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gdcsvstodcm.sh
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gdcsvstodcm.sh
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#!/bin/sh
#
# Usage: ./gdcsvstodcm.sh projectdirname/filename.svs [outdir]
infile="$1"
outdir="$2"
TMPJSONFILE="/tmp/`basename $0`.$$"
# these persist across invocations ...
FILEMAPPINGSPECIMENIDTOUID="TCGAspecimenIDToUIDMap.csv"
FILEMAPPINGSTUDYIDTOUID="TCGAstudyIDToUIDMap.csv"
FILEMAPPINGSTUDYIDTODATETIME="TCGAstudyIDToDateTimeMap.csv"
UIDMAPPINGFILE="tcga_tabulateduids.csv"
TMPSLIDEUIDFILE="slideuid.csv"
#JHOVE="${HOME}/work/jhove/jhove"
#PIXELMEDDIR="${HOME}/work/pixelmed/imgbook"
PIXELMEDDIR="/idc-wsi-conversion"
PATHTOADDITIONAL="${PIXELMEDDIR}/lib/additional"
filename=`basename "${infile}" '.svs'`
echo "$filename"
# "TCGA-GBM/TCGA-12-0819-01A-01-TS1.f94b9687-a5b8-4390-bd23-c913769e45be.svs"
# "TCGA-BRCA/TCGA-A2-A1G0-01Z-00-DX1.9ECB0B8A-EF4E-45A9-82AC-EF36375DEF65.svs"
# "TCGA-DLBC/0c159ca4-c2ed-4a69-bc8d-59611f2122ec/TCGA-GR-A4D9-01A-01-TS1.53C66BD8-5D6B-4685-9A6B-CABDEEC126ED.svs"
# "TCGA-DLBC/0c159ca4-c2ed-4a69-bc8d-59611f2122ec/TCGA-GR-A4D9-01A-01-TS1.53C66BD8-5D6B-4685-9A6B-CABDEEC126ED.svs"
# "TCGA-PRAD/dae680cf-fc39-4da7-8326-ffbb82af9f35/TCGA-HC-7819-01A-01-TS1.svs" ... very occasionally the uuid after the Tissue slide ID and number is missing
# the project name is NOT in the file name ...
tcgaproject=`dirname "${infile}" | sed -e 's/^.*\(TCGA-[A-Z][A-Z]*\).*$/\1/'`
if [ -z "${outdir}" ]
then
#outdir="Converted/${tcgaproject}/${filename}"
outdir=/idc-wsi-conversion/Data/DcmConv
fi
tcgatissuesourcesite=`echo "${filename}" | sed -e 's/^TCGA-\([0-9A-Z]*\).*$/\1/'`
tcgaparticipant=`echo "${filename}" | sed -e 's/^TCGA-[0-9A-Z]*-\([0-9A-Z]*\).*$/\1/'`
tcgasample=`echo "${filename}" | sed -e 's/^TCGA-[0-9A-Z]*-[0-9A-Z]*-\([0-9]*\).*$/\1/'`
tcgavial=`echo "${filename}" | sed -e 's/^TCGA-[0-9A-Z]*-[0-9A-Z]*-[0-9]*\([A-Z]*\).*$/\1/'`
tcgaportion=`echo "${filename}" | sed -e 's/^TCGA-[0-9A-Z]*-[0-9A-Z]*-[0-9]*[A-Z]*-\([0-9]*\).*$/\1/'`
# tcgaanalyte seems to be missing for slides
tcgaanalyte=`echo "${filename}" | sed -e 's/^TCGA-[0-9A-Z]*-[0-9A-Z]*-[0-9]*[A-Z]*-[0-9]*\([A-Z]*\).*$/\1/'`
# "Tissue slide ID can be 'TS' ('Top Slide'), 'BS' ('Bottom Slide') or 'MS' ('Middle slide'), followed by a number or letter to indicate slide order"
# "The difference can be found by looking at the particular filename, where files with “TS#” or “BS#”, where # is an integer, is a frozen slide ... While files with “DX#”, again where # is an integer, is an FFPE slide"
# do not insist on [.] after Tissue slide ID and number, else will fail when trailing uuid is missing
tcgatissueslideidtype=`echo "${filename}" | sed -e 's/^TCGA-[0-9A-Z]*-[0-9A-Z]*-[0-9]*[A-Z]*-[0-9]*[A-Z]*-\([TBMD][SX]\)[0-9A-Z]*.*$/\1/'`
tcgatissueslideidnumber=`echo "${filename}" | sed -e 's/^TCGA-[0-9A-Z]*-[0-9A-Z]*-[0-9]*[A-Z]*-[0-9]*[A-Z]*-[TBMD][SX]\([0-9A-Z]*\).*$/\1/'`
tcgafileguid=`echo "${filename}" | sed -e 's/^TCGA-[0-9A-Z]*-[0-9A-Z]*-[0-9A-Z-]*[.]\([0-9a-fA-F-]*\)$/\1/'`
echo "infile = ${infile}"
echo "filename = ${filename}"
echo "tcgaproject = ${tcgaproject}"
echo "tcgatissuesourcesite = ${tcgatissuesourcesite}"
echo "tcgaparticipant = ${tcgaparticipant}"
echo "tcgasample = ${tcgasample}"
echo "tcgavial = ${tcgavial}"
echo "tcgaportion = ${tcgaportion}"
echo "tcgaanalyte = ${tcgaanalyte}"
echo "tcgatissueslideidtype = ${tcgatissueslideidtype}"
echo "tcgatissueslideidnumber = ${tcgatissueslideidnumber}"
echo "tcgafileguid = ${tcgafileguid}"
slidefilenameforuid="${filename}"
echo "slidefilenameforuid = ${slidefilenameforuid}"
echo "TMPSLIDEUIDFILE = ${TMPSLIDEUIDFILE}"
rm -f "${TMPSLIDEUIDFILE}"
uidarg=""
if [ -f "${UIDMAPPINGFILE}" ]
then
egrep "(Filename|${slidefilenameforuid})" "${UIDMAPPINGFILE}" > "${TMPSLIDEUIDFILE}"
uidarg="UIDFILE ${TMPSLIDEUIDFILE}"
fi
echo "uidarg = ${uidarg}"
# TCIA pattern for radiology is same string for PatientName and PatientID
# GDC and TCIA do not include project in patient ID, i.e., do not use ${tcgaproject} as prefix, but just "TCGA"
dicompatientid="TCGA-${tcgatissuesourcesite}-${tcgaparticipant}"
dicompatientname="${dicompatientid}"
# make study, accession same as case (patient)
# ideally would make sure these are no longer than 16 chars ... assume it for now :(
dicomstudyid="${dicompatientid}"
dicomaccessionnumber="${dicompatientid}"
# specimen is the tissue section on the slide
dicomspecimenidentifier="${dicompatientid}-${tcgasample}${tcgavial}-${tcgaportion}${tcgaanalyte}-${tcgatissueslideidtype}${tcgatissueslideidnumber}"
# container is the slide
dicomcontaineridentifier="${dicomspecimenidentifier}"
# parent specimen that is assumed to be block (for fixation) is portionanalyte
dicomparentspecimenportionanalyteidentifier="${dicompatientid}-${tcgasample}${tcgavial}-${tcgaportion}${tcgaanalyte}"
# parent specimen that of portionanalyte block is vial
dicomparentspecimenvialidentifier="${dicompatientid}-${tcgasample}${tcgavial}"
# parent specimen that of vial block is sample
dicomparentspecimensampleidentifier="${dicompatientid}-${tcgasample}"
#dicomclinicaltrialcoordinatingcentername="GDC (IDC)"
dicomclinicaltrialcoordinatingcentername="NCI Genomic Data Commons (GDC) - Imaging Data Commons (IDC)"
dicomclinicaltrialsponsorname="TCGA"
dicomclinicalprotocolid="${tcgaproject}"
anatomycodevalue=""
anatomycsd="SCT"
anatomycodemeaning=""
# https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations
# should make this a table lookupo from a separate text file :
if [ "${tcgaproject}" = "TCGA-LAML" ]
then
dicomclinicalprotocolname="TCGA Acute Myeloid Leukemia"
anatomycodevalue="14016003"
anatomycodemeaning="Bone marrow"
elif [ "${tcgaproject}" = "TCGA-ACC" ]
then
dicomclinicalprotocolname="TCGA Adrenocortical carcinoma"
# not in SNOMED-DICOM subset - need CP to add it :(
anatomycodevalue="68594002"
anatomycodemeaning="Adrenal cortex"
elif [ "${tcgaproject}" = "TCGA-BLCA" ]
then
dicomclinicalprotocolname="TCGA Bladder Urothelial Carcinoma"
anatomycodevalue="89837001"
anatomycodemeaning="Bladder"
elif [ "${tcgaproject}" = "TCGA-LGG" ]
then
dicomclinicalprotocolname="TCGA Brain Lower Grade Glioma"
anatomycodevalue="12738006"
anatomycodemeaning="Brain"
elif [ "${tcgaproject}" = "TCGA-BRCA" ]
then
dicomclinicalprotocolname="TCGA Breast invasive carcinoma"
anatomycodevalue="76752008"
anatomycodemeaning="Breast"
elif [ "${tcgaproject}" = "TCGA-CESC" ]
then
dicomclinicalprotocolname="TCGA Cervical squamous cell, endocervical adeno, carcinoma"
anatomycodevalue="71252005"
anatomycodemeaning="Cervix"
elif [ "${tcgaproject}" = "TCGA-CHOL" ]
then
dicomclinicalprotocolname="TCGA Cholangiocarcinoma"
anatomycodevalue="28273000"
anatomycodemeaning="Bile duct"
elif [ "${tcgaproject}" = "TCGA-LCML" ]
then
dicomclinicalprotocolname="TCGA Chronic Myelogenous Leukemia"
anatomycodevalue="14016003"
anatomycodemeaning="Bone marrow"
elif [ "${tcgaproject}" = "TCGA-COAD" ]
then
dicomclinicalprotocolname="TCGA Colon adenocarcinoma"
anatomycodevalue="71854001"
anatomycodemeaning="Colon"
elif [ "${tcgaproject}" = "TCGA-CNTL" ]
then
dicomclinicalprotocolname="TCGA Controls"
elif [ "${tcgaproject}" = "TCGA-ESCA" ]
then
dicomclinicalprotocolname="TCGA Esophageal carcinoma"
anatomycodevalue="32849002"
anatomycodemeaning="Esophagus"
elif [ "${tcgaproject}" = "TCGA-FPPP" ]
then
dicomclinicalprotocolname="TCGA FFPE Pilot Phase II"
elif [ "${tcgaproject}" = "TCGA-GBM" ]
then
dicomclinicalprotocolname="TCGA Glioblastoma multiforme"
anatomycodevalue="12738006"
anatomycodemeaning="Brain"
elif [ "${tcgaproject}" = "TCGA-HNSC" ]
then
dicomclinicalprotocolname="TCGA Head and Neck squamous cell carcinoma"
anatomycodevalue="774007"
anatomycodemeaning="Head and Neck"
elif [ "${tcgaproject}" = "TCGA-KICH" ]
then
dicomclinicalprotocolname="TCGA Kidney Chromophobe"
anatomycodevalue="64033007"
anatomycodemeaning="Kidney"
elif [ "${tcgaproject}" = "TCGA-KIRC" ]
then
dicomclinicalprotocolname="TCGA Kidney renal clear cell carcinoma"
anatomycodevalue="64033007"
anatomycodemeaning="Kidney"
elif [ "${tcgaproject}" = "TCGA-KIRP" ]
then
dicomclinicalprotocolname="TCGA Kidney renal papillary cell carcinoma"
anatomycodevalue="64033007"
anatomycodemeaning="Kidney"
elif [ "${tcgaproject}" = "TCGA-LIHC" ]
then
dicomclinicalprotocolname="TCGA Liver hepatocellular carcinoma"
anatomycodevalue="10200004"
anatomycodemeaning="Liver"
elif [ "${tcgaproject}" = "TCGA-LUAD" ]
then
dicomclinicalprotocolname="TCGA Lung adenocarcinoma"
anatomycodevalue="39607008"
anatomycodemeaning="Lung"
elif [ "${tcgaproject}" = "TCGA-LUSC" ]
then
dicomclinicalprotocolname="TCGA Lung squamous cell carcinoma"
anatomycodevalue="39607008"
anatomycodemeaning="Lung"
elif [ "${tcgaproject}" = "TCGA-DLBC" ]
then
dicomclinicalprotocolname="TCGA Lymphoid Neoplasm Diffuse Large B-cell Lymphoma"
anatomycodevalue="6969002"
anatomycodemeaning="Lymphoid tissue"
elif [ "${tcgaproject}" = "TCGA-MESO" ]
then
dicomclinicalprotocolname="TCGA Mesothelioma"
# do not assume pleura
# not in SNOMED-DICOM subset - need CP to add it :(
anatomycodevalue="71400007"
anatomycodemeaning="Mesothelium"
elif [ "${tcgaproject}" = "TCGA-MISC" ]
then
dicomclinicalprotocolname="TCGA Miscellaneous"
elif [ "${tcgaproject}" = "TCGA-OV" ]
then
dicomclinicalprotocolname="TCGA Ovarian serous cystadenocarcinoma"
anatomycodevalue="15497006"
anatomycodemeaning="Ovary"
elif [ "${tcgaproject}" = "TCGA-PAAD" ]
then
dicomclinicalprotocolname="TCGA Pancreatic adenocarcinoma"
anatomycodevalue="15776009"
anatomycodemeaning="Pancreas"
elif [ "${tcgaproject}" = "TCGA-PCPG" ]
then
dicomclinicalprotocolname="TCGA Pheochromocytoma and Paraganglioma"
elif [ "${tcgaproject}" = "TCGA-PRAD" ]
then
dicomclinicalprotocolname="TCGA Prostate adenocarcinoma"
anatomycodevalue="41216001"
anatomycodemeaning="Prostate"
elif [ "${tcgaproject}" = "TCGA-READ" ]
then
dicomclinicalprotocolname="TCGA Rectum adenocarcinoma"
anatomycodevalue="34402009"
anatomycodemeaning="Rectum"
elif [ "${tcgaproject}" = "TCGA-SARC" ]
then
dicomclinicalprotocolname="TCGA Sarcoma"
elif [ "${tcgaproject}" = "TCGA-SKCM" ]
then
dicomclinicalprotocolname="TCGA Skin Cutaneous Melanoma"
anatomycodevalue="39937001"
anatomycodemeaning="Skin"
elif [ "${tcgaproject}" = "TCGA-STAD" ]
then
dicomclinicalprotocolname="TCGA Stomach adenocarcinoma"
anatomycodevalue="69695003"
anatomycodemeaning="Stomach"
elif [ "${tcgaproject}" = "TCGA-TGCT" ]
then
dicomclinicalprotocolname="TCGA Testicular Germ Cell Tumors"
anatomycodevalue="40689003"
anatomycodemeaning="Testis"
elif [ "${tcgaproject}" = "TCGA-THYM" ]
then
dicomclinicalprotocolname="TCGA Thymoma"
anatomycodevalue="9875009"
anatomycodemeaning="Thymus"
elif [ "${tcgaproject}" = "TCGA-THCA" ]
then
dicomclinicalprotocolname="TCGA Thyroid carcinoma"
anatomycodevalue="69748006"
anatomycodemeaning="Thyroid"
elif [ "${tcgaproject}" = "TCGA-UCS" ]
then
dicomclinicalprotocolname="TCGA Uterine Carcinosarcoma"
anatomycodevalue="35039007"
anatomycodemeaning="Uterus"
elif [ "${tcgaproject}" = "TCGA-UCEC" ]
then
dicomclinicalprotocolname="TCGA Uterine Corpus Endometrial Carcinoma"
anatomycodevalue="35039007"
anatomycodemeaning="Uterus"
elif [ "${tcgaproject}" = "TCGA-UVM" ]
then
dicomclinicalprotocolname="TCGA Uveal Melanoma"
# not in SNOMED-DICOM subset - need CP to add it :(
anatomycodevalue="74862005"
anatomycodemeaning="Uvea"
else
dicomclinicalprotocolname="${tcgaproject}"
fi
dicomclinicaltrialsiteid="TCGA-${tcgatissuesourcesite}"
# could populate site name from https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tissue-source-site-codes :(
# should make this a table lookupo from a separate text file :
if [ "${tcgatissuesourcesite}" = "01" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "02" ]
then
dicomclinicaltrialsitename="MD Anderson Cancer Center"
elif [ "${tcgatissuesourcesite}" = "04" ]
then
dicomclinicaltrialsitename="Gynecologic Oncology Group"
elif [ "${tcgatissuesourcesite}" = "05" ]
then
dicomclinicaltrialsitename="Indivumed"
elif [ "${tcgatissuesourcesite}" = "06" ]
then
dicomclinicaltrialsitename="Henry Ford Hospital"
elif [ "${tcgatissuesourcesite}" = "07" ]
then
dicomclinicaltrialsitename="TGen"
elif [ "${tcgatissuesourcesite}" = "08" ]
then
dicomclinicaltrialsitename="UCSF"
elif [ "${tcgatissuesourcesite}" = "09" ]
then
dicomclinicaltrialsitename="UCSF"
elif [ "${tcgatissuesourcesite}" = "10" ]
then
dicomclinicaltrialsitename="MD Anderson Cancer Center"
elif [ "${tcgatissuesourcesite}" = "11" ]
then
dicomclinicaltrialsitename="MD Anderson Cancer Center"
elif [ "${tcgatissuesourcesite}" = "12" ]
then
dicomclinicaltrialsitename="Duke"
elif [ "${tcgatissuesourcesite}" = "13" ]
then
dicomclinicaltrialsitename="Memorial Sloan Kettering"
elif [ "${tcgatissuesourcesite}" = "14" ]
then
dicomclinicaltrialsitename="Emory University"
elif [ "${tcgatissuesourcesite}" = "15" ]
then
dicomclinicaltrialsitename="Mayo Clinic - Rochester"
elif [ "${tcgatissuesourcesite}" = "16" ]
then
dicomclinicaltrialsitename="Toronto Western Hospital"
elif [ "${tcgatissuesourcesite}" = "17" ]
then
dicomclinicaltrialsitename="Washington University"
elif [ "${tcgatissuesourcesite}" = "18" ]
then
dicomclinicaltrialsitename="Princess Margaret Hospital (Canada)"
elif [ "${tcgatissuesourcesite}" = "19" ]
then
dicomclinicaltrialsitename="Case Western"
elif [ "${tcgatissuesourcesite}" = "1Z" ]
then
dicomclinicaltrialsitename="Johns Hopkins"
elif [ "${tcgatissuesourcesite}" = "20" ]
then
dicomclinicaltrialsitename="Fox Chase Cancer Center"
elif [ "${tcgatissuesourcesite}" = "21" ]
then
dicomclinicaltrialsitename="Fox Chase Cancer Center"
elif [ "${tcgatissuesourcesite}" = "22" ]
then
dicomclinicaltrialsitename="Mayo Clinic - Rochester"
elif [ "${tcgatissuesourcesite}" = "23" ]
then
dicomclinicaltrialsitename="Cedars Sinai"
elif [ "${tcgatissuesourcesite}" = "24" ]
then
dicomclinicaltrialsitename="Washington University"
elif [ "${tcgatissuesourcesite}" = "25" ]
then
dicomclinicaltrialsitename="Mayo Clinic - Rochester"
elif [ "${tcgatissuesourcesite}" = "26" ]
then
dicomclinicaltrialsitename="University of Florida"
elif [ "${tcgatissuesourcesite}" = "27" ]
then
dicomclinicaltrialsitename="Milan - Italy, Fondazione IRCCS Instituto Neuroligico C. Besta"
elif [ "${tcgatissuesourcesite}" = "28" ]
then
dicomclinicaltrialsitename="Cedars Sinai"
elif [ "${tcgatissuesourcesite}" = "29" ]
then
dicomclinicaltrialsitename="Duke"
elif [ "${tcgatissuesourcesite}" = "2A" ]
then
dicomclinicaltrialsitename="Memorial Sloan Kettering Cancer Center"
elif [ "${tcgatissuesourcesite}" = "2E" ]
then
dicomclinicaltrialsitename="University of Kansas Medical Center"
elif [ "${tcgatissuesourcesite}" = "2F" ]
then
dicomclinicaltrialsitename="Erasmus MC"
elif [ "${tcgatissuesourcesite}" = "2G" ]
then
dicomclinicaltrialsitename="Erasmus MC"
elif [ "${tcgatissuesourcesite}" = "2H" ]
then
dicomclinicaltrialsitename="Erasmus MC"
elif [ "${tcgatissuesourcesite}" = "2J" ]
then
dicomclinicaltrialsitename="Mayo Clinic"
elif [ "${tcgatissuesourcesite}" = "2K" ]
then
dicomclinicaltrialsitename="Greenville Health System"
elif [ "${tcgatissuesourcesite}" = "2L" ]
then
dicomclinicaltrialsitename="Technical University of Munich"
elif [ "${tcgatissuesourcesite}" = "2M" ]
then
dicomclinicaltrialsitename="Technical University of Munich"
elif [ "${tcgatissuesourcesite}" = "2N" ]
then
dicomclinicaltrialsitename="Technical University of Munich"
elif [ "${tcgatissuesourcesite}" = "2P" ]
then
dicomclinicaltrialsitename="University of California San Diego"
elif [ "${tcgatissuesourcesite}" = "2V" ]
then
dicomclinicaltrialsitename="University of California San Diego"
elif [ "${tcgatissuesourcesite}" = "2W" ]
then
dicomclinicaltrialsitename="University of New Mexico"
elif [ "${tcgatissuesourcesite}" = "2X" ]
then
dicomclinicaltrialsitename="ABS IUPUI"
elif [ "${tcgatissuesourcesite}" = "2Y" ]
then
dicomclinicaltrialsitename="Moffitt Cancer Center"
elif [ "${tcgatissuesourcesite}" = "2Z" ]
then
dicomclinicaltrialsitename="Moffitt Cancer Center"
elif [ "${tcgatissuesourcesite}" = "30" ]
then
dicomclinicaltrialsitename="Harvard"
elif [ "${tcgatissuesourcesite}" = "31" ]
then
dicomclinicaltrialsitename="Imperial College"
elif [ "${tcgatissuesourcesite}" = "32" ]
then
dicomclinicaltrialsitename="St. Joseph's Hospital (AZ)"
elif [ "${tcgatissuesourcesite}" = "33" ]
then
dicomclinicaltrialsitename="Johns Hopkins"
elif [ "${tcgatissuesourcesite}" = "34" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "35" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "36" ]
then
dicomclinicaltrialsitename="BC Cancer Agency"
elif [ "${tcgatissuesourcesite}" = "37" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "38" ]
then
dicomclinicaltrialsitename="UNC"
elif [ "${tcgatissuesourcesite}" = "39" ]
then
dicomclinicaltrialsitename="MSKCC"
elif [ "${tcgatissuesourcesite}" = "3A" ]
then
dicomclinicaltrialsitename="Moffitt Cancer Center"
elif [ "${tcgatissuesourcesite}" = "3B" ]
then
dicomclinicaltrialsitename="Moffitt Cancer Center"
elif [ "${tcgatissuesourcesite}" = "3C" ]
then
dicomclinicaltrialsitename="Columbia University"
elif [ "${tcgatissuesourcesite}" = "3E" ]
then
dicomclinicaltrialsitename="Columbia University"
elif [ "${tcgatissuesourcesite}" = "3G" ]
then
dicomclinicaltrialsitename="MD Anderson Cancer Center"
elif [ "${tcgatissuesourcesite}" = "3H" ]
then
dicomclinicaltrialsitename="MD Anderson Cancer Center"
elif [ "${tcgatissuesourcesite}" = "3J" ]
then
dicomclinicaltrialsitename="Carle Cancer Center"
elif [ "${tcgatissuesourcesite}" = "3K" ]
then
dicomclinicaltrialsitename="Boston Medical Center"
elif [ "${tcgatissuesourcesite}" = "3L" ]
then
dicomclinicaltrialsitename="Albert Einstein Medical Center"
elif [ "${tcgatissuesourcesite}" = "3M" ]
then
dicomclinicaltrialsitename="University of Kansas Medical Center"
elif [ "${tcgatissuesourcesite}" = "3N" ]
then
dicomclinicaltrialsitename="Greenville Health System"
elif [ "${tcgatissuesourcesite}" = "3P" ]
then
dicomclinicaltrialsitename="Greenville Health System"
elif [ "${tcgatissuesourcesite}" = "3Q" ]
then
dicomclinicaltrialsitename="Greenville Health Systems"
elif [ "${tcgatissuesourcesite}" = "3R" ]
then
dicomclinicaltrialsitename="University of New Mexico"
elif [ "${tcgatissuesourcesite}" = "3S" ]
then
dicomclinicaltrialsitename="University of New Mexico"
elif [ "${tcgatissuesourcesite}" = "3T" ]
then
dicomclinicaltrialsitename="Emory University"
elif [ "${tcgatissuesourcesite}" = "3U" ]
then
dicomclinicaltrialsitename="University of Chicago"
elif [ "${tcgatissuesourcesite}" = "3W" ]
then
dicomclinicaltrialsitename="University of California San Diego"
elif [ "${tcgatissuesourcesite}" = "3X" ]
then
dicomclinicaltrialsitename="Alberta Health Services"
elif [ "${tcgatissuesourcesite}" = "3Z" ]
then
dicomclinicaltrialsitename="Mary Bird Perkins Cancer Center - Our Lady of the Lake"
elif [ "${tcgatissuesourcesite}" = "41" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "42" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "43" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "44" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "46" ]
then
dicomclinicaltrialsitename="St. Joseph's Medical Center (MD)"
elif [ "${tcgatissuesourcesite}" = "49" ]
then
dicomclinicaltrialsitename="Johns Hopkins"
elif [ "${tcgatissuesourcesite}" = "4A" ]
then
dicomclinicaltrialsitename="Mary Bird Perkins Cancer Center - Our Lady of the Lake"
elif [ "${tcgatissuesourcesite}" = "4B" ]
then
dicomclinicaltrialsitename="Mary Bird Perkins Cancer Center - Our Lady of the Lake"
elif [ "${tcgatissuesourcesite}" = "4C" ]
then
dicomclinicaltrialsitename="Mary Bird Perkins Cancer Center - Our Lady of the Lake"
elif [ "${tcgatissuesourcesite}" = "4D" ]
then
dicomclinicaltrialsitename="Molecular Response"
elif [ "${tcgatissuesourcesite}" = "4E" ]
then
dicomclinicaltrialsitename="Molecular Response"
elif [ "${tcgatissuesourcesite}" = "4G" ]
then
dicomclinicaltrialsitename="Sapienza University of Rome"
elif [ "${tcgatissuesourcesite}" = "4H" ]
then
dicomclinicaltrialsitename="Proteogenex, Inc."
elif [ "${tcgatissuesourcesite}" = "4J" ]
then
dicomclinicaltrialsitename="Proteogenex, Inc."
elif [ "${tcgatissuesourcesite}" = "4K" ]
then
dicomclinicaltrialsitename="Proteogenex, Inc."
elif [ "${tcgatissuesourcesite}" = "4L" ]
then
dicomclinicaltrialsitename="Proteogenex, Inc."
elif [ "${tcgatissuesourcesite}" = "4N" ]
then
dicomclinicaltrialsitename="Mary Bird Perkins Cancer Center - Our Lady of the Lake"
elif [ "${tcgatissuesourcesite}" = "4P" ]
then
dicomclinicaltrialsitename="Duke University"
elif [ "${tcgatissuesourcesite}" = "4Q" ]
then
dicomclinicaltrialsitename="Duke University"
elif [ "${tcgatissuesourcesite}" = "4R" ]
then
dicomclinicaltrialsitename="Duke University"
elif [ "${tcgatissuesourcesite}" = "4S" ]
then
dicomclinicaltrialsitename="Duke University"
elif [ "${tcgatissuesourcesite}" = "4T" ]
then
dicomclinicaltrialsitename="Duke University"
elif [ "${tcgatissuesourcesite}" = "4V" ]
then
dicomclinicaltrialsitename="Hospital Louis Pradel"
elif [ "${tcgatissuesourcesite}" = "4W" ]
then
dicomclinicaltrialsitename="University of Miami"
elif [ "${tcgatissuesourcesite}" = "4X" ]
then
dicomclinicaltrialsitename="Yale University"
elif [ "${tcgatissuesourcesite}" = "4Y" ]
then
dicomclinicaltrialsitename="Medical College of Wisconsin"
elif [ "${tcgatissuesourcesite}" = "4Z" ]
then
dicomclinicaltrialsitename="Barretos Cancer Hospital"
elif [ "${tcgatissuesourcesite}" = "50" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "51" ]
then
dicomclinicaltrialsitename="UNC"
elif [ "${tcgatissuesourcesite}" = "52" ]
then
dicomclinicaltrialsitename="University of Miami"
elif [ "${tcgatissuesourcesite}" = "53" ]
then
dicomclinicaltrialsitename="University of Miami"
elif [ "${tcgatissuesourcesite}" = "55" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "56" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "57" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "58" ]
then
dicomclinicaltrialsitename="Thoraxklinik at University Hospital Heidelberg"
elif [ "${tcgatissuesourcesite}" = "59" ]
then
dicomclinicaltrialsitename="Roswell Park"
elif [ "${tcgatissuesourcesite}" = "5A" ]
then
dicomclinicaltrialsitename="Wake Forest University"
elif [ "${tcgatissuesourcesite}" = "5B" ]
then
dicomclinicaltrialsitename="Medical College of Wisconsin"
elif [ "${tcgatissuesourcesite}" = "5C" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "5D" ]
then
dicomclinicaltrialsitename="University of Miami"
elif [ "${tcgatissuesourcesite}" = "5F" ]
then
dicomclinicaltrialsitename="Duke University"
elif [ "${tcgatissuesourcesite}" = "5G" ]
then
dicomclinicaltrialsitename="Cleveland Clinic Foundation"
elif [ "${tcgatissuesourcesite}" = "5H" ]
then
dicomclinicaltrialsitename="Retina Consultants Houston"
elif [ "${tcgatissuesourcesite}" = "5J" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "5K" ]
then
dicomclinicaltrialsitename="St. Joseph's Hospital AZ"
elif [ "${tcgatissuesourcesite}" = "5L" ]
then
dicomclinicaltrialsitename="University of Sao Paulo"
elif [ "${tcgatissuesourcesite}" = "5M" ]
then
dicomclinicaltrialsitename="University of Sao Paulo"
elif [ "${tcgatissuesourcesite}" = "5N" ]
then
dicomclinicaltrialsitename="University Hospital Erlangen"
elif [ "${tcgatissuesourcesite}" = "5P" ]
then
dicomclinicaltrialsitename="University Hospital Erlangen"
elif [ "${tcgatissuesourcesite}" = "5Q" ]
then
dicomclinicaltrialsitename="Proteogenex, Inc"
elif [ "${tcgatissuesourcesite}" = "5R" ]
then
dicomclinicaltrialsitename="Proteogenex, Inc"
elif [ "${tcgatissuesourcesite}" = "5S" ]
then
dicomclinicaltrialsitename="Holy Cross"
elif [ "${tcgatissuesourcesite}" = "5T" ]
then
dicomclinicaltrialsitename="Holy Cross"
elif [ "${tcgatissuesourcesite}" = "5U" ]
then
dicomclinicaltrialsitename="Regina Elena National Cancer Institute"
elif [ "${tcgatissuesourcesite}" = "5V" ]
then
dicomclinicaltrialsitename="Roswell Park"
elif [ "${tcgatissuesourcesite}" = "5W" ]
then
dicomclinicaltrialsitename="University of Alabama"
elif [ "${tcgatissuesourcesite}" = "5X" ]
then
dicomclinicaltrialsitename="University of Alabama"
elif [ "${tcgatissuesourcesite}" = "60" ]
then
dicomclinicaltrialsitename="Roswell Park"
elif [ "${tcgatissuesourcesite}" = "61" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "62" ]
then
dicomclinicaltrialsitename="Thoraxklinik at University Hospital Heidelberg"
elif [ "${tcgatissuesourcesite}" = "63" ]
then
dicomclinicaltrialsitename="Ontario Institute for Cancer Research"
elif [ "${tcgatissuesourcesite}" = "64" ]
then
dicomclinicaltrialsitename="Fox Chase"
elif [ "${tcgatissuesourcesite}" = "65" ]
then
dicomclinicaltrialsitename="Roswell Park"
elif [ "${tcgatissuesourcesite}" = "66" ]
then
dicomclinicaltrialsitename="Indivumed"
elif [ "${tcgatissuesourcesite}" = "67" ]
then
dicomclinicaltrialsitename="St Joseph's Medical Center (MD)"
elif [ "${tcgatissuesourcesite}" = "68" ]
then
dicomclinicaltrialsitename="Washington University - Cleveland Clinic"
elif [ "${tcgatissuesourcesite}" = "69" ]
then
dicomclinicaltrialsitename="Washington University - Cleveland Clinic"
elif [ "${tcgatissuesourcesite}" = "6A" ]
then
dicomclinicaltrialsitename="University of Kansas"
elif [ "${tcgatissuesourcesite}" = "6D" ]
then
dicomclinicaltrialsitename="University of Oklahoma HSC"
elif [ "${tcgatissuesourcesite}" = "6G" ]
then
dicomclinicaltrialsitename="University of Sao Paulo"
elif [ "${tcgatissuesourcesite}" = "6H" ]
then
dicomclinicaltrialsitename="Test For lcml"
elif [ "${tcgatissuesourcesite}" = "70" ]
then
dicomclinicaltrialsitename="ILSBio"
elif [ "${tcgatissuesourcesite}" = "71" ]
then
dicomclinicaltrialsitename="ILSBio"
elif [ "${tcgatissuesourcesite}" = "72" ]
then
dicomclinicaltrialsitename="NCH"
elif [ "${tcgatissuesourcesite}" = "73" ]
then
dicomclinicaltrialsitename="Roswell Park"
elif [ "${tcgatissuesourcesite}" = "74" ]
then
dicomclinicaltrialsitename="Swedish Neurosciences"
elif [ "${tcgatissuesourcesite}" = "75" ]
then
dicomclinicaltrialsitename="Ontario Institute for Cancer Research (OICR)"
elif [ "${tcgatissuesourcesite}" = "76" ]
then
dicomclinicaltrialsitename="Thomas Jefferson University"
elif [ "${tcgatissuesourcesite}" = "77" ]
then
dicomclinicaltrialsitename="Prince Charles Hospital"
elif [ "${tcgatissuesourcesite}" = "78" ]
then
dicomclinicaltrialsitename="Prince Charles Hospital"
elif [ "${tcgatissuesourcesite}" = "79" ]
then
dicomclinicaltrialsitename="Ontario Institute for Cancer Research (OICR)/Ottawa"
elif [ "${tcgatissuesourcesite}" = "80" ]
then
dicomclinicaltrialsitename="Ontario Institute for Cancer Research (OICR)/Ottawa"
elif [ "${tcgatissuesourcesite}" = "81" ]
then
dicomclinicaltrialsitename="CHI-Penrose Colorado"
elif [ "${tcgatissuesourcesite}" = "82" ]
then
dicomclinicaltrialsitename="CHI-Penrose Colorado"
elif [ "${tcgatissuesourcesite}" = "83" ]
then
dicomclinicaltrialsitename="CHI-Penrose Colorado"
elif [ "${tcgatissuesourcesite}" = "85" ]
then
dicomclinicaltrialsitename="Asterand"
elif [ "${tcgatissuesourcesite}" = "86" ]
then
dicomclinicaltrialsitename="Asterand"
elif [ "${tcgatissuesourcesite}" = "87" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "90" ]
then
dicomclinicaltrialsitename="ABS - IUPUI"
elif [ "${tcgatissuesourcesite}" = "91" ]
then
dicomclinicaltrialsitename="ABS - IUPUI"
elif [ "${tcgatissuesourcesite}" = "92" ]
then
dicomclinicaltrialsitename="Washington University - St. Louis"
elif [ "${tcgatissuesourcesite}" = "93" ]
then
dicomclinicaltrialsitename="Washington University - St. Louis"
elif [ "${tcgatissuesourcesite}" = "94" ]
then
dicomclinicaltrialsitename="Washington University - Emory"
elif [ "${tcgatissuesourcesite}" = "95" ]
then
dicomclinicaltrialsitename="Washington University - Emory"
elif [ "${tcgatissuesourcesite}" = "96" ]
then
dicomclinicaltrialsitename="Washington University - NYU"
elif [ "${tcgatissuesourcesite}" = "97" ]
then
dicomclinicaltrialsitename="Washington University - NYU"
elif [ "${tcgatissuesourcesite}" = "98" ]
then
dicomclinicaltrialsitename="Washington University - Alabama"
elif [ "${tcgatissuesourcesite}" = "99" ]
then
dicomclinicaltrialsitename="Washington University - Alabama"
elif [ "${tcgatissuesourcesite}" = "A1" ]
then
dicomclinicaltrialsitename="UCSF"
elif [ "${tcgatissuesourcesite}" = "A2" ]
then
dicomclinicaltrialsitename="Walter Reed"
elif [ "${tcgatissuesourcesite}" = "A3" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "A4" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "A5" ]
then
dicomclinicaltrialsitename="Cedars Sinai"
elif [ "${tcgatissuesourcesite}" = "A6" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "A7" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "A8" ]
then
dicomclinicaltrialsitename="Indivumed"
elif [ "${tcgatissuesourcesite}" = "AA" ]
then
dicomclinicaltrialsitename="Indivumed"
elif [ "${tcgatissuesourcesite}" = "AB" ]
then
dicomclinicaltrialsitename="Washington University"
elif [ "${tcgatissuesourcesite}" = "AC" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "AD" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "AF" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "AG" ]
then
dicomclinicaltrialsitename="Indivumed"
elif [ "${tcgatissuesourcesite}" = "AH" ]
then
dicomclinicaltrialsitename="International Genomics Consortium"
elif [ "${tcgatissuesourcesite}" = "AJ" ]
then
dicomclinicaltrialsitename="International Genomics Conosrtium"
elif [ "${tcgatissuesourcesite}" = "AK" ]
then
dicomclinicaltrialsitename="Fox Chase"
elif [ "${tcgatissuesourcesite}" = "AL" ]
then
dicomclinicaltrialsitename="Fox Chase"
elif [ "${tcgatissuesourcesite}" = "AM" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "AN" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "AO" ]
then
dicomclinicaltrialsitename="MSKCC"
elif [ "${tcgatissuesourcesite}" = "AP" ]
then
dicomclinicaltrialsitename="MSKCC"
elif [ "${tcgatissuesourcesite}" = "AQ" ]
then
dicomclinicaltrialsitename="UNC"
elif [ "${tcgatissuesourcesite}" = "AR" ]
then
dicomclinicaltrialsitename="Mayo"
elif [ "${tcgatissuesourcesite}" = "AS" ]
then
dicomclinicaltrialsitename="St. Joseph's Medical Center-(MD)"
elif [ "${tcgatissuesourcesite}" = "AT" ]
then
dicomclinicaltrialsitename="St. Joseph's Medical Center-(MD)"
elif [ "${tcgatissuesourcesite}" = "AU" ]
then
dicomclinicaltrialsitename="St. Joseph's Medical Center-(MD)"
elif [ "${tcgatissuesourcesite}" = "AV" ]
then
dicomclinicaltrialsitename="NCH"
elif [ "${tcgatissuesourcesite}" = "AW" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "AX" ]
then
dicomclinicaltrialsitename="Gynecologic Oncology Group"
elif [ "${tcgatissuesourcesite}" = "AY" ]
then
dicomclinicaltrialsitename="UNC"
elif [ "${tcgatissuesourcesite}" = "AZ" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "B0" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "B1" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "B2" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "B3" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "B4" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "B5" ]
then
dicomclinicaltrialsitename="Duke"
elif [ "${tcgatissuesourcesite}" = "B6" ]
then
dicomclinicaltrialsitename="Duke"
elif [ "${tcgatissuesourcesite}" = "B7" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "B8" ]
then
dicomclinicaltrialsitename="UNC"
elif [ "${tcgatissuesourcesite}" = "B9" ]
then
dicomclinicaltrialsitename="UNC"
elif [ "${tcgatissuesourcesite}" = "BA" ]
then
dicomclinicaltrialsitename="UNC"
elif [ "${tcgatissuesourcesite}" = "BB" ]
then
dicomclinicaltrialsitename="Johns Hopkins"
elif [ "${tcgatissuesourcesite}" = "BC" ]
then
dicomclinicaltrialsitename="UNC"
elif [ "${tcgatissuesourcesite}" = "BD" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "BF" ]
then
dicomclinicaltrialsitename="Cureline"
elif [ "${tcgatissuesourcesite}" = "BG" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "BH" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "BI" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "BJ" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "BK" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "BL" ]
then
dicomclinicaltrialsitename="Christiana Healthcare"
elif [ "${tcgatissuesourcesite}" = "BM" ]
then
dicomclinicaltrialsitename="UNC"
elif [ "${tcgatissuesourcesite}" = "BP" ]
then
dicomclinicaltrialsitename="MSKCC"
elif [ "${tcgatissuesourcesite}" = "BQ" ]
then
dicomclinicaltrialsitename="MSKCC"
elif [ "${tcgatissuesourcesite}" = "BR" ]
then
dicomclinicaltrialsitename="Asterand"
elif [ "${tcgatissuesourcesite}" = "BS" ]
then
dicomclinicaltrialsitename="University of Hawaii"
elif [ "${tcgatissuesourcesite}" = "BT" ]
then
dicomclinicaltrialsitename="University of Pittsburgh"
elif [ "${tcgatissuesourcesite}" = "BW" ]
then
dicomclinicaltrialsitename="St. Joseph's Medical Center-(MD)"
elif [ "${tcgatissuesourcesite}" = "C4" ]