diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 8f71ff415aa60f09156048a4bf26759dee0c628a..8320a0d9454c0823b0a63bb5ab6f9b62834f5290 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -29,14 +29,15 @@ getData: parseMetadata: stage: unit script: - - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID - - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID - - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID - - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta - - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual - - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded - - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike - - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species + - rep=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID + - exp=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID + - study=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID + - endsMeta=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta + - endsManual=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual + - stranded=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded + - spike=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike + - species=singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species + - pytest -m pareseMetadata inferMetadata: stage: unit diff --git a/workflow/tests/test_parseMetadata.py b/workflow/tests/test_parseMetadata.py new file mode 100644 index 0000000000000000000000000000000000000000..a87d244ef752e39484572a51258f6474af786c69 --- /dev/null +++ b/workflow/tests/test_parseMetadata.py @@ -0,0 +1,24 @@ +#!/usr/bin/env python3 + +import pytest +import pandas as pd +from io import StringIO +import os + +test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ + '/../../' + +@pytest.mark.parseMetadata +def test_parseMetadata(): + assert os.path.exists(os.path.join(test_output_path, 'design.csv')) + assert readLine(os.path.join(test_output_path, 'design.csv')) + +def readLine(fileName): + data = False + file = open(fileName, "r") + for line in file: + if file.readlines() == "uk,se,no,no,Homo sapiens,Experiment_RID,Study_RID,Replicate_RID": + data = True + break + + return data