsid="WON301A292"/>
    <reagent-label name="Fecal"/>
    <udf:field type="Numeric" name="Concentration">6.6054</udf:field>
    <workflow-stages/>
</art:artifact>
"""