import string,re,sys,itertools ''' cut pasted from hss.py cookbook ''' class Sql(object): @staticmethod def compile(dbname,querytxt): conn = sqlite3.connect(dbname) try: cur = conn.cursor() cur.executescript(querytxt) conn.commit() except Exception as e: logging.error(e) return conn def __init__(self): self.conn = False def _connect(self): if not self.conn: self.conn = sqlite3.connect(':memory:', check_same_thread=False, isolation_level=None) return self def compile(self,querytxt): self._connect() try: cur = self.conn.cursor() cur.executescript(querytxt) self.conn.commit() except Exception as e: logging.error(e) logging.info(e) return self def attach(self,dbfile,dbname): if os.path.exists(dbfile+'-journal'): os.remove(dbfile+'-journal') self._connect() for db in self.query('PRAGMA database_list;'): if db['name'] == dbname: return self.conn.cursor().execute("ATTACH DATABASE '%(dbfile)s' AS %(dbname)s;" % {'dbfile':dbfile,'dbname':dbname}) self.conn.commit() return self def query(self,querytxt,*args): self._connect() result=[] try: cur = self.conn.cursor() cur.execute(querytxt,args) col = [ attr[0] for attr in cur.description ] if cur.description else [] for row in cur.fetchall(): if cur.description: yield dict(zip(col,row)) else: yield list(row) except Exception as e: logging.error(e) def update(self,querytxt,*args): self._connect() try: cur = self.conn.cursor() cur.execute(querytxt,args) self.conn.commit() return cur.lastrowid except Exception as e: if not 'UNIQUE' in str(e): logging.error(e) def bulk(self,querytxt,blk=[]): self._connect() try: cur = self.conn.cursor() cur.execute('BEGIN TRANSACTION;') cur.executemany(querytxt,blk) cur.execute('COMMIT;') self.conn.commit() except Exception as e: if not 'UNIQUE' in str(e): logging.error(e) ''' the thing ''' def floodTheShit(src): #from highSpeedSandwitch.hss import Sql sql = Sql() sql.attach(src,'hl7') from hl7 import SqlHl7 _, sqlload = SqlHl7(Sql()) def getTrg(src,seq): for tp in sql.query('select VAL from hl7.HL7 where SRC = ? and SEQ = ? and ROW = 0 and COL = 8 and COM = 0',src,seq): for tr in sql.query('select VAL from hl7.HL7 where SRC = ? and SEQ = ? and ROW = 0 and COL = 8 and COM = 1',src,seq): for trg in sql.query('select MessageStructureId, GRP from hl7.TRG where MessageType = ? and MessageTrigger = ?',tp['VAL'],tr['VAL']): return trg['MessageStructureId'] def getGrp(seg,grpT=[],hnt=[]): for i in range(len(grpT)): for r in sql.query('select HNT,SEG,HED from hl7.GRP WHERE SEG!=HNT and GRP = ?',grpT[i]): grp = r['HNT'] hed = r['HED'] grpTT = [grp] + grpT[i:] if not grp in hnt: hnt.append(grp) for chld in getGrp(seg, grpTT, hnt): yield chld if r['SEG'] == seg: yield grpTT yield grpT def Frst(a=[],default=None): for e in a: return e return default def PerCol(it): SEG = 'MSH' for VAL,_,_,COL,COM,SUB,REP,_ in it: if COL == 0: SEG = VAL yield 'SEG', VAL key = ("%s_%d_%d_%d__%d" % (SEG,COL,COM,SUB,REP)).replace('__0','') yield key , VAL def inCtx(src,seq, it): #st = getTrg(src,seq) dick = {} #grpT = [st] for row,itt in itertools.groupby(it, lambda t : t[2]): nudick = dict(PerCol(itt)) #attempt to make thing well for key in set(dick): if key.startswith(nudick['SEG']): dick.pop(key,None) dick.update(nudick) #grpT = Frst( getGrp(dick['SEG'] , []+grpT ) , []+grpT) #dick['GRP'] = grpT[0] print(src,seq,row,dick['SEG']) #,grpT[0]) yield row,dick['SEG'],dick for msh,it in itertools.groupby(sqlload(), lambda t : (t[7],t[1]) ): src,seq = msh yield src,seq, inCtx(src,seq, it) templateCatalog = dict({ 'Patient': { 'MSH' : [''' var patient = GetPatient("$PID_3_0_0"); if (patient == null) { Assert.Inconclusive("patient not found"); } //Assert.AreEqual( null , patient.ModificationDate ); //Assert.AreEqual( null , patient.ModificationUser ); Assert.AreEqual( null , patient.RAMQ ); Assert.AreEqual( null , patient.DateOfDeath ); Assert.AreEqual( "$PID_5_1_0" , patient.FirstName ); Assert.AreEqual( "$PID_5_2_0" , patient.MiddleName ); Assert.AreEqual( "$PID_5_0_0" , patient.LastName ); Assert.AreEqual( "$PID_8_0_0" , patient.Gender ); Assert.AreEqual( new DateTime("$PID_7_0_0") , patient.Birthday ); //Assert.AreEqual( new DateTime("$MSH_6_0_0") , patient.DateLastMessage ); //Assert.AreEqual( "rule specific" , patient.PrimaryExternalCode ); ''',], }, 'PatientExternalCode' : { 'MSH' : [''' var patient = GetPatient("$PID_3_0_0"); if (patient == null) { Assert.Inconclusive("patient not found"); } var patientExternalCodeCnt = 0; '''], 'PID' : [''' { var patientExternalCode = patient.PatientExternalCodes.ElementAt(patientExternalCodeCnt++); //Assert.AreEqual( null , patientExternalCode.ModificationUser ); //Assert.AreEqual( null , patientExternalCode.ModificationDate ); // PID 3.x.y Patient Identifier List Assert.AreEqual( "$PID_3_0_0" , patientExternalCode.ExternalCode ); //Assert.AreEqual( "$PID_3_3_0" , patientExternalCode.AssigningAuthority ); //Assert.AreEqual( "$PID_3_4_0" , patientExternalCode.IdentifierCode ); //Assert.AreEqual( "$PID_3_5_0" , patientExternalCode.Facility ); Assert.AreEqual( "ALGI01CH" , patientExternalCode.AssigningAuthority , "constant chicoutimi"); Assert.AreEqual( "PRI" , patientExternalCode.IdentifierCode , "constant chicoutimi" ); Assert.AreEqual( "51218394" , patientExternalCode.Facility , "constant chicoutimi"); } ''',''' { if (patient.PatientExternalCodes.Count() <= patientExternalCodeCnt) { Assert.Inconclusive("alternate id not mapped"); } var patientExternalCode = patient.PatientExternalCodes.ElementAt(patientExternalCodeCnt++); //Assert.AreEqual( null , patientExternalCode.ModificationUser ); //Assert.AreEqual( null , patientExternalCode.ModificationDate ); // PID 4.x.y Alternate Patient Identifier Assert.AreEqual( "$PID_4_0_0" , patientExternalCode.ExternalCode ); //Assert.AreEqual( "$PID_4_3_0" , patientExternalCode.AssigningAuthority ); //Assert.AreEqual( "$PID_4_4_0" , patientExternalCode.IdentifierCode ); //Assert.AreEqual( "$PID_4_5_0" , patientExternalCode.Facility ); } ''']+[''' { if (patient.PatientExternalCodes.Count() <= patientExternalCodeCnt) { Assert.Inconclusive("repeated alternate id not mapped"); } var patientExternalCode = patient.PatientExternalCodes.ElementAt(patientExternalCodeCnt++); //Assert.AreEqual( null , patientExternalCode.ModificationUser ); //Assert.AreEqual( null , patientExternalCode.ModificationDate ); // PID 4.x.y Alternate Patient Identifier Repetition Assert.AreEqual( "$PID_4_0_0__$REP" , patientExternalCode.ExternalCode ); //Assert.AreEqual( "$PID_4_3_0__$REP" , patientExternalCode.AssigningAuthority ); //Assert.AreEqual( "$PID_4_4_0__$REP" , patientExternalCode.IdentifierCode ); //Assert.AreEqual( "$PID_4_5_0__$REP" , patientExternalCode.Facility ); } '''.replace('$REP', str(i)) for i in range(4) ], }, 'PatientAddresses' : { 'MSH' : [''' var patient = GetPatient("$PID_3_0_0"); if (patient == null) { Assert.Inconclusive("patient not found"); } var patientAddressCnt = 0; '''], 'PID' : [''' { if (patient.PatientAddresses.Count() <= patientAddressCnt) { Assert.Inconclusive("not mapped"); } var patientAddress = patient.PatientAddresses.ElementAt(patientAddressCnt++); //Assert.AreEqual( null , patientAddress.ModificationUser ); //Assert.AreEqual( null , patientAddress.ModificationDate ); Assert.AreEqual( new DateTime("$MSH_6_0_0") , patientAddress.DateOfMessage ); Assert.AreEqual( "" , patientAddress.AddressType ); Assert.AreEqual( "" , patientAddress.Street1 ); Assert.AreEqual( "" , patientAddress.Street2 ); Assert.AreEqual( "" , patientAddress.City ); Assert.AreEqual( "" , patientAddress.Province ); Assert.AreEqual( "" , patientAddress.PostalCode ); Assert.AreEqual( "" , patientAddress.CountryCode ); Assert.AreEqual( "" , patientAddress.PatientHospitalizationExternalCode ); } '''], }, 'PatientHospitalizations' : { 'MSH' : [''' var patient = GetPatient("$PID_3_0_0"); if (patient == null) { Assert.Inconclusive("patient not found"); } var patientHospitalizationCnt = 0; '''], 'PV1' : [''' if (patient.PatientHospitalizations.Count() <= patientHospitalizationCnt) { Assert.Inconclusive("not mapped"); } var patientHospitalization = patient.PatientHospitalizations.ElementAt(patientHospitalizationCnt++); var eventDate = new DateTime("$EVN_6_0_0"); //Assert.AreEqual( null , patientHospitalization.ModificationUser ); //Assert.AreEqual( null , patientHospitalization.ModificationDate ); //Assert.AreEqual( eventDate , patientHospitalization.End ); //Assert.AreEqual( eventDate , patientHospitalization.Start ); Assert.AreEqual( "$PV1_2_0_0" , patientHospitalization.PatientClass ); Assert.AreEqual( "$PV1_19_0_0" , patientHospitalization.ExternalCode ); //Assert.AreEqual( new DateTime("$MSH_6_0_0") , patientHospitalization.DateLastMessage ); var patientHospitalizationBedCnt = 0; var patientHospitalizationTransferCnt = 0; var patientHospitalizationInfectiologistCnt = 0; var patientHospitalizationReasonOfAdmissionCnt = 0; var patientHospitalizationPhysicianCnt = 0; var patientHospitalizationScreeningQuestionCnt = 0; var patientHospitalizationTriageCnt = 0; var patientHospitalizationPhysicianHistoryCnt = 0; ''',''' { var patientHospitalizationReasonOfAdmission = patientHospitalization.PatientHospitalizationReasonOfAdmissions.ElementAt(patientHospitalizationReasonOfAdmissionCnt++); //Assert.AreEqual( null , patientHospitalizationReasonOfAdmission.ModificationDate ); //Assert.AreEqual( null , patientHospitalizationReasonOfAdmission.ModificationUser ); Assert.AreEqual( "" , patientHospitalizationReasonOfAdmission.CodingSystem ); Assert.AreEqual( "" , patientHospitalizationReasonOfAdmission.ReasonOfAdmissionCode ); Assert.AreEqual( "" , patientHospitalizationReasonOfAdmission.ReasonOfAdmission ); //Assert.AreEqual( patientHospitalization.DateLastMessage , patientHospitalizationReasonOfAdmission.DateOfMessage ); //Assert.AreEqual( true , patientHospitalizationReasonOfAdmission.IsEnabled ); } ''',''' { var patientHospitalizationPhysician = patientHospitalization.PatientHospitalizationPhysicians.ElementAt(patientHospitalizationPhysicianCnt++); //Assert.AreEqual( null , patientHospitalizationPhysician.ModificationDate ); //Assert.AreEqual( null , patientHospitalizationPhysician.ModificationUser ); //Assert.AreEqual( true , patientHospitalizationPhysician.IsEnabled ); Assert.AreEqual( null , patientHospitalizationPhysician.Physician.PhoneNumber ); Assert.AreEqual( null , patientHospitalizationPhysician.Physician.PagerNumber ); Assert.AreEqual( null , patientHospitalizationPhysician.Physician.Comment ); //Assert.AreEqual( patientHospitalization.DateLastMessage , patientHospitalizationPhysician.DateOfMessage ); //Assert.AreEqual( eventDate , patientHospitalizationPhysician.Date ); //Assert.AreEqual( patientHospitalization.DateLastMessage , patientHospitalizationPhysician.Date, "CUSM" ); Assert.AreEqual( "$PV1_7_2_0" , patientHospitalizationPhysician.Physician.FirstName ); Assert.AreEqual( "$PV1_7_3_0" , patientHospitalizationPhysician.Physician.MiddleName ); Assert.AreEqual( "$PV1_7_1_0" , patientHospitalizationPhysician.Physician.LastName ); //Assert.AreEqual( "$PV1_7_0_0" , patientHospitalizationPhysician.Physician.ExternalCode ); } ''',''' { if (patientHospitalization.PatientHospitalizationBeds.Count() <= patientHospitalizationBedCnt) { Assert.Inconclusive("bed not mapped"); } var patientHospitalizationBed = patientHospitalization.PatientHospitalizationBeds.ElementAt(patientHospitalizationBedCnt++); //Assert.AreEqual( null , patientHospitalizationBed.ModificationDate ); //Assert.AreEqual( null , patientHospitalizationBed.ModificationUser ); //Assert.AreEqual( patientHospitalization.End , patientHospitalizationBed.End ); //Assert.AreEqual( eventDate , patientHospitalizationBed.Start ); //Assert.AreEqual( patientHospitalization.DateLastMessage , patientHospitalizationBed.DateLastMessage ); // chicoutimi special edition Assert.AreEqual( "$PV1_3_2_0" ?? patientHospitalizationBed.Bed.Room.RoomCode , patientHospitalizationBed.Bed.BedCode ); Assert.AreEqual( "$PV1_3_1_0" ?? patientHospitalizationBed.HospitalUnit.Code, patientHospitalizationBed.Bed.Room.RoomCode ); Assert.AreEqual( "$PV1_3_0_0" ?? patientHospitalizationBed.HospitalUnit.Hospital.Code, patientHospitalizationBed.HospitalUnit.Code ); Assert.AreEqual( "$PV1_3_3_0" , patientHospitalizationBed.HospitalUnit.Hospital.Code ); } ''',''' { var patientHospitalizationTransfer = patientHospitalization.PatientHospitalizationTransfers.ElementAt(patientHospitalizationTransferCnt++); //Assert.AreEqual( null , patientHospitalizationTransfer.ModificationUser ); //Assert.AreEqual( null , patientHospitalizationTransfer.ModificationDate ); Assert.AreEqual( eventDate , patientHospitalizationTransfer.ArrivalDate ); Assert.AreEqual( "" , patientHospitalizationTransfer.ReasonOfAdmission ); Assert.AreEqual( "" , patientHospitalizationTransfer.RelevantAntecedents ); Assert.AreEqual( "" , patientHospitalizationTransfer.OriginalHospital ); Assert.AreEqual( "" , patientHospitalizationTransfer.Specifications ); Assert.AreEqual( null , patientHospitalizationTransfer.ReanimationAllowed ); Assert.AreEqual( null , patientHospitalizationTransfer.IntubationAllowed ); Assert.AreEqual( null , patientHospitalizationTransfer.TransferStatusTypeId ); } ''',''' { var patientHospitalizationInfectiologist = patientHospitalization.PatientHospitalizationInfectiologists.ElementAt(patientHospitalizationInfectiologistCnt++); //Assert.AreEqual( null , patientHospitalizationInfectiologist.ModificationDate ); //Assert.AreEqual( null , patientHospitalizationInfectiologist.ModificationUser ); //Assert.AreEqual( eventDate , patientHospitalizationInfectiologist.Start ); //Assert.AreEqual( null , patientHospitalizationInfectiologist.End ); } ''',''' { var patientHospitalizationScreeningQuestion = patientHospitalization.PatientHospitalizationScreeningQuestions.ElementAt(patientHospitalizationScreeningQuestionCnt++); //Assert.AreEqual( null , patientHospitalizationScreeningQuestion.ModificationDate ); //Assert.AreEqual( null , patientHospitalizationScreeningQuestion.ModificationUser ); Assert.AreEqual( "" , patientHospitalizationScreeningQuestion.QuestionId ); Assert.AreEqual( "" , patientHospitalizationScreeningQuestion.QuestionText ); Assert.AreEqual( "" , patientHospitalizationScreeningQuestion.Answer ); //Assert.AreEqual( patientHospitalization.DateLastMessage , patientHospitalizationScreeningQuestion.DateOfMessage ); //Assert.AreEqual( eventDate , patientHospitalizationScreeningQuestion.EnabledFrom ); Assert.AreEqual( null , patientHospitalizationScreeningQuestion.EnabledTo ); Assert.AreEqual( true , patientHospitalizationScreeningQuestion.IsEnabled ); } ''',''' { var patientHospitalizationTriage = patientHospitalization.PatientHospitalizationTriages.ElementAt(patientHospitalizationTriageCnt++); //Assert.AreEqual( null , patientHospitalizationTriage.ModificationUser ); //Assert.AreEqual( null , patientHospitalizationTriage.ModificationDate ); Assert.AreEqual( eventDate , patientHospitalizationTriage.TriageDate ); Assert.AreEqual( "" , patientHospitalizationTriage.TriageLevel ); //Assert.AreEqual( patientHospitalization.DateLastMessage , patientHospitalizationTriage.DateOfMessage ); } ''',''' { var patientHospitalizationPhysicianHistory = patientHospitalization.PatientHospitalizationPhysicianHistories.ElementAt(patientHospitalizationPhysicianHistoryCnt++); //Assert.AreEqual( null , patientHospitalizationPhysicianHistory.ModificationUser ); //Assert.AreEqual( null , patientHospitalizationPhysicianHistory.ModificationDate ); //Assert.AreEqual( patientHospitalization.DateLastMessage , patientHospitalizationPhysicianHistory.DateOfMessage ); Assert.AreEqual( "" , patientHospitalizationPhysicianHistory.PhysicianRoleKey ); Assert.AreEqual( true , patientHospitalizationPhysicianHistory.IsEnabled ); Assert.AreEqual( "" , patientHospitalizationPhysicianHistory.ExternalCode ); Assert.AreEqual( "" , patientHospitalizationPhysicianHistory.FirstName ); Assert.AreEqual( "" , patientHospitalizationPhysicianHistory.MiddleName ); Assert.AreEqual( "" , patientHospitalizationPhysicianHistory.LastName ); } '''], }, 'PatientLabOrders' : { 'MSH' : [''' var patient = GetPatient("$PID_3_0_0"); if (patient == null) { Assert.Inconclusive("patient not found"); } var patientLabOrderCnt = 0; var patientLabResultCnt = 0; var patientLabOrderNoteCnt = 0; '''], 'OBR' : [''' if (patient.PatientLabOrders.Count() <= patientLabOrderCnt) { Assert.Inconclusive("not mapped"); } var patientLabOrder = patient.PatientLabOrders.ElementAt(patientLabOrderCnt++); //Assert.AreEqual( null , patientLabOrder.ModificationDate ); //Assert.AreEqual( null , patientLabOrder.ModificationUser ); Assert.AreEqual( null , patientLabOrder.IsVisible ); Assert.AreEqual( true , patientLabOrder.IsEnabled ); //Assert.AreEqual( new DateTime("$OBR_7_0_0") , patientLabOrder.Date ); //Assert.AreEqual( new DateTime("$MSH_6_0_0") , patientLabOrder.DateOfMessage ); Assert.AreEqual( "" , patientLabOrder.ExternalCode ); //Assert.AreEqual( "$OBR_4_0_0" , patientLabOrder.GroupOrderNumber ); //Assert.AreEqual( "$OBR_3_0_0".Split(':')[0] , patientLabOrder.GroupOrderNumber , "chicoutimi" ); Assert.AreEqual( "$OBR_4_1_0" , patientLabOrder.Name ); Assert.AreEqual( "$OBR_25_0_0" , patientLabOrder.State ); //Assert.AreEqual( "$OBR_11_0_0" , patientLabOrder.LisOrderType ); '''], }, 'PatientSerumLevels' : { 'MSH' : [''' var patient = GetPatient("$PID_3_0_0"); if (patient == null) { Assert.Inconclusive("patient not found"); } var patientSerumLevelCnt = 0; '''], 'OBX' : [''' if (patient.PatientSerumLevels.Count() <= patientSerumLevelCnt) { Assert.Inconclusive("not mapped"); } var patientSerumLevel = patient.PatientSerumLevels.ElementAt(patientSerumLevelCnt++); //Assert.AreEqual( null , patientSerumLevel.ModificationDate ); //Assert.AreEqual( null , patientSerumLevel.ModificationUser ); //Assert.AreEqual( "$OBX_5_0_0" , patientSerumLevel.Value ); Assert.AreEqual( "$OBX_5_0_0" , patientSerumLevel.ValueStr ); Assert.AreEqual( "$OBX_3_1_0" , patientSerumLevel.Name ); Assert.AreEqual( "$OBX_11_0_0" , patientSerumLevel.State ); //Assert.AreEqual( "$NTE_3_0_0" , patientSerumLevel.Notes ); Assert.AreEqual( "$OBX_7_0_0" , patientSerumLevel.ReferenceRange ); Assert.AreEqual( "$OBX_6_0_0" , patientSerumLevel.Unit ); //Assert.AreEqual( "$OBX_11_0_0" , patientSerumLevel.AbnormalFlag ); //Assert.AreEqual( new DateTime("$OBX_14_0_0") , patientSerumLevel.Date ); //Assert.AreEqual( patientLabOrder.DateOfMessage , patientSerumLevel.LastMessageDate ); Assert.AreEqual( null , patientSerumLevel.EnabledTo ); Assert.AreEqual( null , patientSerumLevel.EnabledFrom ); Assert.AreEqual( true , patientSerumLevel.IsEnabled ); Assert.AreEqual( null , patientSerumLevel.IsManualEntry );'''], }, 'PatientLabResults' : { 'MSH' : [''' var patient = GetPatient("$PID_3_0_0"); if (patient == null) { Assert.Inconclusive("patient not found"); } var patientLabResultCnt = 0; '''], 'OBX' : [''' if (patient.PatientLabResults.Count() <= patientLabResultCnt) { Assert.Inconclusive("not mapped"); } var patientLabResult = patient.PatientLabResults.ElementAt(patientLabResultCnt++); //Assert.AreEqual( null , patientLabResult.ModificationDate ); //Assert.AreEqual( null , patientLabResult.ModificationUser ); Assert.AreEqual( null , patientLabResult.IsManualEntry ); Assert.AreEqual( true , patientLabResult.IsEnabled ); //Assert.AreEqual( new DateTime("$OBX_14_0_0") , patientLabResult.Date ); Assert.AreNotEqual( null , patientLabResult.EnabledFrom ); Assert.AreEqual( null , patientLabResult.EnabledTo ); Assert.AreEqual( $OBX_1_0_0 , patientLabResult.Index ); Assert.AreEqual( "$OBX_3_1_0" , patientLabResult.Name ); Assert.AreEqual( "$OBX_5_0_0" , patientLabResult.ValueStr ); //Assert.AreEqual( "$OBX_5_0_0" , patientLabResult.Value ); Assert.AreEqual( "$OBX_11_0_0" , patientLabResult.State ); Assert.AreEqual( "$NTE_3_0_0" , patientLabResult.Notes ); Assert.AreEqual( "$OBX_7_0_0" , patientLabResult.ReferenceRange ); Assert.AreEqual( "$OBX_6_0_0" , patientLabResult.Unit ); //Assert.AreEqual( "$OBX_3_0_0" , patientLabResult.Mnemonic ); //Assert.AreEqual( "$OBX_11_0_0" , patientLabResult.AbnormalFlag ); '''], }, 'PatientMicrobiologyResults' : { 'MSH' : [''' var patient = GetPatient("$PID_3_0_0"); if (patient == null) { Assert.Inconclusive("patient not found"); } var patientMicrobiologyResultCnt = 0; var patientMicrobiologyResultHistoryDescriptionCnt = 0; var patientMicrobiologyResultHistoryPathogenCnt = 0; var patientMicrobiologyResultHistoryPathogenSensitivityCnt = 0; var patientMicrobiologyResultHistoryScreeningCnt = 0; ''',''' /* Assert.AreEqual(patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryDescriptions) .Count() , patientMicrobiologyResultHistoryDescriptionCnt); Assert.AreEqual(patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens) .Count() , patientMicrobiologyResultHistoryPathogenCnt); Assert.AreEqual(patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens) .SelectMany(patientMicrobiologyResultHistoryPathogen => patientMicrobiologyResultHistoryPathogen.PatientMicrobiologyResultHistoryPathogenSensitivities) .Count() , patientMicrobiologyResultHistoryPathogenSensitivityCnt); */ '''], 'OBR' : [''' if (patient.PatientMicrobiologyResults.Count() <= patientMicrobiologyResultCnt) { Assert.Inconclusive("PatientMicrobiologyResults not mapped as far as {0}", patientMicrobiologyResultCnt); } var patientMicrobiologyResult = patient.PatientMicrobiologyResults.ElementAt(patientMicrobiologyResultCnt++); //Assert.AreEqual( null , patientMicrobiologyResult.ModificationDate ); //Assert.AreEqual( null , patientMicrobiologyResult.ModificationUser ); //Assert.AreEqual( "$OBX_3_0_0" , patientMicrobiologyResult.ExternalCode ); Assert.AreEqual( "$ORC_3_0_0" ?? "${OBX_5_0_0}$OBX_14_0_0" , patientMicrobiologyResult.ExternalCode, "chicoutimi" ); //Assert.AreEqual( "$OBX_5_0_0__1" ?? "$OBR_4_1_0 : $OBR_15_0_1 - $OBR_15_3_1" , patientMicrobiologyResult.ProcedureName ); Assert.AreEqual( null , patientMicrobiologyResult.GroupOrderNumber ); //Assert.AreEqual( "$OBX_11_0_0" , patientMicrobiologyResult.NosocomialStateKey ); //Assert.AreEqual( 0 , patientMicrobiologyResult.SampleType ); //Assert.AreEqual( new DateTime("$MSH_6_0_0") , patientMicrobiologyResult.LastMessageDate ); //Assert.AreEqual( new DateTime("$OBX_14_0_0") , patientMicrobiologyResult.Date ); //Assert.AreEqual( new [] { new DateTime("$ORC_9_0_0"), new DateTime("$OBR_22_0_0") ,new DateTime("$OBX_14_0_0"), new DateTime("$OBR_7_0_0") }.Where(date => date > new DateTime(2000,1,1)).First() , patientMicrobiologyResult.Date, "chicoutimi" ); var patientMicrobiologyResultHistoryCnt = 0; ''',''' if("$OBX_11_0_0" != null) // chicoutimi { if (patientMicrobiologyResult.PatientMicrobiologyResultHistories.Count() <= patientMicrobiologyResultHistoryCnt) { Assert.Inconclusive("PatientMicrobiologyResultHistory not mapped as far as {0}", patientMicrobiologyResultHistoryCnt); } var patientMicrobiologyResultHistory = patientMicrobiologyResult.PatientMicrobiologyResultHistories.ElementAt(patientMicrobiologyResultHistoryCnt++); //Assert.AreEqual( null , patientMicrobiologyResultHistory.ModificationDate ); //Assert.AreEqual( null , patientMicrobiologyResultHistory.ModificationUser ); Assert.AreEqual( "$OBX_11_0_0" , patientMicrobiologyResultHistory.ProgressStateKey ); //Assert.AreEqual( patientMicrobiologyResult.LastMessageDate , patientMicrobiologyResultHistory.DateOfMessage ); //Assert.AreEqual( patientMicrobiologyResult.Date , patientMicrobiologyResultHistory.Date ); //Assert.AreEqual( new DateTime("$OBR_14_0_0") , patientMicrobiologyResultHistory.Date , "chicoutimi"); //Assert.AreEqual( new DateTime("$OBR_22_0_0") , patientMicrobiologyResultHistory.Date , "chicoutimi"); //Assert.AreEqual( new DateTime("$OBX_14_0_0") , patientMicrobiologyResultHistory.Date , "chicoutimi"); //Assert.AreEqual( new DateTime("$OBR_7_0_0") , patientMicrobiologyResultHistory.Date , "chicoutimi"); } '''], 'OBX' : [''' { if (patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryDescriptions) .Count() <= patientMicrobiologyResultHistoryDescriptionCnt) { Assert.Inconclusive("PatientMicrobiologyResultHistoryDescriptions not mapped as far as {0}", patientMicrobiologyResultHistoryDescriptionCnt); } var patientMicrobiologyResultHistoryDescription = patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryDescriptions) .ElementAt(patientMicrobiologyResultHistoryDescriptionCnt++); //Assert.AreEqual( null , patientMicrobiologyResultHistoryDescription.ModificationDate ); //Assert.AreEqual( null , patientMicrobiologyResultHistoryDescription.ModificationUser ); Assert.AreEqual( "$OBX_3_1_0" , patientMicrobiologyResultHistoryDescription.FieldName ); //Assert.AreEqual( "$OBX_5_0_0" , patientMicrobiologyResultHistoryDescription.Description ); //Assert.AreEqual( true , patientMicrobiologyResultHistoryDescription.IsVisible ); //Assert.AreEqual( 0 , patientMicrobiologyResultHistoryDescription.LineNumber ); } ''',''' if("$OBX_2_0_0" == "CE") // chicoutimi { if (patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens) .Count() <= patientMicrobiologyResultHistoryPathogenCnt) { Assert.Inconclusive("PatientMicrobiologyResultHistoryPathogens not mapped as far as {0}",patientMicrobiologyResultHistoryPathogenCnt); } var patientMicrobiologyResultHistoryPathogen = patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens) .ElementAt(patientMicrobiologyResultHistoryPathogenCnt++); //Assert.AreEqual( null , patientMicrobiologyResultHistoryPathogen.ModificationDate ); //Assert.AreEqual( null , patientMicrobiologyResultHistoryPathogen.ModificationUser ); Assert.AreEqual( "$OBX_5_1_0" , patientMicrobiologyResultHistoryPathogen.PathogenType.SystemName ); Assert.AreEqual( "$OBX_5_1_0" , patientMicrobiologyResultHistoryPathogen.OrganismRaw ); //Assert.AreEqual( "" , patientMicrobiologyResultHistoryPathogen.OrganismIdentifier ); //Assert.AreEqual( "" , patientMicrobiologyResultHistoryPathogen.PathogenType.SpinCode ); //Assert.AreEqual( "" , patientMicrobiologyResultHistoryPathogen.PathogenType.MylaCode ); Assert.AreEqual( null , patientMicrobiologyResultHistoryPathogen.EnabledTo ); //Assert.AreEqual( true , patientMicrobiologyResultHistoryPathogen.IsSuspected ); Assert.AreEqual( true , patientMicrobiologyResultHistoryPathogen.IsEnabled ); //Assert.AreEqual( patientMicrobiologyResult.Date , patientMicrobiologyResultHistoryPathogen.EnabledFrom ); } ''',''' if("$OBX_2_0_0" == "ST") { if (patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens) .SelectMany(patientMicrobiologyResultHistoryPathogen => patientMicrobiologyResultHistoryPathogen.PatientMicrobiologyResultHistoryPathogenSensitivities) .Count() <= patientMicrobiologyResultHistoryPathogenSensitivityCnt) { Assert.Inconclusive("PatientMicrobiologyResultHistoryPathogenSensitivities not mapped"); } var patientMicrobiologyResultHistoryPathogenSensitivity = patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens) .SelectMany(patientMicrobiologyResultHistoryPathogen => patientMicrobiologyResultHistoryPathogen.PatientMicrobiologyResultHistoryPathogenSensitivities) .ElementAt(patientMicrobiologyResultHistoryPathogenSensitivityCnt++); //Assert.AreEqual( null , patientMicrobiologyResultHistoryPathogenSensitivity.ModificationDate ); //Assert.AreEqual( null , patientMicrobiologyResultHistoryPathogenSensitivity.ModificationUser ); Assert.AreEqual( "$OBX_3_1_0" , patientMicrobiologyResultHistoryPathogenSensitivity.MedicationRaw ); Assert.AreEqual( "$OBX_8_0_0" , patientMicrobiologyResultHistoryPathogenSensitivity.SensitivityRaw ); //Assert.AreEqual( "$OBX_8_0_0" , patientMicrobiologyResultHistoryPathogenSensitivity.Sensitivity ); Assert.AreEqual( "$OBX_5_0_0" , patientMicrobiologyResultHistoryPathogenSensitivity.MicValue ); //Assert.AreEqual( "$NTE_3_0_0" , patientMicrobiologyResultHistoryPathogenSensitivity.Notes ); //Assert.AreEqual( "$OBX_3_1_0" , patientMicrobiologyResultHistoryPathogenSensitivity.MedicationType.SystemName ); //Assert.AreEqual( patientMicrobiologyResult.Date , patientMicrobiologyResultHistoryPathogenSensitivity.EnabledFrom ); Assert.AreEqual( true , patientMicrobiologyResultHistoryPathogenSensitivity.IsEnabled ); Assert.AreEqual( null , patientMicrobiologyResultHistoryPathogenSensitivity.EnabledTo ); Assert.AreEqual( null , patientMicrobiologyResultHistoryPathogenSensitivity.NonReportable ); //Assert.AreEqual( true , patientMicrobiologyResultHistoryPathogenSensitivity.MedicationType.IsAntibiotic ); } ''',''' { if (patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryScreenings) .Count() <= patientMicrobiologyResultHistoryScreeningCnt) { Assert.Inconclusive("PatientMicrobiologyResultHistoryScreenings not mapped"); } var patientMicrobiologyResultHistoryScreening = patient.PatientMicrobiologyResults .SelectMany(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories) .SelectMany(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryScreenings) .ElementAt(patientMicrobiologyResultHistoryScreeningCnt++); //Assert.AreEqual( null , patientMicrobiologyResultHistoryScreening.ModificationUser ); //Assert.AreEqual( null , patientMicrobiologyResultHistoryScreening.ModificationDate ); Assert.AreEqual( "" , patientMicrobiologyResultHistoryScreening.InfectionType.InfectionTypeKey ); Assert.AreEqual( "" , patientMicrobiologyResultHistoryScreening.ScreeningStateKey ); Assert.AreEqual( "" , patientMicrobiologyResultHistoryScreening.InfectionTypeKey ); //Assert.AreEqual( patientMicrobiologyResult.Date , patientMicrobiologyResultHistoryScreening.EnabledFrom ); Assert.AreEqual( null , patientMicrobiologyResultHistoryScreening.EnabledTo ); Assert.AreEqual( true , patientMicrobiologyResultHistoryScreening.IsEnabled ); } '''] } }) if __name__ == '__main__': src = 'hl7.db' if len(sys.argv) > 1: src = sys.argv[1] for src,seq,theShit in floodTheShit(src): d = dict( test='', tests={}, src = src, seq = seq ) for row,seg,dick in theShit: #if seg == 'MSH': # d['name'] = string.Template('${MSH_2_0_0}_${MSH_2_1_0}_${MSH_6_0_0}_${MSH_8_0_0}_${MSH_8_1_0}_${src}_${seq}').safe_substitute(dick) # #sanitize filename # d['name'] = re.sub(r'\$\{?[A-Z][A-Z]{2}(_[0-9]+){3}\}?','',d['name']) for testName in templateCatalog: t = d['tests'][testName] if testName in d['tests'] else '' if seg in templateCatalog[testName]: ttt = '' for tpl in templateCatalog[testName][seg]: tt = string.Template(tpl).safe_substitute(dick) if tt != tpl or seg == 'MSH': # if havent changed at all, no match ttt = ttt + tt # clean up same segment unused tag t = re.sub(r'"\$\{?'+seg+'(_[0-9]+){3}(__[0-9]+)?\}?"','null',t) if ttt: if seg != 'MSH': t = t + '\n' + ' '*12 + '{\n' + ttt + '\n' +' '*12 + '}\n' else: t = t + ttt #maybe and OBX refer to the next NTE d['tests'][testName] = string.Template(t).safe_substitute(dick) d['name'] = string.Template('${MSH_2_0_0}_${MSH_2_1_0}_${PID_3_0_0}_${MSH_6_0_0}_${MSH_8_0_0}_${MSH_8_1_0}').safe_substitute(dick) #sanitize filename d['name'] = re.sub(r'\$\{?[A-Z][A-Z]{2}(_[0-9]+){3}\}?','',d['name']) #wrap c# unit test method for testName in templateCatalog: dtpl = ''' [TestMethod] public void ${name}_Test() { $test } ''' dtest = string.Template(dtpl).safe_substitute(test=d['tests'][testName], name=testName) if len(dtest) - 200 > len(dtpl): d['test'] = d['test'] + dtest #wrap c# unit test class d['test'] = string.Template(''' using Lumed.Common.Data; using Lumed.Data.Entity; using Microsoft.VisualStudio.TestTools.UnitTesting; using System; using System.Data.Entity; using System.Linq; namespace Importer.IntegrationTests.Analysis { [TestClass] public class ${name}_Tests { $test private Patient GetPatient(string externalCode) { using (var dbContext = new CommonEntities()) { return dbContext .DisableLazyLoading() .Patients .AsNoTracking() .Include(patient => patient.PatientExternalCodes) .Include(patient => patient.PatientHospitalizations) .Include(patient => patient.PatientHospitalizations.Select(patientHospitalization => patientHospitalization.PatientHospitalizationBeds)) .Include(patient => patient.PatientHospitalizations.Select(patientHospitalization => patientHospitalization.PatientHospitalizationBeds.Select(patientHospitalizationBed => patientHospitalizationBed.Bed.Room))) .Include(patient => patient.PatientHospitalizations.Select(patientHospitalization => patientHospitalization.PatientHospitalizationBeds.Select(patientHospitalizationBed => patientHospitalizationBed.HospitalUnit.Hospital))) .Include(patient => patient.PatientHospitalizations.Select(patientHospitalization => patientHospitalization.PatientHospitalizationPhysicians)) .Include(patient => patient.PatientHospitalizations.Select(patientHospitalization => patientHospitalization.PatientHospitalizationPhysicians.Select(patientHospitalizationPhysician => patientHospitalizationPhysician.Physician))) .Include(patient => patient.PatientHospitalizations.Select(patientHospitalization => patientHospitalization.PatientHospitalizationReasonOfAdmissions)) .Include(patient => patient.PatientLabResults) .Include(patient => patient.PatientLabOrders.Select(labOrder => labOrder.PatientLabResults)) .Include(patient => patient.PatientLabOrders.Select(labOrder => labOrder.PatientSerumLevels)) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.CurrentPatientMicrobiologyResultHistory)) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.CurrentPatientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryDescriptions)) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.CurrentPatientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens)) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.CurrentPatientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens.Select(patientMicrobiologyResultHistoryPathogen => patientMicrobiologyResultHistoryPathogen.PathogenType))) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.CurrentPatientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens.Select(patientMicrobiologyResultHistoryPathogen => patientMicrobiologyResultHistoryPathogen.PatientMicrobiologyResultHistoryPathogenSensitivities.Select(patientMicrobiologyPathogenSensivity => patientMicrobiologyPathogenSensivity.MedicationType)))) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.CurrentPatientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens.Select(patientMicrobiologyResultHistoryPathogen => patientMicrobiologyResultHistoryPathogen.PatientMicrobiologyResultHistoryPathogenSensitivities))) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.CurrentPatientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryScreenings)) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories)) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories.Select(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryDescriptions))) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories.Select(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens))) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories.Select(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens.Select(patientMicrobiologyResultHistoryPathogen => patientMicrobiologyResultHistoryPathogen.PathogenType)))) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories.Select(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens.Select(patientMicrobiologyResultHistoryPathogen => patientMicrobiologyResultHistoryPathogen.PatientMicrobiologyResultHistoryPathogenSensitivities.Select(patientMicrobiologyPathogenSensivity => patientMicrobiologyPathogenSensivity.MedicationType))))) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories.Select(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryPathogens.Select(patientMicrobiologyResultHistoryPathogen => patientMicrobiologyResultHistoryPathogen.PatientMicrobiologyResultHistoryPathogenSensitivities)))) .Include(patient => patient.PatientMicrobiologyResults.Select(patientMicrobiologyResult => patientMicrobiologyResult.PatientMicrobiologyResultHistories.Select(patientMicrobiologyResultHistory => patientMicrobiologyResultHistory.PatientMicrobiologyResultHistoryScreenings))) .FirstOrDefault(patient => patient.PatientExternalCodes.Any(p => p.ExternalCode == externalCode)); } } } } ''').safe_substitute(d) t = d['test'] #clean up unused token t = re.sub(r'"\$\{?[A-Z][A-Z0-9]{2}(_[0-9]+){3}(__[0-9]+)?\}?"','null',t) #date are better that way t = re.sub(r'DateTime\(""\)', r'DateTime()', t) t = re.sub(r'DateTime\(null\)', r'DateTime()', t) t = re.sub(r'DateTime\("([0-9]{4})([0-9]{2})([0-9]{2})"\)', r'DateTime(\1, \2, \3)', t) t = re.sub(r'DateTime\("([0-9]{4})([0-9]{2})([0-9]{2})([0-9]{2})([0-9]{2})"\)', r'DateTime(\1, \2, \3, \4, \5, 0)', t) t = re.sub(r'DateTime\("([0-9]{4})([0-9]{2})([0-9]{2})([0-9]{2})([0-9]{2})([0-9]{2})"\)', r'DateTime(\1, \2, \3, \4, \5, \6)', t) #chicoutimi do wierd thing t = re.sub(r'GetPatient\("[CP]([A-Z][^"]*)"\)', r'GetPatient("\1")', t) t = re.sub(r'AreEqual\( "[CP]([A-Z][^"]*)" , patientExternalCode.ExternalCode \)', r'AreEqual( "\1" , patientExternalCode.ExternalCode )', t) #sanitize generated text #t = re.sub(r'\\S\\',r'\\\\S\\\\',t) # hl7 escaped character #t = re.sub(r'\\.br\\',r'\\\\.br\\\\',t) # hl7 escaped character t = re.sub(r'\\',r'\\\\',t) # hl7 escaped character t = re.sub(r'""""',r'""',t) # hl7 escaped character d['test'] = t import os if not os.path.exists('AnalyseTests'): os.makedirs('AnalyseTests') open('AnalyseTests/'+d['name']+'.cs','w').write(d['test']) print(d['name'])