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mvdbeek 9c7025aacd Replace GitHub raw content URLs with local mock HTTP server in tests 
Remove skip_if_github_down decorators from 20 tests across 9 files by
serving test data from the local mock HTTP server. Enhances the mock
server with file_path support, HEAD requests, and HTTP range requests
(206 Partial Content). For unit tests that run data_fetch.main()
directly, writes a file_sources.json with 127.0.0.0/24 in the
fetch_url_allowlist so the local server passes URI validation.
2026-03-13 12:19:55 +01:00
..
bwa_mem2_index
Fix directory uploads, use `__FETCH_DATA__` api
2025-02-25 18:10:10 +01:00
exports
Legacy history export tests and infrastructure.
2019-03-11 10:56:25 -04:00
highdicom
Employ more diverse DICOM test data
2026-01-19 17:56:27 +01:00
library
Fix library security functional tests.
2014-04-25 15:29:56 -04:00
rules
Rules - test case for apply rules tutorial.
2018-05-05 16:52:02 -04:00
users
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1.axt
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1.bam
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1.bed
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1.bed.spaces
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1.bedgraph
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1.bigbed
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1.bigwig
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1.csv
WIP: metadata validation.
2023-06-06 10:02:29 +02:00
1.ct
Add connectivity table test dataset
2022-11-18 18:24:54 -05:00
1.customtrack
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1.fasta
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1.fasta.gz
Add test-data
2019-04-07 23:15:35 +02:00
1.fastq
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1.fastqsanger
Add missing newline at end of some test files
2017-11-28 17:13:18 +00:00
1.fastqsanger.bz2
add fastq(*).bz2 datatypes and converters
2016-11-24 15:37:51 +01:00
1.fastqsanger.gz
Create a BaseFastq class and add test tools
2016-11-11 16:13:18 +01:00
1.fastqsolexa
Add missing newline at end of some test files
2017-11-28 17:13:18 +00:00
1.interval
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1.lav
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1.pileup
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1.RData
Add missing file from previous commit.
2015-09-23 15:10:06 +01:00
1.sam
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1.sam.gz
Configuration tests for the last few upload enhancements.
2017-08-12 07:13:05 -04:00
1.scf
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1.sff
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1.tabular
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1.tiff
Some more upload/sniff tests.
2018-05-24 10:31:28 -04:00
1.txt
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1.wig
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1.yaml
added sniffer for yaml
2021-09-20 13:07:20 -07:00
2.bed
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2.cram
Update pysam depedency to 0.20.0
2023-01-01 03:37:53 +00:00
2.csv
Use consistent naming for added test csv
2025-05-04 09:04:15 -04:00
2.fasta
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2.tabular
make 2nd column of 2.tabular test data unique values
2021-01-12 13:44:58 +01:00
2gen.fastq
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3.bam
More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16
2016-02-02 13:54:24 -05:00
3.bed
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3.maf
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3unsorted.bam
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4.bed
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4.bed.bz2
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4.bed.gz
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4.bed.zip
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5_Ig-like.gff
Cope with GFF3 as well as legacy GFF.
2017-06-26 11:16:06 +01:00
5.bed
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5.gff
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5.gff3
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6.bed
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7.bed
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8.bed
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9.bed
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11.tabular
Test dumping multiple="false" data_column param as json
2018-06-30 09:11:42 -07:00
454Score.pdf
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454Score.png
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a.tab
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a.txt
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asian_chars_1.txt
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bad.html.gz
Configuration tests for the last few upload enhancements.
2017-08-12 07:13:05 -04:00
bam_from_sam.bam
Add sam-to-bam conversion test tool
2016-11-16 22:01:47 +01:00
bam_native_from_sam.bam
add new test file
2017-12-10 15:23:26 +01:00
bcf_index_metadata_test.bcf
Added test for bcf index creation.
2015-04-28 13:45:33 -04:00
bcf_index_metadata_test.txt
Fix `metadata_bcf` framework test
2021-03-11 20:21:00 +00:00
biom1_metadata_test.txt
Add test for failing handling of BIOM1 metadata.
2016-06-07 12:02:09 -04:00
chebi_57262.v3k.mol
move test data for molecules converters
2021-06-29 14:06:39 +02:00
chopper.h5
Add support for visualizing HDF5 datasets. This contribution is split into two parts: the visualization plugin and backend changes. The client code integrates the h5web visualizer into Galaxy (https://h5web.panosc.eu). The backend changes add the ability to access the contents of a dataset without needing to read the whole dataset, which is essential for large files. It is based on the h5grove API (https://github.com/silx-kit/h5grove).
2023-05-04 20:48:15 -04:00
composite_output_expected_log
Improve composite output tool test.
2016-05-16 11:51:03 -04:00
drugbank_drugs.cml
move test data for molecules converters
2021-06-29 14:06:39 +02:00
drugbank_drugs.inchi
move test data for molecules converters
2021-06-29 14:06:39 +02:00
drugbank_drugs.mol
fix the to_inchi converter
2021-07-01 15:08:49 +02:00
drugbank_drugs.mol2
move test data for molecules converters
2021-06-29 14:06:39 +02:00
drugbank_drugs.sdf
move test data for molecules converters
2021-06-29 14:06:39 +02:00
drugbank_drugs.smi
move test data for molecules converters
2021-06-29 14:06:39 +02:00
empty.txt
add empty test file
2021-01-08 12:43:37 +01:00
example-bag.zip
Hierarchical upload API optimized for folders & collections.
2018-03-08 10:33:36 -05:00
filter1_in3.sam
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filter1_in5.tab
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filter1_in6.bed
add test case for fixed bug
2018-04-20 09:44:27 +02:00
filter1_inbad.bed
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filter1_test1.bed
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filter1_test2.bed
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filter1_test3.sam
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filter1_test4.bed
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filter1_test5.tab
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filter1_test6.bed
add test case for fixed bug
2018-04-20 09:44:27 +02:00
filter_labels_1.txt
Implement collection operation for filtering lists from a file.
2017-04-17 17:08:25 -04:00
GRCm38mm10_chr5_34761740-34912521.fa
Moved API tests to live under test/ rather than test/functional/. Removed test for DNAse flanked genes. Added test for UCSC table browser.
2014-04-30 15:35:57 -04:00
html_file.txt
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im1_uint8.png
Add functional test for image_diff
2024-02-27 19:22:33 +01:00
im1_uint8.tif
Add functional test for image_diff
2024-02-27 19:22:33 +01:00
im2_a.png
Add functional test for image_diff
2024-02-27 19:22:33 +01:00
im2_b.png
Add functional test for image_diff
2024-02-27 19:22:33 +01:00
im3_a.png
Fix bugs
2024-02-27 21:54:23 +01:00
im3_b_bool.tiff
Add test for content assertions with bool image
2026-01-03 11:59:13 +01:00
im3_b.tif
Fix bugs
2024-02-27 21:54:23 +01:00
im4_float.tif
Add float TIFF test case (fails with Pillow)
2024-03-19 22:03:34 +01:00
im5_uint8.tif
Add support for YXCS axes in asserts/image.py
2024-09-25 13:21:47 +02:00
im6_uint8.tif
Add test for ZCYX axes
2024-09-25 16:59:32 +02:00
im7_uint8.tif
Add test for ZYX axes
2024-09-25 17:11:26 +02:00
im8_uint16.tif
Make im8_uint16.tif tiled so we have a test for is_tiled=True
2025-03-25 14:36:42 +01:00
im9_multiseries.tif
Rename im9_multipage.tif -> im9_multiseries.tif
2025-03-25 14:36:42 +01:00
im_empty.tif
Add test for empty TIFF file (no metadata available)
2024-10-09 08:45:38 +02:00
input_taxonomy.biom1
Add test for failing handling of BIOM1 metadata.
2016-06-07 12:02:09 -04:00
joiner_header_in1.tab
join with header: add test
2017-06-26 15:11:51 +02:00
joiner_header_in2.tab
join with header: add test
2017-06-26 15:11:51 +02:00
joiner_out1.bed
join with header: add test-data output files
2017-06-26 15:11:39 +02:00
joiner_out2.bed
join with header: add test-data output files
2017-06-26 15:11:39 +02:00
joiner_out3.bed
join with header: add test-data output files
2017-06-26 15:11:39 +02:00
joiner_out4.bed
join with header: add test-data output files
2017-06-26 15:11:39 +02:00
joiner_out5.tab
join with header: add test
2017-06-26 15:11:51 +02:00
joiner_out6.tab
join with header: add a use case with a fill value
2017-06-26 15:12:21 +02:00
joiner_out7.tab
join with header: add a regression test
2017-06-26 15:12:15 +02:00
matrix.cool
add test-data for new hdf5 based tool test
2019-02-05 04:23:13 +01:00
MTBLS6.zip
Start writing upload test for isa-tab.
2018-06-07 12:07:35 +01:00
neostore.zip
added tests
2017-06-13 16:09:00 +02:00
new_element_sort_order.txt
Allow sorting collection elements based on file
2018-01-08 08:49:26 +01:00
new_labels_1.txt
Start work on a relabelling collection operation.
2017-04-13 23:11:49 -04:00
new_labels_2.txt
Add possibility to rename collection items from a tabular file
2017-04-13 23:11:49 -04:00
new_labels_3.txt
Fix linting and add test
2024-10-21 13:35:15 +02:00
new_labels_bad_1.txt
Various improvements to relabel from file collection operation.
2017-04-13 23:15:56 -04:00
new_labels_bad_2.txt
Fix relabel_from_file collection operation error handling if duplicate identifiers.
2017-04-17 13:12:57 -04:00
new_tags_1.txt
add a bit of docs to the add tags tool
2021-04-21 11:45:07 +02:00
phiX.fasta
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qname_sorted.bam
Add queryname sorted and input sorted datatypes
2018-02-22 19:59:55 +01:00
qualscores.qual454
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qualscores.qualsolid
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random-file
Configuration tests for the last few upload enhancements.
2017-08-12 07:13:05 -04:00
rgenetics.bed
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rgenetics.bim
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rgenetics.fam
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rgenetics.map
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rgenetics.ped
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rocrate-test.zip
Replace GitHub raw content URLs with local mock HTTP server in tests
2026-03-13 12:19:55 +01:00
safe_relative_symlink.tar
Add test case and use assertRaises()
2019-04-12 12:41:48 +01:00
safetar_with_symlink.tar
Fix security problems when extracting untrusted tar files.
2018-10-04 11:32:52 -04:00
sam_with_header.sam
use unsorted sam file for tests
2017-12-10 15:23:26 +01:00
selenium-test-notebook.ipynb
Update ruff to 0.6.1
2024-08-17 18:58:38 +01:00
shrimp_cs_test1.csfasta
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simple_line_alternative.txt
Add missing newline at end of some test files
2017-11-28 17:13:18 +00:00
simple_line_no_newline.txt
Fix Galaxy tool/workflow staging and refactor for reuse in Planemo.
2020-08-01 10:34:46 -04:00
simple_line_x2_windows.txt
Display dataset source transform information.
2021-11-12 11:42:21 -05:00
simple_line_x2.txt
Rework test framework testing and tools.
2014-04-28 11:48:51 -05:00
simple_line_x3.txt
Rework test framework testing and tools.
2014-04-28 11:48:51 -05:00
simple_line_x5.txt
Rework test framework testing and tools.
2014-04-28 11:48:51 -05:00
simple_line.txt
Rework test framework testing and tools.
2014-04-28 11:48:51 -05:00
simple_lines_both.txt
Add framework test tool that has both data and data_collection param - with test case.
2014-05-07 15:39:03 -05:00
simple_lines_interleaved.txt
Add missing newline at end of some test files
2017-11-28 17:13:18 +00:00
simple.xml
added functional test for <is_valid_xml>
2017-02-01 21:17:07 -06:00
sort_out1.bed
sort with header: add test-data for the state of art
2017-06-26 17:00:13 +02:00
sort_out2.bed
sort with header: add test-data for the state of art
2017-06-26 17:00:13 +02:00
sort_out3.tab
sort with header: add test-data for the state of art
2017-06-26 17:00:13 +02:00
sort_out4.sam
sort with header: done
2017-06-26 19:07:14 +02:00
test.vcf
Add VCF_BGZIP to VCF converter
2020-07-25 01:33:02 +01:00
test.vcf.gz
Added test file
2017-07-07 18:29:05 +03:00
testdir1.tar
SQUASH: Adding in other archive containers
2019-02-26 16:43:23 -07:00
testdir1.tar.gz
SQUASH: Adding in other archive containers
2019-02-26 16:43:23 -07:00
testdir1.zip
Hierarchical upload API optimized for folders & collections.
2018-03-08 10:33:36 -05:00
testdir.tar
Fix security problems when extracting untrusted tar files.
2018-10-04 11:32:52 -04:00
tinywga.bed
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tinywga.bim
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tinywga.fam
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tinywga.map
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tinywga.ped
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tinywga.ped.space_to_tab
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unsafe_relative_symlink.tar
Fix security problems when extracting untrusted tar files.
2018-10-04 11:32:52 -04:00
unsafe.tar
Fix security problems when extracting untrusted tar files.
2018-10-04 11:32:52 -04:00
unsafe.zip
Fix security problems when extracting untrusted tar files.
2018-10-04 11:32:52 -04:00