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dcc_xml.py
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# -*- coding: utf-8 -*-
"""
This module is responsible for generating the XML files for the DCC upload.
There are two XMLs to be generated:
J.YYYY-MM-DD.NN.specimen.impc.xml for specimens
and
J.YYYY-MM-DD.NN.experiment.impc.xml for experiments
This module queries CLIMB for data based on a filter
set up by the user. It then gathers DCC-specific information from
a table in the MySQL schema `komp` table names `dccparameterdetails` +and
`taskimpccodes`.
Given that information it can create the XML files.
It determines the XML file name and writes it out to the working directory.
@author: michaelm
"""
import json
import glob
import pandas as pd
import argparse
from datetime import datetime
from os import listdir
from os.path import isfile, join, basename
import zipfile
from zipfile import ZipFile
import xml.etree.ElementTree as ET
import read_config as cfg
# Our code
import jaxlims_api as db
import climb_api as c
import validate_procedure as v
import core_api as pfs
import omero_api
import my_logger
# Globals - set either from the command line or config file
g_ImpcCode = ''
g_ColonyId =''
g_DataSrc = '' # CLIMB, PFS, or JAXLIMS Set on command line
g_dataDir = '' # Set from config file
g_filterFileName = 'microct-fix.json' # Set on command line
g_image_dir = '.' # Currentoly unused
g_DryRun = None
# "environment variables"
# From YAML file
def getDatadir():
global g_dataDir
return g_dataDir
def setClimbFilterFile(filename:str):
global g_filterFileName
g_filterFileName = filename
def getClimbFilterFile():
global g_filterFileName
return g_filterFileName
def setDataDir(datadir:str):
global g_dataDir
g_dataDir = datadir
def getDataSrc():
global g_DataSrc
return g_DataSrc
def setDataSrc(sourceName:str):
# sourceName: JAXLIMS, PFS, or CLIMB
global g_DataSrc
g_DataSrc = sourceName
def getFtpServer():
return 'sftp://bhjlk02lp.jax.org/' # Probably should come from config file
# Global map: Look up a proc status string and return the IMPC code
procedure_status_message_map = {
'Incomplete' : 'IMPC_PSC_015',
'Removed' : 'IMPC_PSC_001',
'Cancelled' : 'IMPC_PSC_006',
'Incomplete' : 'IMPC_PSC_015',
'Cancelled - Pipeline stopped - scheduling' : 'IMPC_PSC_006',
'Cancelled - Pipeline stopped - welfare' : 'IMPC_PSC_005',
'Cancelled - Single procedure not performed - welfare' : 'IMPC_PSC_003',
'Incomplete - Procedure Failed - Equipment Failed' : 'IMPC_PSC_007',
'Incomplete - Single procedure not performed - schedule' : ' IMPC_PSC_004',
'Procedure Failed - Insufficient Sample' : 'IMPC_PSC_009',
'Procedure Failed - Process Failed' : 'IMPC_PSC_010',
'Procedure Failed - Sample Lost' : 'IMPC_PSC_008',
'Procedure QC Failed' : 'IMPC_PSC_011',
'Removed - Mouse culled' : 'IMPC_PSC_002',
'Removed - Mouse died' : 'IMPC_PSC_001',
'LIMS not ready' : 'IMPC_PSC_012',
'Software failure' : 'IMPC_PSC_013',
'Uncooperative mouse' : 'IMPC_PSC_014',
'Incomplete - see comments' : 'IMPC_PSC_015:Wrong_pipeline',
'Withdrawn' : 'IMPC_PSC_015:Withdrawn'
}
# Global map: Look up a output status string and return the IMPC code
output_status_message_map = {
'Parameter not measured - Equipment Failed' : 'IMPC_PARAMSC_001',
'Parameter not measured - Sample Lost' : 'IMPC_PARAMSC_002',
'Parameter not measured - Insufficient sample' : 'IMPC_PARAMSC_003',
'Parameter not recorded - welfare issue' : 'IMPC_PARAMSC_004',
'Free Text of Issues' : 'IMPC_PARAMSC_005',
'Extra Information' : 'IMPC_PARAMSC_006',
'Parameter not measured - not in SOP' : 'IMPC_PARAMSC_007',
'Above upper limit of quantitation' : 'IMPC_PARAMSC_008',
'Below lower limit of quantitation' : 'IMPC_PARAMSC_009',
'Parameter QC Failed' : 'IMPC_PARAMSC_010',
'LIMS not ready yet' : 'IMPC_PARAMSC_011',
'Software failure' : 'IMPC_PARAMSC_012',
'Uncooperative mouse' : 'IMPC_PARAMSC_013'
}
def setProcedureImpcCode(code):
global g_ImpcCode
g_ImpcCode=code
def getProcedureImpcCode():
global g_ImpcCode
return g_ImpcCode
def getColonyId():
global g_ColonyId
return g_ColonyId
def setColonyId(colonyId):
global g_ColonyId
g_ColonyId = colonyId
# By convention if a task with no mice needs to record the line
# then she stores it in an output named "JR". But she only stores the five digit code
def findColonyId(proc):
outputLs = proc["outputs"]
if outputLs == None or len(outputLs) == 0:
return ""
for output in outputLs:
# For line calls we need the JR# - or Stock Number - so lets store it for later -- just one more kluge
if output["outputName"] == "JR":
setColonyId('JR' + output["outputValue"])
elif output["outputName"] == "Stock Number":
# Different formats of JRs and Stock Numbers!!
sn = output["outputValue"]
if sn[0] == '0':
sn = sn[1:]
setColonyId('JR' + sn)
return getColonyId()
def getBackgroundStrainId():
# C57BL/6NJ
return 'MGI:3056279'
# XML XML XML
def createSpecimenXML(animalLs):
# Upper limit of 2500 entries will never be reached, I assume
root = createSpecimenRoot()
centerNode = createSpecimenCentre(root)
generateSpecimenXML(animalLs, centerNode)
# Write it out
tree = ET.ElementTree(indent(root))
specimenFileName = getNextSpecimenFilename(getDatadir())
tree.write(specimenFileName, xml_declaration=True, encoding='utf-8')
my_logger.info("Creating specimen file {0}".format(specimenFileName))
# Now zip it up.
zipfilename = specimenFileName.replace('specimen.','').replace('xml','zip')
with ZipFile(zipfilename,'w',zipfile.ZIP_DEFLATED) as zipper:
zipper.write(specimenFileName,basename(specimenFileName))
zipper.close()
def createExperimentXML(experimentLs, procedureHasAnimals):
startRecord = 0
maxRecords = 2500 # The xml file will be failed by the crawler if it contains more than 2500 entries
while startRecord < len(experimentLs):
endRecord = startRecord + maxRecords
if endRecord > len(experimentLs):
endRecord = len(experimentLs)
experimentChunk = experimentLs[startRecord:endRecord]
startRecord = endRecord
root = createProcedureRoot()
centerNode = createCentre(root)
if procedureHasAnimals:
numberOfProcs = generateExperimentXML(experimentChunk, centerNode)
else:
numberOfProcs = generateLineCallExperimentXML(experimentChunk, centerNode)
expFileName = getNextExperimentFilename(getDatadir())
my_logger.info("Creating experiment file {0}".format(expFileName))
if(numberOfProcs > 0): # write the new XML file
tree = ET.ElementTree(indent(root))
tree.write(expFileName, xml_declaration=True, encoding='utf-8')
# Now zip it up.
zipfilename = expFileName.replace('experiment.','').replace('xml','zip')
with ZipFile(zipfilename,'w',zipfile.ZIP_DEFLATED) as zipper:
zipper.write(expFileName,basename(expFileName))
zipper.close()
# Now record it.
recordSubmission(experimentChunk,expFileName)
def createProcedureRoot():
root = ET.Element('centreProcedureSet', {'xmlns':'http://www.mousephenotype.org/dcc/exportlibrary/datastructure/core/procedure'})
return root
def createSpecimenRoot():
root = ET.Element('centreSpecimenSet', {'xmlns':'http://www.mousephenotype.org/dcc/exportlibrary/datastructure/core/specimen'})
return root
def createCentre(root):
centerNode = ET.SubElement(root, 'centre', {'centreID':'J', 'pipeline':'JAX_001', 'project':'JAX'})
return centerNode
def createSpecimenCentre(root):
centerNode = ET.SubElement(root, 'centre', {'centreID':'J'})
return centerNode
def createCentreSpecimenSet(root):
centerNode = ET.SubElement(root, 'centreSpecimenSet', {'centreID':'J', 'pipeline':'JAX_001', 'project':'JAX'})
return centerNode
def convert_date(date_str: str) -> str:
# Assume the date is in the format mm/dd/yyyy and convert to yyyy-mm-dd
date_str = date_str[0:10] # Remove hh:ms if present
try:
# Parse the input date string to a datetime object
date_obj = datetime.strptime(date_str, "%m/%d/%Y")
formatted_date = date_obj.strftime("%Y-%m-%d") # Changed to match the DCC format
return formatted_date # Strip off minutes, etc
except Exception as e:
# Non-standard date format
#my_logger.info(repr(e))
#my_logger.info("Returning: " + date_str)
return date_str
def createExperiment(centerNode, expName, expDate,taskInstanceKey):
# Generate the bones of the experiment node. No procedure or specimen info yet
experimentDictKeys = [ "experimentID", "dateOfExperiment" ]
experimentDict = dict.fromkeys(experimentDictKeys)
experimentDict["experimentID"] = expName
experimentDict["dateOfExperiment"] = expDate if '/' in expDate == False else convert_date(expDate) # Kind of a weak check
if 'body' in expName.lower() and 'weight' in expName.lower():
experimentDict["sequenceID"] = str(taskInstanceKey)
experimentNode = ET.SubElement(centerNode, 'experiment', experimentDict)
return experimentNode
def createSpecimen(experimentNode,animalName):
specimenNode = ET.SubElement(experimentNode, 'specimenID')
specimenNode.text = animalName
return experimentNode # experimentNode
def createColonyId(experimentNode,colonyId):
lineNode = ET.SubElement(experimentNode, 'line', {'colonyID': '{jr}'.format(jr=colonyId)} )
return lineNode # experimentNode
def createProcedure(experimentNode, procId):
procedureNode = ET.SubElement(experimentNode, 'procedure', {'procedureID': '{proc}'.format(proc=procId) })
return procedureNode # procedureNode
def createMetadata(procedureNode,impcCode, strVal):
paramNode = ET.SubElement(procedureNode, 'procedureMetadata', { 'parameterID': '{code}'.format(code=impcCode)})
valueNode = ET.SubElement(paramNode, 'value')
valueNode.text = strVal
return procedureNode
def createSimpleParameter(procedureNode,impcCode, strVal,statusCode):
paramNode = ET.SubElement(procedureNode, 'simpleParameter', { 'parameterID': '{code}'.format(code=impcCode)})
if len(statusCode) > 0:
statusNode = ET.SubElement(paramNode,'parameterStatus')
statusNode.text = statusCode
else:
valueNode = ET.SubElement(paramNode, 'value')
valueNode.text = strVal
return procedureNode
def createOntologyParameter(procedureNode,impcCode, strVal,statusCode):
paramNode = ET.SubElement(procedureNode, 'ontologyParameter', { 'parameterID': '{code}'.format(code=impcCode)})
if len(statusCode) > 0:
statusNode = ET.SubElement(paramNode,'parameterStatus')
statusNode.text = statusCode
else:
valueNode = ET.SubElement(paramNode, 'value')
valueNode.text = strVal
return procedureNode
# <seriesMediaParameter parameterID="IMPC_XRY_048_001">
# <value incrementValue="1" URI="ftp://images/image1.jpg" fileType="img/jpg">
# <value incrementValue="1" URI="ftp://images/image1.jpg" fileType="img/jpg">
#</seriesMediaParameter>
# Must be included just before the metadata!!!
def createSeriesMediaParameter(procedureNode,impc_code, strVal,procedureImpcCode,taskKey):
if strVal == None:
return procedureNode # bail
# strVal is a string but must be a dict with the increment as the key and the output value as the value
dictVal = validateSeriesParameter(strVal) # e.g. { "1" : "/path/image1.jpg", "2" : "image2.jpg" } - returns None if not a dict
if dictVal == None: # Nothing to do
return procedureNode
# The value is a dictionary with the key as the increment and the value as the value
paramNode = ET.SubElement(procedureNode, 'seriesMediaParameter', { 'parameterID': '{code}'.format(code=impc_code)})
for key in dictVal:
image = dictVal[key] # Looks like \\jax\jax\phenotype\EKG\KOMP\images\blah.jpg or https://omeroweb.jax.org/webgateway/img_detail/69917
if '-1' in image: # -1 is a flag for None. TODO make it None
continue
filenameOnly = get_filename_only(image) # e.g. blah.jpg
ET.SubElement(paramNode, 'value', {'incrementValue': str(key), 'URI': getFtpServer() + 'images/' + procedureImpcCode + "/" + filenameOnly})
db.recordMediaSubmission(image, (getFtpServer() + 'images/' + procedureImpcCode + "/" + filenameOnly) ,taskKey,impc_code)
return procedureNode
def get_filename_only(fullyqualified_path:str) -> str:
filenameOnly = ''
try:
if fullyqualified_path != None:
if omero_api.is_omero_url(fullyqualified_path):
filenameOnly = omero_api.get_upload_image_filename(fullyqualified_path)
else:
filenameOnly_ls = fullyqualified_path.split('\\')
filenameOnly = filenameOnly_ls[len(filenameOnly_ls)-1]
filenameOnly = filenameOnly.replace(' ','_',) # Replace spaces with underscores
except Exception as e:
my_logger.info(repr(e))
return filenameOnly
def createMediaParameter(procedureNode,impc_code, image,procedureImpcCode,taskKey, statusCode):
if image == None:
return procedureNode # bail
filenameOnly = get_filename_only(image) # e.g. \\jax\jax\phenotype\EKG\KOMP\images\blah.jpg return blah.jpg
# The value is a dictionary with the key as the increment and the value as the value
param = {}
param['parameterID'] = impc_code
param['URI'] = getFtpServer() + 'images/' + procedureImpcCode + "/" + filenameOnly
param['fileType'] = 'application/pdf'
paramNode = ET.SubElement(procedureNode, 'mediaParameter', param)
if len(statusCode) > 0:
statusNode = ET.SubElement(paramNode,'parameterStatus')
statusNode.text = statusCode
db.recordMediaSubmission(image, (getFtpServer() + 'images/' + procedureImpcCode + "/" + filenameOnly) ,taskKey,impc_code)
return procedureNode
def validateSeriesParameter(seriesValue: str): # Comes in a str, returns a dict
# series parameters must be in dict format. If not make it so.
# Both key and value need to be strings!!!
# Returns None if not valid
paramDict = {}
try:
if "None" in seriesValue: # Can't handle Nones. Should never see.
return None
seriesValue = seriesValue.replace("\'","\"") # Single quote check
paramDict = json.loads(seriesValue) # Turn to dict
# Values need to be str's!
for k,v in paramDict.items():
paramDict[k] = str(v)
# TODO : Handle viability -> paramDict["noLitter"] = seriesValue # VIA only for now
except Exception as e:
my_logger.info(repr(e))
return paramDict
# e.g. for Primary Viability
"""
<seriesParameter parameterID="IMPC_VIA_037_001">
<value incrementValue="litterID1">RIKEN-Rln1-AB5_01</value>
<value incrementValue="litterID2">RIKEN-Rln1-AB5_01</value>
<value incrementValue="litterID3">RIKEN-Rln1-AB5_03</value>
</seriesParameter>
"""
def createSeriesParameter(procedureNode, impcCode, strVal):
if strVal == None:
return procedureNode # bail
# strVal is a string but must be a dict with the increment as the key and the output value as the value
dictVal = validateSeriesParameter(strVal) # returns None if can't be converted
if dictVal == None: # Nothing to do
return procedureNode
# The value is a dictionary with the key as the increment and the value as the value
paramNode = ET.SubElement(procedureNode, 'seriesParameter', { 'parameterID': '{code}'.format(code=impcCode)})
for key in dictVal:
valueNode = ET.SubElement(paramNode, 'value', {'incrementValue': key})
valueNode.text = dictVal[key]
return procedureNode
def createStatusCode(procedureNode, statusCode):
statusNode = ET.SubElement(procedureNode, 'statusCode')
statusNode.text = statusCode
return procedureNode
def createSpecimenRecord(specimenRecord,specimenSetNode,statusCode):
# fairly weak check but it is true
isEmbryo = specimenRecord["generation"][0] == 'E'
if v.validateMouseFields(specimenRecord) == True:
# A little preprocessing...if zygosity is +/+ then it is baseline. No colony ID
if specimenRecord["zygosity"] == 'wild type':
specimenRecord["isBaseline"] = 'true'
specimenRecord["colonyId"] = ''
if isEmbryo == True:
paramNode = ET.SubElement(specimenSetNode, 'embryo', {
'stage': '{stage}'.format(stage=specimenRecord["generation"][1:]),
'stageUnit': 'DPC',
'isBaseline': '{isBaseline}'.format(isBaseline=str(specimenRecord["isBaseline"]).lower()),
'colonyID': '{colonyID}'.format(colonyID=specimenRecord["colonyId"]),
'strainID': '{strainID}'.format(strainID=getBackgroundStrainId()),
'specimenID': '{specimenID}'.format(specimenID=specimenRecord["specimenID"]),
'gender': '{gender}'.format(gender=specimenRecord["gender"].lower()),
'zygosity': '{zygosity}'.format(zygosity=specimenRecord["zygosity"]),
'litterId': '{litterId}'.format(litterId=specimenRecord["litterId"]),
'pipeline': '{pipeline}'.format(pipeline=specimenRecord["pipeline"]),
'productionCentre': '{productionCentre}'.format(productionCentre=specimenRecord["productionCenter"]),
'phenotypingCentre': '{phenotypingCentre}'.format(phenotypingCentre=specimenRecord["phenotypingCenter"]),
'project': '{project}'.format(project=specimenRecord["project"]) })
else:
paramNode = ET.SubElement(specimenSetNode, 'mouse', {
'DOB': '{dob}'.format(dob=specimenRecord["dob"]),
'colonyID': '{colonyID}'.format(colonyID=specimenRecord["colonyId"]),
'isBaseline': '{isBaseline}'.format(isBaseline=str(specimenRecord["isBaseline"]).lower()),
'strainID': '{strainID}'.format(strainID=getBackgroundStrainId()),
'specimenID': '{specimenID}'.format(specimenID=specimenRecord["specimenID"]),
'gender': '{gender}'.format(gender=specimenRecord["gender"].lower()),
'zygosity': '{zygosity}'.format(zygosity=specimenRecord["zygosity"]),
'litterId': '{litterId}'.format(litterId=specimenRecord["litterId"]),
'pipeline': '{pipeline}'.format(pipeline=specimenRecord["pipeline"]),
'productionCentre': '{productionCentre}'.format(productionCentre=specimenRecord["productionCenter"]),
'phenotypingCentre': '{phenotypingCentre}'.format(phenotypingCentre=specimenRecord["phenotypingCenter"]),
'project': '{project}'.format(project=specimenRecord["project"]) })
if len(statusCode) > 0:
statusNode = ET.SubElement(paramNode,'parameterStatus')
statusNode.text = statusCode
return specimenSetNode
# BEGIN -- KLUGE KLUGE KLUGE KLUGE KLUGE KLUGE because these tests were created with no inputs. Yuck
# Hopefully this will be temporary
def embryoKluge(taskName, parentNode):
# If this is an embryo gross morphology or placenta task
# we may have to create the metadata because there were many tasks
# created before the inputs were created.
expName = "Kristy"
expId = db.databaseGetExperimenterIdCode(expName)
if taskName == "E9.5 Embryo Gross Morphology":
createMetadata(parentNode,"IMPC_GEL_045_001", expId)
createMetadata(parentNode,"IMPC_GEL_046_001", "0")
createMetadata(parentNode,"IMPC_GEL_047_001", "Leica")
createMetadata(parentNode,"IMPC_GEL_048_001", "MC170HD")
createMetadata(parentNode,"IMPC_GEL_049_001", "4% PFA")
createMetadata(parentNode,"IMPC_GEL_050_001", "12:00")
createMetadata(parentNode,"IMPC_GEL_051_001", "48")
createMetadata(parentNode,"IMPC_GEL_052_001", "19:00")
createMetadata(parentNode,"IMPC_GEL_053_001", "07:00")
elif taskName == "E9.5 Placenta Morphology":
createMetadata(parentNode,"IMPC_GPL_008_001", expId)
createMetadata(parentNode,"IMPC_GPL_009_001", "0")
createMetadata(parentNode,"IMPC_GPL_010_001", "Leica")
createMetadata(parentNode,"IMPC_GPL_011_001", "MC170HD")
createMetadata(parentNode,"IMPC_GPL_012_001", "4% PFA")
createMetadata(parentNode,"IMPC_GPL_013_001", "12:00")
createMetadata(parentNode,"IMPC_GPL_014_001", "48")
createMetadata(parentNode,"IMPC_GPL_015_001", "19:00")
createMetadata(parentNode,"IMPC_GPL_016_001", "07:00")
elif taskName == "E12.5 Embryo Gross Morphology":
createMetadata(parentNode,"IMPC_GEM_050_001", expId)
createMetadata(parentNode,"IMPC_GEM_051_001", "0")
createMetadata(parentNode,"IMPC_GEM_052_001", "Leica")
createMetadata(parentNode,"IMPC_GEM_053_001", "MC170HD")
createMetadata(parentNode,"IMPC_GEM_054_001", "4% PFA")
createMetadata(parentNode,"IMPC_GEM_055_001", "12:00")
createMetadata(parentNode,"IMPC_GEM_056_001", "48")
createMetadata(parentNode,"IMPC_GEM_057_001", "19:00")
createMetadata(parentNode,"IMPC_GEM_058_001", "07:00")
elif taskName == "E12.5 Placenta Morphology":
createMetadata(parentNode,"IMPC_GPM_008_001", expId)
createMetadata(parentNode,"IMPC_GPM_009_001", "0")
createMetadata(parentNode,"IMPC_GPM_010_001", "Leica")
createMetadata(parentNode,"IMPC_GPM_011_001", "MC170HD")
createMetadata(parentNode,"IMPC_GPM_012_001", "4% PFA")
createMetadata(parentNode,"IMPC_GPM_013_001", "12:00")
createMetadata(parentNode,"IMPC_GPM_014_001", "48")
createMetadata(parentNode,"IMPC_GPM_015_001", "19:00")
createMetadata(parentNode,"IMPC_GPM_016_001", "07:00")
elif taskName == "E15.5 Embryo Gross Morphology":
createMetadata(parentNode,"IMPC_GEO_051_001", expId)
createMetadata(parentNode,"IMPC_GEO_052_001", "0")
createMetadata(parentNode,"IMPC_GEO_053_001", "Leica")
createMetadata(parentNode,"IMPC_GEO_054_001", "MC170HD")
createMetadata(parentNode,"IMPC_GEO_055_001", "4% PFA")
createMetadata(parentNode,"IMPC_GEO_056_001", "12:00")
createMetadata(parentNode,"IMPC_GEO_057_001", "48")
createMetadata(parentNode,"IMPC_GEO_058_001", "19:00")
createMetadata(parentNode,"IMPC_GEO_059_001", "07:00")
elif taskName == "E15.5 Placenta Morphology":
createMetadata(parentNode,"IMPC_GPO_008_001", expId)
createMetadata(parentNode,"IMPC_GPO_009_001", "0")
createMetadata(parentNode,"IMPC_GPO_010_001", "Leica")
createMetadata(parentNode,"IMPC_GPO_011_001", "MC170HD")
createMetadata(parentNode,"IMPC_GPO_012_001", "4% PFA")
createMetadata(parentNode,"IMPC_GPO_013_001", "12:00")
createMetadata(parentNode,"IMPC_GPO_014_001", "48")
createMetadata(parentNode,"IMPC_GPO_015_001", "19:00")
createMetadata(parentNode,"IMPC_GPO_016_001", "07:00")
elif taskName == "E18.5 Embryo Gross Morphology":
createMetadata(parentNode,"IMPC_GEP_065_001", expId)
createMetadata(parentNode,"IMPC_GEP_066_001", "0")
createMetadata(parentNode,"IMPC_GEP_067_001", "Leica")
createMetadata(parentNode,"IMPC_GEP_068_001", "MC170HD")
createMetadata(parentNode,"IMPC_GEP_069_001", "4% PFA")
createMetadata(parentNode,"IMPC_GEP_070_001", "12:00")
createMetadata(parentNode,"IMPC_GEP_071_001", "48")
createMetadata(parentNode,"IMPC_GEP_072_001", "19:00")
createMetadata(parentNode,"IMPC_GEP_073_001", "07:00")
elif taskName == "E18.5 Placenta Morphology":
createMetadata(parentNode,"IMPC_GPP_008_001", expId)
createMetadata(parentNode,"IMPC_GPP_009_001", "0")
createMetadata(parentNode,"IMPC_GPP_010_001", "Leica")
createMetadata(parentNode,"IMPC_GPP_011_001", "MC170HD")
createMetadata(parentNode,"IMPC_GPP_012_001", "4% PFA")
createMetadata(parentNode,"IMPC_GPP_013_001", "12:00")
createMetadata(parentNode,"IMPC_GPP_014_001", "48")
createMetadata(parentNode,"IMPC_GPP_015_001", "19:00")
createMetadata(parentNode,"IMPC_GPP_016_001", "07:00")
else:
return False
return True
# End -- of embryo metadata kluge
# Create experiment XMLs
def generateExperimentXML(taskInfoLs, centerNode):
# Given a dictionary parse out the animal info and the procedure info
# It looks like "taskInfo" [ { "animal" [] , "taskInstance" : [] }, { "animal" [] , "taskInstance" : [] }, ...]
# If an animal has multiple procedures the animal will only appear once.
# Get the list of mouse info. For KOMP it should always be 1 element
if taskInfoLs == None or len(taskInfoLs) == 0:
return 0
# otherwise, we have some data
# Go to database once for needed DCC data
# e.g. BWT
threeLetterImpcCode = extractThreeLetterCode(db.databaseSelectProcedureCode(taskInfoLs[0]["taskInstance"][0]['workflowTaskName']))
# Returns a list of tuples (impccode, climb_key, dccType_key) from komp.cv_dcctypes
parameterDefLs = db.databaseSelectImpcData(threeLetterImpcCode,False, False)
# Now get the full code e.g. IMPC_BWT_001
procedureImpcCode = db.databaseSelectProcedureCode(taskInfoLs[0]["taskInstance"][0]['workflowTaskName'])
numberOfProcs = 0
for exps in taskInfoLs:
# For each animal thee are one or more tasks
mouseInfoLs = exps["animal"]
for mouseInfo in mouseInfoLs:
procLs = exps["taskInstance"]
for proc in procLs:
if proc["taskStatus"] == "Failed QC" or proc["taskStatus"] == "Already submitted":
my_logger.info("XML generation: Experiment not processed for " + mouseInfo['animalName'] + ". Task status:" + proc["taskStatus"] )
continue # We failed it or we've already submitted it.
my_logger.info("Generating XML for " + (proc['workflowTaskName'] + ' - ' + mouseInfo['animalName'] + ' - ' + str(proc["taskInstanceKey"])))
# for each procedure in the list build up the XML
numberOfProcs += 1
experimentNode = createExperiment(centerNode,(proc['workflowTaskName'] + ' - ' + mouseInfo['animalName'] + ' - ' + str(proc["taskInstanceKey"])), proc['dateComplete'],proc["taskInstanceKey"])
experimentNode = createSpecimen(experimentNode,mouseInfo['animalName'])
procedureNode = createProcedure(experimentNode,procedureImpcCode)
# Now create the metadata from the inputs and outputs
procedureNode = buildParameters(procedureNode,proc,parameterDefLs,procedureImpcCode)
procedureNode = buildMetadata(procedureNode,proc)
experimentNode = buildExperimentStatusCode(experimentNode,getProcedureStatusCode(proc))
# CALL the new function
return numberOfProcs
# Create experiment XMLs
def generateLineCallExperimentXML(taskInfoLs, centerNode):
# Given a dictionary parse out the animal info and the procedure info
# It looks like "taskInfo" [ { "animal" [] , "taskInstance" : [] }, { "animal" [] , "taskInstance" : [] }, ...]
# If an animal has multiple procedures the animal will only appear once.
# Get the list of mouse info. For KOMP it should always be 1 element
if taskInfoLs == None:
return 0
# e.g. BWT
threeLetterImpcCode = extractThreeLetterCode(db.databaseSelectProcedureCode(taskInfoLs[0]["taskInstance"][0]['workflowTaskName']))
# Returns a list of tuples (impccode, climb_key, dccType_key) from komp.cv_dcctypes
parameterDefLs = db.databaseSelectImpcData(threeLetterImpcCode,False, False)
# Now get the full code e.g. IMPC_BWT_001
procedureImpcCode = db.databaseSelectProcedureCode(taskInfoLs[0]["taskInstance"][0]['workflowTaskName'])
# Else we have some data
numberOfProcs = 0
for exps in taskInfoLs:
procLs = exps["taskInstance"]
for proc in procLs:
if proc["taskStatus"] == "Failed QC" or proc["taskStatus"] == "Already submitted":
continue # We failed it or we've already submitted it.
findColonyId(proc)
# for each procedure in the list build up the XML
numberOfProcs += 1
lineNode = createColonyId(centerNode,getColonyId())
procedureNode = createProcedure(lineNode,db.databaseSelectProcedureCode(proc['workflowTaskName']))
# Now create the metadata from the inputs and outputs
procedureNode = buildParameters(procedureNode,proc,parameterDefLs,procedureImpcCode)
procedureNode = buildMetadata(procedureNode,proc)
lineNode = buildExperimentStatusCode(lineNode,getProcedureStatusCode(proc))
return numberOfProcs
def buildMetadata(procedureNode,proc):
# Ugly - If there are no inputs then this may be an embryo lethal task that was unfortunately created with no inputs.
if len(proc['inputs']) == 0:
embryoKluge(proc['workflowTaskName'],procedureNode)
return procedureNode
# Returns a list of tuples (impccode, climb_key, dccType_key)
setProcedureImpcCode(extractThreeLetterCode(db.databaseSelectProcedureCode(proc['workflowTaskName'])))
# Get inputs -- last boolean = true
metadataDefLs = db.databaseSelectImpcData(getProcedureImpcCode(), True, True)
# Merge with metadata from the outputs (last boolean = false)
metadataDefLs = metadataDefLs + db.databaseSelectImpcData(getProcedureImpcCode(), True, False)
# Go through the inputs and if there is a climb_key match add the value
inputLs = proc['inputs']
for input in inputLs:
inputKey = input['inputKey']
impcCode = None
for i, v in enumerate(metadataDefLs):
if v[1] == inputKey: # If the climb key matches, store the IMPC code
impcCode = v[0] # For the input
if not impcCode == None:
# Get the value from input
if input['inputValue'] is not None:
inputVal = input['inputValue'].strip()
if len(inputVal) > 0: # only if there is a value there.
if db.isExperimenterID(impcCode) == True: # Can't use real names. Must insert numerical value
inputVal = db.databaseGetExperimenterIdCode(inputVal)
if len(inputVal) == 0:
my_logger.info("Couldn't resolve experimenter ID for " + input['inputValue'].strip())
elif db.isDate(impcCode) == True: # Format YYYY-MM-DD
inputVal = str(pd.to_datetime(inputVal))[0:10]
my_logger.info("Reformating date:"+ input['inputValue'].strip() + " to " + inputVal)
elif db.isDateTime(impcCode) == True: # Format YYYY-M-DD hh:mm:ss
inputVal = str(pd.to_datetime(inputVal))[0:19]
my_logger.info("Reformating datetime:"+ input['inputValue'].strip() + " to " + inputVal)
procedureNode = createMetadata(procedureNode, impcCode, inputVal)
# Go through the outputs and if there is a climb_key match add the value
# We have to do this because CLIMB and PFS do not allow importation of inputs so some matadata are outputs
outputLs = proc['outputs']
for output in outputLs:
outputKey = output['outputKey']
impcCode = None
for i, v in enumerate(metadataDefLs):
if v[1] == outputKey:
impcCode = v[0]
if not impcCode == None:
if output['outputValue'] is not None:
# Get the IMPC code from metadataDefLs and the value from input
outputVal = str(output['outputValue']).strip()
if len(outputVal) > 0: # only if there is a value there.
if db.isExperimenterID(impcCode) == True: # Can't use real names. Must insert numerical value
#my_logger.info("Looking up " + outputVal + " for experimenterID.")
outputVal = db.databaseGetExperimenterIdCode(outputVal)
if len(outputVal) == 0:
my_logger.info(" Couldn't resolve experimenter ID")
elif db.isDate(impcCode) == True: # Format YYYY-MM-DD
outputVal = str(pd.to_datetime(outputVal))[0:10]
my_logger.info("Reformating date:"+ output['outputValue'].strip() + " to " + outputVal)
elif db.isDateTime(impcCode) == True: # Format YYYY-M-DD hh:mm:ss
outputVal = str(pd.to_datetime(outputVal))[0:19]
my_logger.info("Reformating datetime:"+ output['outputValue'].strip() + " to " + outputVal)
procedureNode = createMetadata(procedureNode, impcCode, outputVal)
return procedureNode
def getProcedureStatusCode(proc:dict):
impc_status_code = ""
if 'taskStatus' in proc and proc['taskStatus'] is not None:
if proc['taskStatus'] in procedure_status_message_map:
impc_status_code = procedure_status_message_map[proc['taskStatus']]
return impc_status_code
# For adding to XML
def buildExperimentStatusCode(experimentNode, status_code):
if status_code != '':
status_node = ET.SubElement(experimentNode,'statusCode')
status_node.text = status_code
return experimentNode
def getOutputStatusCode(output:dict):
impc_status_code = ""
if 'statusCode' in output and \
output['statusCode'] is not None and \
output['statusCode'] in output_status_message_map:
impc_status_code = output_status_message_map[output['statusCode']]
return impc_status_code
def buildParameters(procedureNode,proc,parameterDefLs,procedureImpcCode):
# Get the data from the Outputs
output_status_code = ''
# Go through the outputs and if there is a climb_key match add the value
outputLs = proc['outputs']
# Sorted by _DccType_key because simples must precede ontology that must precede series
for i, v in enumerate(parameterDefLs):
impcCode = None
dccType = None
for output in outputLs:
outputKey = output['outputKey']
if v[1] == outputKey:
impcCode = v[0]
dccType = v[2]
break
outputVal=None
if not impcCode == None and output['outputValue'] is not None:
# Get the IMPC code from metadataDefLs and the value from output
outputVal = output['outputValue']
output_status_code = getOutputStatusCode(output)
# No value and no status code
if len(output_status_code) == 0 and (outputVal is None or len(str(outputVal)) == 0):
continue
if type(outputVal) != type(""): # TODO - Handle floats and ints
outputVal = str(outputVal)
if len(outputVal) > 0:
if dccType == 1:
procedureNode = createSimpleParameter(procedureNode, impcCode, outputVal,output_status_code)
elif dccType == 2: # Ontology TBD
procedureNode = createOntologyParameter(procedureNode, impcCode, outputVal,output_status_code)
elif dccType == 3: # Media - ABR (014) and ERG (047)
taskKey = int(proc["taskInstanceKey"])
procedureNode = createMediaParameter(procedureNode,impcCode, outputVal,procedureImpcCode,taskKey,output_status_code)
elif dccType == 4: # Series
outputVal = outputVal.replace("\'","\"") # TODO - will this handle VIABILITY?
procedureNode = createSeriesParameter(procedureNode, impcCode, json.loads(json.dumps(outputVal)))
elif dccType == 5: # SeriesMedia
taskKey = int(proc["taskInstanceKey"])
procedureNode = createSeriesMediaParameter(procedureNode, impcCode, outputVal,procedureImpcCode,taskKey)
elif dccType == 8: # colony ids are stored as ouputs for line calls
setColonyId(outputVal)
elif dccType == 6: # MediaSample - unsupported
my_logger.info("MediaSample for an output type? Output key:" + str(outputKey))
else:
my_logger.info("Metadata for an output? Output key:" + str(outputKey))
return procedureNode
# SPECIMEN
def removeDuplicates(animalInfoLs):
# We only want one of each specimen in the specimen file
animalNames = {''} # A set
animalInfoLs = animalInfoLs[::-1]
i=0
for animalInfo in animalInfoLs:
animal = animalInfo["animal"]
if animal['animalName'] in animalNames:
animalInfoLs.pop(i)
else:
animalNames.add(animal['animalName'])
i += 1
return animalInfoLs
def generateSpecimenXML(animalInfoLs, centerNode): # List of dictionaries
if animalInfoLs == None:
return
if len(animalInfoLs) == 0:
return
# Otherwise we have some data
# Remove duplicates - if any
animalInfoLs = removeDuplicates(animalInfoLs)
specimenRecord = {}
# Hardcoded / constants
specimenRecord["pipeline"] = 'JAX_001'
specimenRecord["productionCenter"] = 'J'
specimenRecord["phenotypingCenter"] = 'J'
specimenRecord["project"] = 'JAX'
for animalInfo in animalInfoLs:
# Get the four entities
animal = animalInfo["animal"]
line = animalInfo["line"]
litter = animalInfo["litter"]
genotypes = animalInfo["genotypes"] # List of dicts with keys genotypeKey, date, assay, genotype, modifiedBy, dateModified.
specimenRecord["specimenID"] = animal["animalName"]
if animal["dateBorn"] is not None:
specimenRecord["dob"] = animal["dateBorn"][0:10]
specimenRecord["gender"] = animal["sex"]
specimenRecord["isBaseline"] = line["stock"] == '005304'
if specimenRecord["isBaseline"] == False:
specimenRecord["colonyId"] = "JR" + line["stock"][1:6]
else:
specimenRecord["colonyId"] = ""
genotype_str = extractGenotype(genotypes) # must be present
if genotype_str == None:
my_logger.info("Could not resolve zygosity for" + animal['animalName'])
continue
specimenRecord["zygosity"] = genotype_str
specimenRecord["generation"] = animal['generation']
if litter != None: # Not required
specimenRecord["litterId"] = litter['birthID']
else:
specimenRecord["litterId"] = ''
createSpecimenRecord(specimenRecord,centerNode,"")
return # root
# UTILITIES
def getNextExperimentFilename(dataDir):
filename = ''
# The experiment filename has a format of
# J.YYYY-MM-DD.NN.experiment.impc.xml
filter = 'J.' + datetime.today().strftime('%Y-%m-%d') + '.{counterVal}.experiment.impc.xml'.format(counterVal='*')
fileLs = glob.glob(dataDir + filter)
max = 49
for a in fileLs:
parts = a.split('.')
cntr = parts[2]
if max < int(cntr):
max = int(cntr)
newFileName = 'J.' + datetime.today().strftime('%Y-%m-%d') + '.{counterVal}.experiment.impc.xml'.format(counterVal=str(max+1))
return dataDir + newFileName;
def getNextSpecimenFilename(dataDir):
filename = ''
# The specimen filename has a format of
# J.YYYY-MM-DD.NN.specimen.impc.xml
filter = 'J.' + datetime.today().strftime('%Y-%m-%d') + '.{counterVal}.specimen.impc.xml'.format(counterVal='*')
fileLs = glob.glob(dataDir + filter)
max = 0
for a in fileLs:
parts = a.split('.')
cntr = parts[2]
if max < int(cntr):
max = int(cntr)
newFileName = 'J.' + datetime.today().strftime('%Y-%m-%d') + '.{counterVal}.specimen.impc.xml'.format(counterVal='{:02d}'.format(max+1))
return dataDir + newFileName;
# Take something like IMPC_BWT_001 and return BWT
def extractThreeLetterCode(s):
try:
return s[(s.index('_') + 1):(s.index('_') + 4)]
except ValueError:
my_logger.info("Could not resolve three letter code for" + s)
return ""
"""
genotypes = List of dicts with keys genotypeKey, date, assay, genotype, modifiedBy, dateModified.
"""
def extractGenotype(genotypes):
zygosity = None
for genotype in genotypes:
if genotype["genotype"] == '+/+':
zygosity = 'wild type'
elif genotype["genotype"] == '-/+' or genotype["genotype"] == '+/-' :
zygosity = 'heterozygous'
elif genotype["genotype"] == '-/-':
zygosity = 'homozygous'
elif genotype["genotype"] == '-/Y':
zygosity = 'hemizygous'
elif genotype["genotype"] == '+/Y':
zygosity = 'anzygous'
return zygosity
lineCallProcedures = ["Viability E18.5 Secondary Screen", "Viability E15.5 Secondary Screen",
"Viability E12.5 Secondary Screen", "Viability E9.5 Secondary Screen",
"Fertility of Homozygous Knock-out Mice", "Viability Primary Screen v2"]
# Check it against a list of possible line-based procedures
def procedureHasAnimals(climbFilter):
taskName = climbFilter.get("taskInstance").get("workflowTaskName")
hasAnimals = True
if taskName in lineCallProcedures:
hasAnimals = False
return hasAnimals
def getAnimalNameFromTaskInfo(task):
animalName = '' # Not all tasks have animals
if "animal" in task:
animalName = task["animal"][0]["animalName"] # This one does
else: # line based procedure. No animal - need JR number / colony ID
animalName = findColonyId(task["taskInstance"][0]) # It' too bad but the colony id is stored at the output level rather than the task level. Thanks CLIMB!
return animalName
#pretty print method
def indent(elem, level=0):
i = "\n" + level*" "
j = "\n" + (level-1)*" "
if len(elem):
if not elem.text or not elem.text.strip():
elem.text = i + " "
if not elem.tail or not elem.tail.strip():
elem.tail = i
for subelem in elem:
indent(subelem, level+1)
if not elem.tail or not elem.tail.strip():
elem.tail = j
else:
if level and (not elem.tail or not elem.tail.strip()):
elem.tail = j
return elem
def handleClimbData():
# For CORE PFS komp mice
mycfg = cfg.parse_config(path="config.yml")
# Setup credentials for database
setDataDir(mycfg['directories']['dest'])
my_logger.info("Attempting to buils XMLs from CLIMB.")