Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

add test showing error during import job preparion with latest Galaxy #51

Merged
merged 7 commits into from
Jan 29, 2024
Merged

add test showing error during import job preparion with latest Galaxy #51

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
7ae4b68
add test showing error during import job preparion
bernt-matthias Jan 22, 2024
d5569e2
working test for 23.0
bernt-matthias Jan 23, 2024
87b8fb1
hack showing that staging_path_and_source_path
bernt-matthias Jan 23, 2024
8d265c5
add test for laneless
bernt-matthias Jan 24, 2024
ff65965
Revert "hack showing that staging_path_and_source_path"
bernt-matthias Jan 26, 2024
9a15f2b
better fix
bernt-matthias Jan 26, 2024
f3a8ece
bump tool version
bernt-matthias Jan 26, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ on:
# MODIFIED END
env:
GALAXY_FORK: galaxyproject
GALAXY_BRANCH: release_22.05 # MODIFIED
GALAXY_BRANCH: release_23.1 # MODIFIED
MAX_CHUNKS: 40
jobs:
setup:
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/pr.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ on:
# MODIFIED END
env:
GALAXY_FORK: galaxyproject
GALAXY_BRANCH: release_22.05 # MODIFIED
GALAXY_BRANCH: release_23.1 # MODIFIED
MAX_CHUNKS: 10 # MODIFIED
jobs:
# the setup job does two things:
Expand Down
67 changes: 63 additions & 4 deletions tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ This tool was automatically generated by:
for:
qiime2 (version: 2023.5.1)
-->
<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause">
<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.3" profile="22.05" license="BSD-3-Clause">
<description>Import data into a QIIME 2 artifact</description>
<requirements>
<container type="docker">quay.io/qiime2/core:2023.5</container>
Expand All @@ -20,6 +20,7 @@ for:
<configfile name="inputs">&lt;%
# This is an exercise in cheating the Cheetah
import json
from collections.abc import MutableMapping

def expand_collection(collection):
# All of this work is just to extract the
Expand All @@ -28,7 +29,7 @@ def expand_collection(collection):
for d in collection]

def stringify(obj):
if type(obj) is dict:
if isinstance(obj, MutableMapping):
new = {}
for key, value in obj.items():
if (key.startswith('__') and key.endswith('__')
Expand Down Expand Up @@ -969,7 +970,7 @@ write(json.dumps(inputs))
<option value="individual">Associate individual files</option>
</param>
<when value="collection">
<param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
<param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
<conditional name="__q2galaxy__GUI__cond__add_ext__">
<param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
<option value="no">No, use element identifiers as is</option>
Expand Down Expand Up @@ -1146,7 +1147,7 @@ write(json.dumps(inputs))
<option value="individual">Associate individual files</option>
</param>
<when value="collection">
<param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/>
<param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/>
<conditional name="__q2galaxy__GUI__cond__add_ext__">
<param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
<option value="no">No, use element identifiers as is</option>
Expand Down Expand Up @@ -1657,6 +1658,64 @@ write(json.dumps(inputs))
<outputs>
<data name="imported_data" format="qza" from_work_dir="imported_data.qza"/>
</outputs>
<tests>
<test>
<conditional name="import_root">
<param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/>
<conditional name="__q2galaxy__GUI__cond__format__">
<param name="format" value="CasavaOneEightLanelessPerSampleDirFmt"/>
<section name="import_sequences">
<conditional name="__q2galaxy__GUI__cond__sequences__">
<param name="__q2galaxy__GUI__select__picker__" value="collection"/>
<param name="elements">
<collection type="list">
<element name="YY_S49_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" />
<element name="YY_S49_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" />
</collection>
</param>
<conditional name="__q2galaxy__GUI__cond__add_ext__">
<param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/>
<param name="ext" label="fastq.gz"/>
</conditional>
</conditional>
</section>
</conditional>
</conditional>
<output name="imported_data">
<assert_contents>
<has_size min="1"/>
</assert_contents>
</output>
</test>
<test>
<conditional name="import_root">
<param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/>
<conditional name="__q2galaxy__GUI__cond__format__">
<param name="format" value="CasavaOneEightSingleLanePerSampleDirFmt"/>
<section name="import_sequences">
<conditional name="__q2galaxy__GUI__cond__sequences__">
<param name="__q2galaxy__GUI__select__picker__" value="collection"/>
<param name="elements">
<collection type="list">
<element name="YY_S49_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" />
<element name="YY_S49_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" />
</collection>
</param>
<conditional name="__q2galaxy__GUI__cond__add_ext__">
<param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/>
<param name="ext" label="fastq.gz"/>
</conditional>
</conditional>
</section>
</conditional>
</conditional>
<output name="imported_data">
<assert_contents>
<has_size min="1"/>
</assert_contents>
</output>
</test>
</tests>
<help>
QIIME 2: tools import
=====================
Expand Down
Binary file added tools/suite_qiime2_core__tools/test-data/YY/YY_S49_R1_001.fastq.gz
View file
Open in desktop
Binary file not shown.
Binary file added tools/suite_qiime2_core__tools/test-data/YY/YY_S49_R2_001.fastq.gz
View file
Open in desktop
Binary file not shown.
Loading