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Merged
merged 2 commits into from
Aug 4, 2023
Merged

don't leave summary file behind #47

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303d527
donot leave summary file behind
antgonza Jul 19, 2023
008b529
server.crt -> ci_rootca.crt
antgonza Aug 3, 2023
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6 changes: 3 additions & 3 deletions .github/workflows/qiita-plugin-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ jobs:
conda create -q --yes -n qtp-sequencing python=3.9 pip pigz quast fqtools
conda activate qtp-sequencing

export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
pip install -U pip
pip install .
Expand All @@ -90,7 +90,7 @@ jobs:
shell: bash -l {0}
run: |
conda activate qiita
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}

Expand Down Expand Up @@ -123,7 +123,7 @@ jobs:
COVER_PACKAGE: ${{ matrix.cover_package }}
run: |
conda activate qtp-sequencing
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg

nosetests --with-doctest --with-coverage -v --cover-package=qtp_sequencing
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2 changes: 2 additions & 0 deletions qtp_sequencing/summary.py
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Expand Up @@ -7,6 +7,7 @@
# -----------------------------------------------------------------------------

from hashlib import md5
from os import remove
from os.path import basename, join, dirname, exists
from base64 import b64encode
from io import BytesIO
Expand Down Expand Up @@ -163,6 +164,7 @@ def _summary_not_demultiplexed(artifact_type, filepaths):
fdata = f'{dirname(fp)}/qtp-sequencing-validate-data.csv'
if exists(fdata):
df = pd.read_csv(fdata, index_col=None)
remove(fdata)

if df is None:
cmd = f'fqtools count {fp}'
Expand Down