import java.text.
SimpleDateFormat;
import sapphire.util.DataSet;
import sapphire.util.SafeSQL;
import sapphire.xml.PropertyList;
import sapphire.SapphireException;
import sapphire.util.StringUtil;
logger.info("######### Starting Frontage File Import DFD #########");
String samplealias = fields.samplealias;
String samplealiastype = fields.samplealiastype;
String primary = fields.primary;
String sstudy = fields.studyid;
String protocol = fields.protocolid;
String subjectalias = fields.subjectaliasid;
String gender = fields.gender;
String dateofbirth = fields.dateofbirth;
String externalparticipantid = fields.externalparticipantid;
String cohort = fields.cohortid;
String sampletype = fields.sampletypeid;
String containertype = fields.containertypeid;
String samplecondition = fields.samplecondition;
String visit = fields.visitlabel;
String timepoint = fields.timepointlabel;
String collectiondt = fields.collectiondate;
String receivedt = fields.receivedate;
String qtyvalue = fields.quantity;
String qtyunit = fields.units;
String studysitedesc = fields.studysitedesc;
String treatment = fields.drugname;
String storage = fields.storageid;
String pkgtracking = fields.pkgtrackingno;
String kitid = fields.kitid;
//// Dataset for all the fields
DataSet valuesds=new DataSet();
valuesds.addColumnValues("samplealias", DataSet.STRING, samplealias, ";", "");
valuesds.addColumnValues("samplealiastype", DataSet.STRING, samplealiastype, ";",
"");
valuesds.addColumnValues("primary", DataSet.STRING, primary, ";", "");
valuesds.addColumnValues("sstudy", DataSet.STRING, sstudy, ";", "");
valuesds.addColumnValues("protocol", DataSet.STRING, protocol, ";", "");
valuesds.addColumnValues("subjectalias", DataSet.STRING, subjectalias, ";", "");
valuesds.addColumnValues("gender", DataSet.STRING, gender, ";", "");
valuesds.addColumnValues("dateofbirth", DataSet.STRING, dateofbirth, ";", "");
valuesds.addColumnValues("externalparticipantid", DataSet.STRING,
externalparticipantid, ";", "");
valuesds.addColumnValues("cohort", DataSet.STRING, cohort, ";", "");
valuesds.addColumnValues("sampletype", DataSet.STRING, sampletype, ";", "");
valuesds.addColumnValues("containertype", DataSet.STRING, containertype, ";", "");
valuesds.addColumnValues("samplecondition", DataSet.STRING, samplecondition, ";",
"");
valuesds.addColumnValues("visit", DataSet.STRING, visit, ";", "");
valuesds.addColumnValues("timepoint", DataSet.STRING, timepoint, ";", "");
valuesds.addColumnValues("collectiondt", DataSet.STRING, collectiondt, ";", "");
valuesds.addColumnValues("receivedt", DataSet.STRING, receivedt, ";", "");
valuesds.addColumnValues("qtyvalue", DataSet.STRING, qtyvalue, ";", "");
valuesds.addColumnValues("qtyunit", DataSet.STRING, qtyunit, ";", "");
valuesds.addColumnValues("studysitedesc", DataSet.STRING, studysitedesc, ";", "");
valuesds.addColumnValues("treatment", DataSet.STRING, treatment, ";", "");
valuesds.addColumnValues("storage", DataSet.STRING, storage, ";", "");
valuesds.addColumnValues("pkgtracking", DataSet.STRING, pkgtracking, ";", "");
valuesds.addColumnValues("kitid", DataSet.STRING, kitid, ";", "");
valuesds.addColumn("subjectid", DataSet.STRING);
valuesds.addColumn("participantid", DataSet.STRING);
valuesds.addColumn("useflag", DataSet.STRING);
StringBuffer subaliassb = new StringBuffer();
StringBuffer gendersb = new StringBuffer();
StringBuffer dobsb = new StringBuffer();
StringBuffer neubjectidsb = new StringBuffer();
StringBuffer studyidsb = new StringBuffer();
StringBuffer studysiteidsb = new StringBuffer();
StringBuffer cpcohortb = new StringBuffer();
StringBuffer expartidb = new StringBuffer();
int flag=0;
int counter=0;
DataSet subjectIDds=new DataSet();
String studyid;
String sampleid;
SafeSQL sf = new SafeSQL();
ConnectionProcessor conp = new
ConnectionProcessor( queryProcessor.getConnectionid());
String deptid = conp.getConnectionInfo().getDefaultDepartment();
String userid = conp.getConnectionInfo().getSysuserId();
logger.info("User ID : "+userid);
logger.info("Department ID : "+deptid);
// Checking Sample and Subject Alias is present or not.
logger.info("####### Starting Validation of Sample and Subject Alias Field
#######");
String sql = "with allsamleps as( \n" +
"select rownum as rno, column_value as allsamples from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("samplealias", ";"),
";") + ")) \n" +
"), allsubjects as( \n" +
"select rownum as rno, column_value as allsubjects from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("subjectalias", ";"),
";") + ")) \n" +
"), alldob as( \n" +
"select rownum as rno, column_value as alldobs from TABLE (sys.odcivarchar2list(" +
sf.addIn(valuesds.getColumnValues("dateofbirth", ";"), ";") + ")) \n" +
"), samplealiases as( \n" +
"select alls.rno, sdcid, keyid1, aliasid, aliastype \n" +
"from sdialias, allsamleps alls \n" +
"where sdcid='Sample' \n" +
"and aliastype in (" + sf.addIn(valuesds.getColumnValues("samplealiastype", ";"),
";") + ") \n" +
"and aliasid in (alls.allsamples) \n" +
"), subjectaliases as( \n" +
"select allsub.rno, sdcid, keyid1, aliasid, aliastype \n" +
"from sdialias, allsubjects allsub \n" +
"where sdcid='LV_Subject' \n" +
"and lower(aliastype)=lower('Patient Id') \n" +
"and aliasid in (allsub.allsubjects) \n" +
"), allstudy as ( \n" +
"select rownum as rno, column_value as allstudies from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("sstudy", ";"), ";") +
")) \n" +
"), allparticipant as( \n" +
"select rownum as rno, column_value as allparticipants from TABLE
(sys.odcivarchar2list(" +
sf.addIn(valuesds.getColumnValues("externalparticipantid", ";"), ";") + ")) \n" +
"), isstudyp as ( \n" +
"select rownum as rno, s_studyid, clinicalflag \n" +
"from s_study, allstudy als \n" +
"where s_studyid in (als.allstudies) \n" +
"), participantdt as ( \n" +
"select ap.rno, isp.s_studyid, isp.clinicalflag, p.s_participantid,
p.externalparticipantid, \n" +
"p.sstudyid, p.studysiteid, p.clinicalprotocolid, p.cpcohortid, p.subjectid \n" +
"from s_participant p, isstudyp isp, allparticipant ap \n" +
"where p.sstudyid = isp.s_studyid \n" +
"and p.externalparticipantid in (ap.allparticipants) \n" +
"and ap.rno = isp.rno \n" +
") \n" +
"select distinct alls.rno, alls.allsamples, allsub.allsubjects, sa.keyid1 sampleid,
suba.keyid1 subid, \n" +
"(case when (length(ad.alldobs)=4) then (to_char(trunc(to_date(ad.alldobs, 'yyyy'),
'YEAR'), 'mm/dd/yyyy')) else (to_char(to_date(ad.alldobs, 'mm/dd/yyyy'),
'mm/dd/yyyy')) end) dob, \n" +
"(select count(aliasid) from samplealiases sa1 where sa1.rno=alls.rno) as
samplefound, \n" +
"(select count(aliasid) from subjectaliases suba1 where suba1.rno=allsub.rno) as
subjectfound, \n" +
"(select suba1.keyid1 from subjectaliases suba1 where suba1.rno=allsub.rno) as
subjectid, \n" +
"st.s_studyid, st.clinicalflag, pa.studysiteid, nvl(pa.s_participantid, '0')
participantid, \n" +
"pa.externalparticipantid, pa.clinicalprotocolid, pa.cpcohortid, pa.subjectid
partsubjectid \n" +
"from allsamleps alls \n" +
"inner join allsubjects allsub \n" +
"on allsub.rno = alls.rno \n" +
"inner join isstudyp st \n" +
"on st.rno = alls.rno \n" +
"inner join alldob ad \n" +
"on ad.rno = alls.rno \n" +
"left outer join samplealiases sa \n" +
"on sa.rno = alls.rno \n" +
"left outer join subjectaliases suba \n" +
"on suba.rno = allsub.rno \n" +
"left outer join participantdt pa \n" +
"on pa.sstudyid = st.s_studyid \n" +
"and pa.rno = st.rno \n" +
"order by alls.rno";
logger.info("*****## Sample and Subject Alias Validation sql : "+sql);
DataSet ds = queryProcessor.getPreparedSqlDataSet(sql, sf.getValues());
sf.reset();
if(ds!=null && ds.getRowCount()>0){
ds.addColumn("useflag", DataSet.STRING);
int smpfound=0;
for(int i=0; i<ds.getRowCount(); i++) {
smpfound=ds.getInt(i, "samplefound", 0);
if((smpfound>0) && (valuesds.getString(i,
"samplealias").equals(ds.getString(i, "allsamples")))){
logger.info("*****!! Sample Alias "+ds.getString(i, "allsamples")
+" already present. Hence Skipping !!*****");
valuesds.setValue(i, "useflag", "S");
ds.setValue(i, "useflag", "S");
}
else {
valuesds.setValue(i, "useflag", "A");
ds.setValue(i, "useflag", "A");
if((0==(ds.getInt(i, "subjectfound"))) && (valuesds.getString(i,
"subjectalias").equals(ds.getString(i, "allsubjects")))){
subaliassb.append(";" + valuesds.getString(i,
"subjectalias", ""));
gendersb.append(";" + valuesds.getString(i, "gender", ""));
dobsb.append(";" + ds.getValue(i, "dob", ""));
studyidsb.append(";" + valuesds.getString(i, "sstudy",
""));
studysiteidsb.append(";" + valuesds.getString(i,
"studysitedesc", ""));
cpcohortb.append(";" + valuesds.getString(i, "cohort",
""));
expartidb.append(";" + valuesds.getString(i,
"externalparticipantid", ""));
flag=1;
counter=counter+1;
}
else{
valuesds.setValue(i, "subjectid", ds.getString(i,
"subjectid", ""));
valuesds.setValue(i, "participantid", ds.getString(i,
"participantid", ""));
logger.info("*****!! Subject Alias "+ds.getString(i,
"allsubjects")+" already present !!*****");
}
}
HashMap hm = new HashMap<>();
hm.put("useflag", "A");
valuesds = valuesds.getFilteredDataSet(hm);
ds = ds.getFilteredDataSet(hm);
if(flag==1){
logger.info("*****!! Subject Alias
"+subaliassb.toString().substring(1)+" not present !!*****");
logger.info("*****!! Creating New Subject with Alias
"+subaliassb.toString().substring(1)+" !!*****");
logger.info("*****!! Gender : "+gendersb.toString().substring(1)+".");
logger.info("*****!! DOB : "+dobsb.toString().substring(1)+".");
//// Creating Subject here
def propsforSubject=[
sdcid: "LV_Subject",
keyid1: "",
keyid2: "",
keyid3: "",
overrideautokey: "N",
genderflag: gendersb.toString().substring(1),
birthdt: dobsb.toString().substring(1),
u_group: cpcohortb.toString().substring(1),
copies: counter,
propsmatch: "Y",
newkeyid1: ""
]
logger.info( "Calling AddSDDI with properties: " +
propsforSubject.toString());
processAction( "AddSDI", propsforSubject);
neubjectidsb.append(";" + propsforSubject.get("newkeyid1"));
def AddSDIAliasprops=[
sdcid: "LV_Subject",
keyid1: neubjectidsb.toString().substring(1),
keyid2: "",
keyid3: "",
aliasid: subaliassb.toString().substring(1),
aliastype: "Patient ID"
]
logger.info( "Calling AddSDIAlias with properties: " +
AddSDIAliasprops.toString())
processAction( "AddSDIAlias", AddSDIAliasprops );
subjectIDds.addColumnValues("subjectid", DataSet.STRING,
AddSDIAliasprops.get("keyid1"), ";", "");
subjectIDds.addColumnValues("subaliasid", DataSet.STRING,
AddSDIAliasprops.get("aliasid"), ";", "");
for(int i=0; i<subjectIDds.getRowCount(); i++) {
valuesds.setValue(valuesds.findRow("subjectalias",
subjectIDds.getString(i, "subaliasid")), "subjectid", subjectIDds.getString(i,
"subjectid", ""));
}
}
logger.info("####### Completed Validation of Sample and Subject Alias Field
#######");
//Checking Participant using external participantid. If not present Enrolling
the subject. Also enrolling the new subjects
logger.info("####### Starting Validation of Participant Field #######");
String isProtocol;
String protocolid;
String cpcohort;
String partid;
for(int i=0; i<ds.getRowCount(); i++) {
isProtocol = ds.getString(i, "clinicalflag", "");
partid = ds.getString(i, "participantid", "0");
if(!("0".equalsIgnoreCase(partid))){
if("Y".equalsIgnoreCase(isProtocol)){
cpcohort = ds.getString(i, "cpcohortid");
protocolid = ds.getString(i, "clinicalprotocolid");
if(!(cpcohort.equals(valuesds.getString(i, "cohort")))){
logger.info("*****!! External Participant
"+ds.getValue(i, "externalparticipantid")+" present for the Study "+ds.getValue(i,
"s_studyid")+". But Mismatch Cohort !!*****");
}
if(!(protocolid.equals(valuesds.getString(i, "protocol"))))
{
logger.info("*****!! External Participant
"+ds.getValue(i, "externalparticipantid")+" present for the Study "+ds.getValue(i,
"s_studyid")+". But Mismatch Protocol !!*****");
//logger.info("####### Completed Validation of
Participant Field #######");
valuesds.setValue(i, "useflag", "S");
ds.setValue(i, "useflag", "S");
//throw new
SapphireException(SapphireException.TYPE_FAILURE, "Protocol "+valuesds.getString(i,
"protocol")+" mismatch for External Participant "+ds.getValue(i,
"externalparticipantid")+".");
}
}
}
logger.info("####### Completed Validation of Participant Field
#######");
if(("0".equalsIgnoreCase(partid)) && ds.getInt(i, "subjectfound")!=0 &&
"A".equalsIgnoreCase(ds.getString(i, "useflag"))){
flag = 1;
neubjectidsb.append(";" + ds.getString(i, "subid", ""));
studyidsb.append(";" + ds.getString(i, "s_studyid", ""));
studysiteidsb.append(";" + valuesds.getString(i, "studysitedesc",
""));
cpcohortb.append(";" + valuesds.getString(i, "cohort", ""));
expartidb.append(";" + valuesds.getString(i,
"externalparticipantid", ""));
}
}
valuesds = valuesds.getFilteredDataSet(hm);
ds = ds.getFilteredDataSet(hm);
if(flag==1){
logger.info("*****!! Enrolling Participants for newly created Subjects
or not Enrolled subjects "+neubjectidsb.toString().substring(1)+" !!*****");
//// Enrolling Participant here
logger.info("*****!! Enrolling Participants for newly created Subjects
or not Enrolled subjects "+neubjectidsb.toString().substring(1)+" !!*****");
def AddUpdateParticipantprops=[
studyid: studyidsb.toString().substring(1),
studycode: "",
siteid: "",
sitename: studysiteidsb.toString().substring(1),
departmentid: "",
protocolrevision: "",
cohortid: cpcohortb.toString().substring(1),
participantid: "",
externalparticipantid: expartidb.toString().substring(1),
subjectid: neubjectidsb.toString().substring(1),
autopartenrollment: "Y",
participantenrollmentdt: "n",
mode: "add",
auditreason: "",
auditactivity: "",
auditsignedflag: "",
newparticipantid: "",
propsmatch: "Y"
]
logger.info( "Calling AddUpdateParticipant with properties: " +
AddUpdateParticipantprops.toString())
processAction( "AddUpdateParticipant", AddUpdateParticipantprops );
subjectIDds.addColumnValues("participant", DataSet.STRING,
AddUpdateParticipantprops.get("newparticipantid"), ";", "");
for(int i=0; i<subjectIDds.getRowCount(); i++) {
valuesds.setValue(valuesds.findRow("subjectalias",
subjectIDds.getString(i, "subaliasid")), "participantid", subjectIDds.getString(i,
"participant", ""));
}
}
//Checking Visit, Timepont and Clinical Event against a study.
logger.info("####### Starting Validation of Visit, Timepont and Clinical Event
against a study #######");
sql = "with allstudy as ( \n" +
"select rownum as rno, column_value as allstudies from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("sstudy", ";"), ";") +
")) \n" +
"), allsite as ( \n" +
"select rownum as rno, column_value as allsites from TABLE (sys.odcivarchar2list("
+ sf.addIn(valuesds.getColumnValues("studysitedesc", ";"), ";") + ")) \n" +
"), allprotocol as ( \n" +
"select rownum as rno, column_value as allprotocols from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("protocol", ";"), ";")
+ ")) \n" +
"), allcohort as ( \n" +
"select rownum as rno, column_value as allcohorts from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("cohort", ";"), ";") +
")) \n" +
"), allvisit as ( \n" +
"select rownum as rno, column_value as allvisits from TABLE (sys.odcivarchar2list("
+ sf.addIn(valuesds.getColumnValues("visit", ";"), ";") + ")) \n" +
"), alltimepoint as ( \n" +
"select rownum as rno, nvl(column_value, 'NA') as alltimepoints from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("timepoint", ";"), ";")
+ ")) \n" +
"), isstudyp as ( \n" +
"select rownum as rno, s_studyid, clinicalflag \n" +
"from s_study, allstudy als \n" +
"where s_studyid in (als.allstudies) \n" +
"), peventtimepoint as ( \n" +
"select st.rno, cp.s_clinicalprotocolid, cp.s_clinicalprotocolversionid,
cp.s_clinicalprotocolrevision, ed.s_eventdefid, ed.eventdeflabel,
nvl(ed.parenteventdeflabel, 'NA') timepoint \n" +
" from isstudyp st, allsite ast, allprotocol ap, allcohort ac, allvisit av,
alltimepoint atp, s_clinicalprotocol cp, s_studysite sts, s_eventdef ed \n" +
" where ast.rno = st.rno \n" +
" and ap.rno = st.rno \n" +
" and ac.rno = st.rno \n" +
" and av.rno = st.rno \n" +
" and atp.rno = st.rno \n" +
" and st.clinicalflag = 'Y' \n" +
" and sts.sstudyid = st.s_studyid \n" +
" and sts.studysitedesc = ast.allsites \n" +
" and sts.clinicalprotocolrevision = ap.allprotocols \n" +
" and cp.sstudyid = sts.sstudyid \n" +
" and cp.s_clinicalprotocolid = sts.clinicalprotocolid \n" +
" and cp.s_clinicalprotocolrevision = sts.clinicalprotocolrevision \n" +
" and cp.versionstatus = 'C' \n" +
" and ed.clinicalprotocolid = cp.s_clinicalprotocolid \n" +
" and ed.clinicalprotocolversionid = cp.s_clinicalprotocolversionid \n" +
" and ed.clinicalprotocolrevision = cp.s_clinicalprotocolrevision \n" +
" and ed.cohortid = ac.allcohorts \n" +
" and ((nvl(ed.parenteventdeflabel, 'NA') = av.allvisits \n" +
" and ed.eventdeflabel = atp.alltimepoints)) \n" +
"), noncpevent as ( \n" +
"select st.rno, ce.clinicaleventdesc \n" +
" from isstudyp st, allvisit npce, s_clinicalevent ce \n" +
" where npce.rno = st.rno \n" +
" and ce.sstudyid = st.s_studyid \n" +
" and st.clinicalflag = 'N' \n" +
" and ce.clinicaleventdesc = npce.allvisits \n" +
") \n" +
"select st.rno, st.s_studyid, st.clinicalflag, ast.allsites, npce.allvisits
clinicalevents, pet.s_eventdefid, \n" +
"(select s_studysiteid from s_studysite where s_studysite.sstudyid = st.s_studyid
and s_studysite.studysitedesc=ast.allsites) studysiteid, \n" +
"(case when st.clinicalflag = 'Y' then pet.s_clinicalprotocolid else null end)
clinicalpid, \n" +
"(case when st.clinicalflag = 'Y' then pet.s_clinicalprotocolversionid else null
end) clinicalpverid, \n" +
"(case when st.clinicalflag = 'Y' then pet.s_clinicalprotocolrevision else null
end) clinicalprev, \n" +
"(case when pet.eventdeflabel is not null then 1 else 0 end) eventfound, \n" +
"(case when pet.timepoint is not null then 1 else 0 end) timepointfound, \n" +
"pet.eventdeflabel pevent, pet.timepoint ptimepoint, \n" +
"(case when npe.clinicaleventdesc is not null then 1 else 0 end) npeventfound, \n"
+
"npe.clinicaleventdesc npevent \n" +
"from isstudyp st \n" +
"left outer join allsite ast \n" +
"on ast.rno = st.rno \n" +
"left outer join allvisit npce \n" +
"on npce.rno = st.rno \n" +
"left outer join peventtimepoint pet \n" +
"on pet.rno = st.rno \n" +
"left outer join noncpevent npe \n" +
"on npe.rno = st.rno \n" +
"order by st.rno";
logger.info("*****## Visit, Timepoint, Clinical Event Validation sql : "+sql);
DataSet ds1 = queryProcessor.getPreparedSqlDataSet(sql, sf.getValues());
sf.reset();
if(ds1!=null && ds1.getRowCount()>0){
for(int i=0; i<ds1.getRowCount(); i++) {
if(("Y".equals(ds1.getString(i, "clinicalflag")))){
if(((ds1.getInt(i, "eventfound", 0))==1) && ((ds1.getInt(i,
"timepointfound", 0))==1)){
logger.info("*****## Event, Timepoint matches ##*****");
}
else {
logger.info("*****!! Event, Timepoint mismatch !!*****");
throw new SapphireException(SapphireException.TYPE_FAILURE,
"Event, Timepoint mismatch !");
}
}
else {
if(((ds1.getInt(i, "npeventfound", 0))==1)){
logger.info("*****## Clinical Event matches ##*****");
}
else {
logger.info("*****!! Clinical Event mismatch !!*****");
throw new SapphireException(SapphireException.TYPE_FAILURE,
"Clinical Event mismatch !");
}
}
}
////////////// Sample Creation //////////////////
logger.info("####### Creating Sample and adding Alias #######");
if(valuesds.getRowCount()>0 && valuesds!=null){
sql="with allqtyunit as ( \n" +
"select rownum as rno, column_value as allqtyunits from TABLE
(sys.odcivarchar2list("+ sf.addIn(valuesds.getColumnValues("qtyunit", ";"), ";")
+")) \n" +
"), allsampletype as ( \n" +
"select rownum as rno, column_value as allsampletypes from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("sampletype", ";"),
";") + ")) \n" +
"), allkit as ( \n" +
"select rownum as rno, column_value as allkits from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("kitid", ";"), ";") +
")) \n" +
"), allpkgtrack as ( \n" +
"select rownum as rno, column_value as allpkgtracks from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("pkgtracking", ";"),
";") + ")) \n" +
"), allstorage as ( \n" +
"select rownum as rno, column_value as allstorages from TABLE
(sys.odcivarchar2list(" + sf.addIn(valuesds.getColumnValues("storage", ";"), ";") +
")) \n" +
"), pkgstorage as ( \n" +
"select ap.rno, sp.s_packageid, su.storageunitid, sp.trackingnumber \n" +
"from allpkgtrack ap, s_package sp, storageunit su \n" +
"where sp.trackingnumber in (ap.allpkgtracks) \n" +
"and su.linksdcid = 'LV_Package' \n" +
"and su.linkkeyid1 = sp.s_packageid \n" +
") \n" +
"select aq.rno, ci.categoryid, ak.allkits, \n" +
"(select u_lab_code from s_sampletype where s_sampletypeid =
ast.allsampletypes) labcode, \n" +
"(select count(t.trackitemid) from trackitem t where t.trackitemlabel =
ak.allkits) haskit, \n" +
"(select t.trackitemid from trackitem t where t.trackitemlabel = ak.allkits)
kittrackitem, \n" +
"(select ps.s_packageid from pkgstorage ps where ps.rno = ap.rno)
packagestorageid, \n" +
"(select count(su.storageunitid) from storageunit su where su.labelpath =
als.allstorages and su.spaceavailflag = 'Y' and maxtiallowed > 0)
storagavailableflag, \n" +
"(select su.storageunitid from storageunit su where su.labelpath =
als.allstorages and su.spaceavailflag = 'Y' and maxtiallowed > 0) storageunitid \n"
+
"from allqtyunit aq, allsampletype ast, allkit ak, allpkgtrack ap, allstorage
als, categoryitem ci \n" +
"where ast.rno = aq.rno \n" +
"and ak.rno = aq.rno \n" +
"and ap.rno = aq.rno \n" +
"and als.rno = aq.rno \n" +
"and ci.sdcid = 'Units' \n" +
"and ci.keyid1 in (aq.allqtyunits) \n" +
"and ci.categoryid in ('MassUnits', 'VolumeUnits', 'ConcUnits') \n" +
"order by aq.rno";
logger.info("*****## Qualtity and Labcode sql : "+sql);
ds.reset();
ds = queryProcessor.getPreparedSqlDataSet(sql, sf.getValues());
sf.reset();
StringBuffer inivolb = new StringBuffer();
StringBuffer inivolunitb = new StringBuffer();
StringBuffer inimassb = new StringBuffer();
StringBuffer inimassunitb = new StringBuffer();
StringBuffer iniconcb = new StringBuffer();
StringBuffer iniconcunitb = new StringBuffer();
StringBuffer custodialuser = new StringBuffer();
StringBuffer custodialdept = new StringBuffer();
int kitfnpflag = 0;
int storageflag = 0;
if(ds!=null && ds.getRowCount()>0){
for(int i=0; i<ds.getRowCount(); i++) {
String qtytype = ds.getString(i, "categoryid", "");
int kitflag = ds.getInt(i, "haskit", 0);
int storageavlflag = ds.getInt(i, "storagavailableflag", 0);
logger.info("*****!! storageavlflag : "+storageavlflag);
if("MassUnits".equalsIgnoreCase(qtytype)){
inimassb.append(";" + valuesds.getString(i, "qtyvalue",
""));
inimassunitb.append(";" + valuesds.getString(i, "qtyunit",
""));
}
else {
inimassb.append(";");
inimassunitb.append(";");
}
if("VolumeUnits".equalsIgnoreCase(qtytype)){
inivolb.append(";" + valuesds.getString(i, "qtyvalue",
""));
inivolunitb.append(";" + valuesds.getString(i, "qtyunit",
""));
}
else {
inivolb.append(";");
inivolunitb.append(";");
}
if("ConcUnits".equalsIgnoreCase(qtytype)){
iniconcb.append(";" + valuesds.getString(i, "qtyvalue",
""));
iniconcunitb.append(";" + valuesds.getString(i, "qtyunit",
""));
}
else {
iniconcb.append(";");
iniconcunitb.append(";");
}
if(kitflag==0){
logger.info("*****!! Kit "+ds.getString(i, "allkits", "")+"
not present !!*****");
}
else {
kitfnpflag = 1;
}
if(storageavlflag==0){
custodialuser.append(";" + userid);
custodialdept.append(";" + deptid);
logger.info("*****!! Custodial User :
"+custodialuser.toString().substring(1)+" !!*****");
logger.info("*****!! Custodial Department :
"+custodialdept.toString().substring(1)+" !!*****");
}
else {
storageflag = 1;
custodialuser.append(";");
custodialdept.append(";");
}
}
}
def AddSDIprops=[
sdcid: "Sample",
templateid: "",
overrideautokey: "",
copies: valuesds.getRowCount(),
keyid1: "",
keyid2: "",
keyid3: "",
eventnotify: "",
auditreason: "",
adduserroles: "",
addtemplateroles: "",
applyworkitems: "Y",
forcenew: "",
newkeyid1: "",
usetemplatedepartment: "",
auditactivity: "",
auditsignedflag: "",
auditdt: "",
templatekeyid1: "",
templatekeyid2: "",
templatekeyid3: "",
templateflag: "",
copyattachment: "",
copyattachmentmode: "",
checkinsdiflag: "",
newkeyid2: "",
newkeyid3: "",
sstudyid: valuesds.getColumnValues("sstudy", ";"),
u_primary: valuesds.getColumnValues("primary", ";"),
sampletypeid: valuesds.getColumnValues("sampletype", ";"),
u_lab_code_sampletype: ds.getColumnValues("labcode", ";"),
u_condition: valuesds.getColumnValues("samplecondition", ";"),
collectiondt: valuesds.getColumnValues("collectiondt", ";"),
receiveddt: valuesds.getColumnValues("receivedt", ";"),
storagestatus: "Received",
concentration: iniconcb.toString().substring(1),
concentrationunits: iniconcunitb.toString().substring(1),
__samplefamily_initialmass: inimassb.toString().substring(1),
__samplefamily_initialmassunits: inimassunitb.toString().substring(1),
__samplefamily_initialvolume: inivolb.toString().substring(1),
__samplefamily_initialvolumeunits: inivolunitb.toString().substring(1),
__samplefamily_collectiondt: valuesds.getColumnValues("collectiondt",
";"),
__samplefamily_studysiteid: ds1.getColumnValues("studysiteid", ";"),
__samplefamily_subjectid: valuesds.getColumnValues("subjectid", ";"),
__samplefamily_externalsubject:
valuesds.getColumnValues("externalparticipantid", ";"),
__samplefamily_participantid: valuesds.getColumnValues("participantid",
";"),
__samplefamily_clinicalevent: valuesds.getColumnValues("visit", ";"),
__samplefamily_clinicalprotocolid: ds1.getColumnValues("clinicalpid",
";"),
__samplefamily_clinicalprotocolversionid:
ds1.getColumnValues("clinicalpverid", ";"),
__samplefamily_clinicalprotocolrevision:
ds1.getColumnValues("clinicalprev", ";"),
__samplefamily_eventdefid: ds1.getColumnValues("s_eventdefid", ";"),
__samplefamily_kittrackitem: ds.getColumnValues("kittrackitem", ";"),
__samplefamily_initialpackageid: ds.getColumnValues("packagestorageid",
";"),
__trackitem_containertypeid: valuesds.getColumnValues("containertype",
";"),
__trackitem_qtycurrent: valuesds.getColumnValues("qtyvalue", ";"),
__trackitem_qtyunits: valuesds.getColumnValues("qtyunit", ";"),
__trackitem_custodialuserid: custodialuser.toString().substring(1),
__trackitem_custodialdepartmentid:
custodialdept.toString().substring(1),
propsmatch: "Y"
]
logger.info( "Calling AddSDI with properties: " + AddSDIprops.toString());
processAction( "AddSDI", AddSDIprops );
sampleid = AddSDIprops.get("newkeyid1");
def AddSDIAliasprops=[
sdcid: "Sample",
keyid1: sampleid,
keyid2: "",
keyid3: "",
aliasid: valuesds.getColumnValues("samplealias", ";"),
aliastype: valuesds.getColumnValues("samplealiastype", ";"),
propsmatch: "Y"
]
logger.info( "Calling AddSDIAlias with properties: " +
AddSDIAliasprops.toString());
processAction( "AddSDIAlias", AddSDIAliasprops );
def AddSDIDetailprops=[
sdcid: "Sample",
keyid1: sampleid,
keyid2: "",
keyid3: "",
linkid: "SampleDetail",
detailtype: "Treatment",
detailvalue: valuesds.getColumnValues("treatment", ";"),
detailsdcid: "LV_Treatment",
applylock: "",
detailkeyid1: valuesds.getColumnValues("treatment", ";"),
eventnotify: "",
auditreason: "Drug Name Added via DFD",
auditactivity: "Add",
auditsignedflag: "N",
separator: ";"
]
logger.info( "Calling AddSDIDetail with properties: " +
AddSDIDetailprops.toString());
processAction( "AddSDIDetail", AddSDIDetailprops );
if(kitfnpflag != 0){
// Update Kit status as Used.
logger.info("####### Update Kit status as Used. #######");
def EditSDIprops=[
sdcid: "TrackItemSDC",
keyid1: ds.getColumnValues("kittrackitem", ";"),
keyid2: "",
keyid3: "",
auditreason: "Kit marked as used via DFD",
eventnotify: "",
applylock: "",
auditactivity: "Update",
auditsignedflag: "N",
auditdt: "",
trackitemstatus: "Used"
]
logger.info( "Calling EditSDI with properties: " +
EditSDIprops.toString());
processAction( "EditSDI", EditSDIprops );
}
// File Samples to the Package
/*logger.info("####### File Samples to the Package. #######");
def AssignPKGStrgprops=[
storageunitid: ds.getColumnValues("packagestorageid", ";"),
sdcid: "Sample",
keyid1: sampleid,
keyid2: "",
keyid3: "",
makeretain: "",
trackitemid: "",
istrackitem: "",
clearstorage: "",
applylock: ""
]
logger.info( "Calling AssignStrgAndReceive with properties: " +
AssignPKGStrgprops.toString())
processAction( "AssignStrgAndReceive", AssignPKGStrgprops );
*/
// File Samples to the Storage Unit
logger.info("####### File Samples to the Storage Unit. #######");
if(storageflag != 0){
def AssignStrgAndReceiveprops=[
storageunitid: ds.getColumnValues("storageunitid", ";"),
sdcid: "Sample",
keyid1: sampleid,
keyid2: "",
keyid3: "",
makeretain: "",
trackitemid: "",
istrackitem: "",
clearstorage: "",
applylock: ""
]
logger.info( "Calling AssignStrgAndReceive with properties: " +
AssignStrgAndReceiveprops.toString())
processAction( "AssignStrgAndReceive", AssignStrgAndReceiveprops );
}
}
else {
logger.info("*****!! No Samples to create !!*****");
}
