diff --git a/tests/perl_tests.bats b/tests/perl_tests.bats index 09efc53..e73ee8c 100755 --- a/tests/perl_tests.bats +++ b/tests/perl_tests.bats @@ -92,7 +92,7 @@ setup() { @test "[atlas-experiment-metadata] Run condense_sdrf.pl" { - run condense_sdrf.pl -z -x $PWD/config/zooma_exclusions.yml -e E-MTAB-9898 -fi $PWD/tests/E-MTAB-9898/E-MTAB-9898.idf.txt -o $PWD + run condense_sdrf.pl -z -x $PWD/tests/zooma_exclusions_for_testing.yml -e E-MTAB-9898 -fi $PWD/tests/E-MTAB-9898/E-MTAB-9898.idf.txt -o $PWD echo "output = ${output}" [ "$status" -eq 0 ] } diff --git a/tests/zooma_exclusions_for_testing.yml b/tests/zooma_exclusions_for_testing.yml new file mode 100644 index 0000000..3d19b82 --- /dev/null +++ b/tests/zooma_exclusions_for_testing.yml @@ -0,0 +1,59 @@ +--- +# This file contains property types, values, and type-value pairs to be +# excluded from being mapped with Zooma. + +# Property types (exclude all values with this property type). +types_to_exclude: + - age + - age at diagnosis + - individual + - exercise + - physical activity + - replicate + - genotype + - clinical history + - clinical information + - biosource provider + - dose + - block + - body weight + - last follow up + - mass + - mitotic rate + - passage + - RNA interference + - sampling time point + - time + - tumor mass + - tumor size + - body mass index + - temperature + - gestational age + - survival time + - technical replicate + - initial time point + - sample lot number + - single cell identifier + - single cell quality + - submitted single cell quality + +# Property values (always exclude this value regardless of property type). +values_to_exclude: + - unknown + - not available + - not specified + - positive + - negative + - unrelated + - unclassified + +# Property type-value pairs. +type_value_pairs_to_exclude: + growth condition: + - cold + phenotype: + - resistant + phenotype: + - susceptible + phenotype: + - tolerant