Update and add tests

tests/complex.test

@@ -38,7 +38,7 @@ rm ~/GitOmmix/$PATIENT -rf
 
 ../../git-ommix add sample --id blood
 ../../git-ommix add data -s blood --id blood data_blood
-../../git-ommix add result -s blood --use blood --id blood result_blood
+../../git-ommix add result -s blood --use blood --id blood --method ddPCR result_blood
 ../../git-ommix add diagnostic --revision_of LungT1 --use blood --id LungT1N1
 ../../git-ommix add diagnostic --revision_of GastricT2 --use blood --id GastricT2N1
 

tests/simple_complete.test

@@ -0,0 +1,28 @@
+#!/bin/env bash
+
+export PATIENT=simple_complete
+export DEBUG=verbose
+
+mkdir -p "tests/$PATIENT"
+cd "tests/$PATIENT"
+
+echo "a" > data
+echo "A" > result
+
+rm ~/GitOmmix/$PATIENT -rf
+
+../../git-ommix add patient --id $PATIENT
+
+../../git-ommix add sample --id sample
+
+../../git-ommix add data -s sample --id data data
+
+../../git-ommix add result -s sample --use data --id result result --provider "Bioinformatician <bioinf@hospital>" --method "Bioinformatics"
+
+echo "a2" > data
+echo "A2" > result
+../../git-ommix add data -s sample --revision_of data --id data2 data
+../../git-ommix add result -s sample --revision_of result --invalidate result --use data2 --id result2 result
+
+../../git-ommix add diagnostic --use result --id diag
+../../git-ommix add diagnostic --revision_of diag --use result2 --id diag2 --provider "MD <md@hospital>" --method "Clinical_acumen"

tests/simple_large.test

@@ -0,0 +1,40 @@
+#!/bin/env bash
+
+export PATIENT=simple_large
+export DEBUG=verbose
+export GIT_OMMIX_LARGE_FILES='largerthan=1Mb'
+
+mkdir -p "tests/$PATIENT"
+cd "tests/$PATIENT"
+
+base64 /dev/urandom | head -c 10MiB > data_a
+base64 /dev/urandom | head -c 10MiB > data_b
+echo "c" > data_c
+echo "A" > result_a
+echo "B" > result_b
+echo "C" > result_c
+
+rm ~/GitOmmix/$PATIENT -rf
+
+../../git-ommix add patient --id $PATIENT
+
+../../git-ommix add sample --id s_a
+../../git-ommix add data -s s_a --id d_a data_a
+../../git-ommix add result -s s_a --use d_a --id r_a result_a
+
+../../git-ommix add sample --id s_b
+../../git-ommix add data -s s_b --id d_b data_b
+../../git-ommix add result -s s_b --use d_b --id r_b result_b
+
+../../git-ommix add sample --id s_c
+../../git-ommix add data -s s_c --id d_c data_c
+../../git-ommix add result -s s_c --use d_c --id r_c result_c
+
+base64 /dev/urandom | head -c 10MiB > data_a
+echo "A2" > result_a
+
+../../git-ommix add data -s s_a --revision_of d_a --id d_a2 data_a
+../../git-ommix add result -s s_a --revision_of r_a --invalidate r_a --use d_a2 --id r_a2 result_a
+
+../../git-ommix add diagnostic --use r_a2 --use r_b --id diag1
+../../git-ommix add diagnostic --revision_of diag1 --use r_c --id diag1b