From b247d7e4b2a843928855075a8c9beb4be2e0325c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 31 Jul 2020 14:03:18 -0500
Subject: [PATCH] Move expected assigned into ci.yml #27
---
.gitlab-ci.yml | 25 +++++++++++++++++++------
workflow/tests/test_consistency.py | 22 ++++++++++------------
2 files changed, 29 insertions(+), 18 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2871cf7..b36504f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -133,13 +133,13 @@ integration_se:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 -with-dag dag.png --ci true
- - find . -type f -name "multiqc_data.json" -exec cp {} ./16-1ZX4_multiqc_data.json \;
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- output/qc/
- - 16-1ZX4_multiqc_data.json
+ - SE_multiqc_data.json
expire_in: 7 days
integration_pe:
@@ -148,21 +148,34 @@ integration_pe:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA -with-dag dag.png --ci true
- - find . -type f -name "multiqc_data.json" -exec cp {} ./Q-Y5JA_multiqc_data.json \;
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- dag.png
- output/qc/
- - Q-Y5JA_multiqc_data.json
+ - PE_multiqc_data.json
expire_in: 7 days
consistency:
stage: consistency
script:
- - grep -m 1 \"Assigned\":.[0-9] 16-1ZX4_multiqc_data.json | grep -oe '\([0-9.]*\)' > assignedSE.txt
- - grep -m 1 \"Assigned\":.[0-9] Q-Y5JA_multiqc_data.json | grep -oe '\([0-9.]*\)' > assignedPE.txt
+ - grep -m 1 \"Assigned\":.[0-9] SE_multiqc_data.json | grep -oe '\([0-9.]*\)' > assignedSE.txt
+ - grep -m 1 \"Assigned\":.[0-9] PE_multiqc_data.json | grep -oe '\([0-9.]*\)' > assignedPE.txt
+ - echo 7742416 > assignedExpectSE.txt
+ - echo 2599149 > assignedExpectPE.txt
- pytest -m consistencySE
- pytest -m consistencyPE
+ artifacts:
+ name: "$CI_JOB_NAME"
+ when: always
+ paths:
+ - SE_multiqc_data.json
+ - PE_multiqc_data.json
+ - assignedSE.txt
+ - assignedPE.txt
+ - assignedExpectSE.txt
+ - assignedExpectPE.txt
+ expire_in: 7 days
diff --git a/workflow/tests/test_consistency.py b/workflow/tests/test_consistency.py
index 4526aa9..7659290 100644
--- a/workflow/tests/test_consistency.py
+++ b/workflow/tests/test_consistency.py
@@ -7,26 +7,24 @@ import os
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
-test_sampleSE = '16-1ZX4'
-test_assignededSE = '7742416'
-test_samplePE = 'Q-Y5JA'
-test_assignedPE = '2599149'
@pytest.mark.consistencySE
def test_consistencySE():
- assert os.path.exists(os.path.join(test_output_path, test_sampleSE, '_multiqc_data.json'))
- assert readAssigned("assignedSE.txt",test_assignedSE)
+ assert os.path.exists(os.path.join(test_output_path, 'SE_multiqc_data.json'))
+ assert readAssigned("assignedSE.txt","assignedExpectSE.txt")
@pytest.mark.consistencyPE
def test_consistencyPE():
- assert os.path.exists(os.path.join(test_output_path, test_samplePE, '_multiqc_data.json'))
- assert readAssigned("assignedPE.txt",test_assignedPE)
+ assert os.path.exists(os.path.join(test_output_path, 'PE_multiqc_data.json'))
+ assert readAssigned("assignedPE.txt","assignedExpectPE.txt")
-def readAssgned(assignedFile,assigned):
+def readAssgned(fileAssigned,fileExpectAssigned):
data = False
- file = open(assignedFile, "r")
- line = file.readline()
- if line.strip() == assigned:
+ assigned = open(fileAssigned, "r")
+ expect = open(fileExpectAssigned, "r")
+ lineAssigned = assigned.readline()
+ lineExpect = expect.readline()
+ if lineAssigned.strip() == lineExpect.strip():
data = True
return data
--
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