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|
#!/bin/sh -e
pkg=q2cli
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cd "${AUTOPKGTEST_TMP}"
export HOME=${HOME:-$PWD}
QZA_SAMPLE="/usr/lib/python3/dist-packages/q2_sample_classifier/tests/data/vaw.qza"
if [ ! -r "$QZA_SAMPLE" ]
then
cat >&2 <<-ERR
error: could not find sample data: $QZA_SAMPLE
Please install q2-sample-classifier
ERR
exit 1
fi
# TODO: same tests but with recommended dependencies!
# This is important since there is a huge change of behavior, and
# extensions may potentially break the qiime command as I am seeing with
# python3-sklearn at the moment.
set -v
# 0. the basics
qiime --version
# 1. help messages
qiime --help
qiime info --help
qiime tools --help
qiime dev --help
qiime tools citations --help
qiime tools export --help
qiime tools extract --help
qiime tools import --help
qiime tools inspect-metadata --help
qiime tools peek --help
qiime tools validate --help
qiime tools view --help
qiime dev export-default-theme --help
qiime dev import-theme --help
qiime dev refresh-cache --help
qiime dev reset-theme --help
# 2. info command
qiime info
# 3. tools commands
qiime tools
qiime tools citations "$QZA_SAMPLE" > citations.bib
file citations.bib | grep -qi 'bibtex'
qiime tools export --input-path "$QZA_SAMPLE" --output-path .
file feature-table.biom | grep -qi 'Hierarchical Data Format'
qiime tools extract --input-path "$QZA_SAMPLE"
cd 861451cc-c250-43fc-818a-ddc2159dbe25
md5sum --check checksums.md5
cd -
qiime tools inspect-metadata "$QZA_SAMPLE" --tsv > metadata.tsv
qiime tools inspect-metadata "$QZA_SAMPLE" --no-tsv
qiime tools peek "$QZA_SAMPLE"
qiime tools import \
--type 'FeatureTable[Frequency]' \
--input-path '861451cc-c250-43fc-818a-ddc2159dbe25/data' \
--output-path artifact.qza
file artifact.qza | grep -qi 'zip archive data'
qiime tools validate artifact.qza
# TODO test qiime tools view, missing Vizualization data at the moment,
# most likely available under the form of *.qvz files.
# 4. dev commands
qiime dev
qiime dev export-default-theme --output-path file.theme
diff file.theme - <<-END
[option]
fg = bright_blue
[type]
fg = green
[default_arg]
fg = magenta
[command]
fg = bright_blue
[emphasis]
underline = True
[problem]
fg = yellow
[warning]
fg = yellow
bold = True
[error]
fg = red
bold = True
[required]
underline = True
[success]
fg = green
END
qiime dev import-theme --theme file.theme
qiime dev refresh-cache
yes | qiime dev reset-theme
echo "\nRESULTS: OK\n"
|
