Page Comparison

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1. Obtaining Authentication Token (replace URL with the CanRisk website address):

   curl -k 'https://{URL}/auth-token/' \
-d '{"username": "XYZ", "password": "ABC"}' \
-H "Content-Type: application/json"

2. Running a breast cancer risk calculation with pedigree data as a JSON parameter (replace with the authentication token):
   
   CanRisk v1 format
   curl -k -XPOST -H "Content-Type: application/json"  -d '{"mut_freq":"UK","cancer_rates":"UK","user_id":"end_user_id","pedigree_data":"##CanRisk 21.0\n##menarche=14=12\n##oc_use=N\n##mht_use=N\n##BMI=2523.6201\n##alcohol=15.4\n##menopause=5244.8\n##height=165.1\n##TL=Y\n##endo=N180.34\n##FamID\tName\tTarget\tIndivID\tFathID\tMothID\tSex\tMZtwin\tDead\tAge\tYob\tBC1\tBC2\tOC\tPRO\tPAN\tAshkn\tBRCA1\tBRCA2\tPALB2\tATM\tCHEK2\tBARD1\tRAD51D\tRAD51C\tBRIP1\tER:PR:HER2:CK14:CK56\nd10nXXXX\t0tpa\t0\tm21\t0\t0\tM\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0:0\t0:0\t0:0\t0:0\t0:0\t0:0\t0:0\t0:0\t0:0\t0:0:0:0:0\nd10nXXXX\t1tma\t0\tf21\t0\t0\tF\t0\t0\t77t0\t1944t0\t67t0\t0\t0\t0\t0\t0\tSt0:N0\tSt0:N0\tSt0:N0\tSt0:N0\tSt0:N0\tSt0:N0\tSt0:N0\tS:N\tS:Nt0:0\t0:0:0:0:0\nd10nXXXX\t2tme\t1\tch1\tm21\tf21\tF\t0\t0\t54t42\t1967t1977\t0t38\t0\t0\t0\t0\t0\t0tS:0N\t0tS:0N\t0tS:0N\t0:0\t0:0tS:N\t0:0\t0:0\t0:0\t0:0\t0:0:0:0:0\n"}' https://{URL}/boadicea/ -H "Authorization: Token <TOKEN>"
   
   or with a pedigree file POSTed as a form
   curl -k -XPOST -F "mut_freq=UK" -F "cancer_rates=UK" -F "user_id=end_user_id" -F "pedigree_data=@/home/xxxx/d10.canrisk2canrisk" https://{URL}/boadicea/ -H "Authorization: <TOKEN>" -H "Accept: application/json"
   
   BOADICEA format
   curl -k -XPOST -H "Content-Type: application/json" \
-H 'Authorization: Token <TOKEN>' -H "Accept: application/json" \
-d '{"mut_freq": "UK", "cancer_rates":"UK", "user_id": "end_user_id",
pedigree_data":"BOADICEA import pedigree file format 4.0\nFamID\tName\tTarget\tIndivID\tFathID\tMothID\tSex\tMZtwin\tDead\tAge\tYob\t1stBrCa\t2ndBrCa\tOvCa\tProCa\tPanCa\tAshkn\tBRCA1t\tBRCA1r\tBRCA2t\tBRCA2r\tPALB2t\tPALB2r\tATMt\tATMr\tCHEK2t\tCHEK2r\tER\tPR\tHER2\tCK14\tCK56\nXXX1 \tF1 \t1\t1 \t3 \t2 \tF\t0\t0\t23 \t1993\t21 \t0 \t0 \t0 \t0 \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\nXXX1 \tF2 \t0\t2 \t0 \t0 \tF\t0\t0\t55 \t1961\t0 \t0 \t0 \t0 \t0 \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\nXXX1 \tM2 \t0\t3 \t0 \t0 \tM\t0\t0\t53 \t1963\t0 \t0 \t0 \t0 \t0 \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0"}' https://{URL}/boadicea/
   

3. Running a ovarian cancer risk calculation with a pedigree file POSTed as a form:
   curl -k -XPOST -F "mut_freq=UK" -F "cancer_rates=UK" \
-F "user_id=end_user_id" \
-F "pedigree_data=@/home/xxx/bwa4_pedigree_data.txt" \
https://{URL}/ovarian/ -H 'Authorization: Token <TOKEN>' -H "Accept: application/json"

4. Obtaining a PRS for breast cancer:
   curl -k -XPOST -F "bc_prs_reference_file=BCAC_313_PRS.prs" -F "sample_name=SampleA" \
-F "vcf_file=@/home/xxx/sample_BCAC_313.vcf" \
https://{URL}/vcf2prs/ \
-H 'Authorization: Token <TOKEN>' -H "Accept: application/json"

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