DCIS/pythonScripts/importXML.py

import os
import sys
import importlib
import json
import lxml.etree

#need labkey interface's importXLS
def getImporter(setup):
    sys.path.append(setup['paths']['nixWrapper'])
    import nixWrapper
    nixWrapper.loadLibrary('labkeyInterface')
    import importXLSX
    importlib.reload(importXLSX)
    return importXLSX

def getFileBrowser(db):
   import nixWrapper
   nixWrapper.loadLibrary('labkeyInterface')
   import labkeyFileBrowser
   return labkeyFileBrowser.labkeyFileBrowser(db.net)

def getVal(xmlRoot,aliasVal,xPath='',aliasReplace={}):
    q=aliasVal.split(':')
    xName=q[0]
    
    for x in aliasReplace:
        xName=xName.replace(x,aliasReplace[x])
    if len(xPath)>0:
        if len(xName)>0:
            elementPath='/'.join([xPath,xName])
        else:
            elementPath=xPath
    else:
        elementPath=xName
    attributeName=q[1]
    try:
        return xmlRoot.find(elementPath).get(attributeName)
    except AttributeError:
        return None
    
def parseJSON(x):
    print(f'Decoding [{x}]')
    try:
        return json.loads(x)
    except TypeError:
        pass
    return {}
                
def readSetup(importXLSX,pars):
    db=importXLSX.getDB(pars)
    ds=db.selectRows(pars['project'],'lists','importSetup',[])
    setupRows=ds['rows']
    for r in setupRows:
        
        r['aliasReplace']=parseJSON(r['aliasReplace'])
        r['presetValues']=parseJSON(r['presetValues'])
    return setupRows
        
    
        
    
def importXML(importXLSX,pars,xmlFile,dryRun=True):
    #def importData(pars,filename,getId=getId,modify=modify,convertLookup=convertLookup,dryRun=True,debug=True):
#master routine that imports data based on pars, 
#applies user supplied functions modify, convertLookup and get Id and 
#updates relevant database

#some useful fields from pars (d is for default value)
# - seqNumOffset specify visit/sequenceNum offset (number, d:0 will result in 1)
# - XPath - xml path to the element to take data from (helpful if multiple elements are present in xml and identical data is sought)
# - additionalKeyColumn - name of the variable/column used for separating data entries (on top of ParticipantId and SequenceNum, helpful in the same cases as XPath)
# - presetVariables - set some of the row variables to this values (same cases as XPath)
# - project - labkey project
# - schema - labkey schema (list/study, d: study)
# - query - labkey query

   #set this is as sequenceNum for entries, or initial seqNum if more than a single entry is in the dataset
    seqNumOffset=pars.get('seqNumOffset',0)
    xPath=pars.get('XPath','')
    keyColumn=pars.get('additionalKeyColumn')
    presetValues=pars.get('presetValues',{})
    aliasReplace=pars.get('aliasReplace',{})
    
    fields=importXLSX.getFields(pars)
    lookupVars=importXLSX.getVariables(fields,fieldType='LOOKUP')
    dateVars=importXLSX.getVariables(fields,fieldType='DATE')
    doubleVars=importXLSX.getVariables(fields,fieldType='DOUBLE')

#convert dates to list
    dateVars=list(dateVars.keys())
    print(f'dateVars: {dateVars}')
    lookupMap={f:importXLSX.getLookupMap(pars,fields,f) for f in lookupVars}
    alias=importXLSX.invertMap(importXLSX.getAlias(fields))
    print(f'aliases: {alias}')
    row={}
    
    tree = lxml.etree.ElementTree(file=xmlFile)
    print(tree.docinfo.xml_version)
    root=tree.getroot()#Element
    #patient id can be either set in pars (takes precedence) or from xml record
    pid=pars.get('id',root.find('Patient/PatientID').get('val'))
    
    row={'ParticipantId':pid,'SequenceNum':seqNumOffset+1}
    row.update(presetValues)
    
    for f in fields:
        try:
            row[f]=getVal(root,alias[f],xPath,aliasReplace)
        except KeyError:
            print(f'Alias for field {f} not found')
            continue
    print(row)
    db=importXLSX.getDB(pars)
    project=pars.get('project','DCIS/Study')
    schema=pars.get('schema','demographics')
    query=pars.get('query','demographics')

    selVal=['ParticipantId','SequenceNum']
    if keyColumn:
        selVal.append(keyColumn)
    qFilter=[{'variable':v,'value':'{}'.format(row[v]),'oper':'eq'} for v in selVal]

    ds=db.selectRows(project,schema,query,qFilter)
    if len(ds['rows'])>0:
        r=ds['rows'][0]
        r.update(row)
        print(f'Updating entry')
        if not dryRun:
            importXLSX.printErr(db.modifyRows('update',project,schema,query,[r]))
        return r
    print(f'Inserting entry')
    if not dryRun:
        importXLSX.printErr(db.modifyRows('insert',project,schema,query,[row]))
    
        


def main(parameterFile):

   with open(parameterFile) as f:
      pars=json.load(f)

   print(pars)

   fhome=os.path.expanduser('~')
   with open(os.path.join(fhome,".labkey","setup.json")) as f:
     setup=json.load(f)

   importXLSX=getImporter(setup)

   #needs server
   db=importXLSX.getDB(pars)
   
   db.net.getCSRF()
   keyFilter={'variable':'Key','value':'{key}'.format(**pars),'oper':'eq'}
#needs project
   ds=db.selectRows(pars['project'],'lists','importXML',[keyFilter])
   r=ds['rows'][0]
   filename=os.path.join(fhome,'temp','DCIS','data.xml')
   url=db.net.connectionConfig['host']+r['_labkeyurl_fileUpload']
   fb=getFileBrowser(db)
   fb.readFileToFile(url,filename)
   #needs project
   setupRows=readSetup(importXLSX,pars)
   setupRows=setupRows[0:1]
   for s in setupRows:
#needs project and schema for queries 
      importXML(importXLSX,pars|s,filename,dryRun=True)



if __name__ == "__main__" :
   main(sys.argv[1])