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461 Commits
Author SHA1 Message Date
Marius van den Beek 9415df899e Merge pull request #17422 from wm75/data_source_tools_fixes 
Fix data_source and data_source_async bugs
 2024-02-15 12:36:25 +01:00
Wolfgang Maier fd3a19afd2 Fix linting 2024-02-09 09:19:33 +01:00
Wolfgang Maier eef015d4e2 Preserve original request params as nested dict 
and use them in final POST request
 2024-02-09 09:14:20 +01:00
Wolfgang Maier 561bf92a1b Format import section with isort 2024-02-08 21:41:19 +01:00
Wolfgang Maier 3c178b559e Fix linting 2024-02-08 16:58:28 +01:00
Wolfgang Maier bd0f257452 Switch data_source.py to modern tool-provided metadata 
Allows moving all data source tools using the script to profile 20.09.
For more recent profiles data_source.py would have to work outside of
Galaxy's Python environment.
 2024-02-08 16:43:39 +01:00
Wolfgang Maier c554023c5e Simply exit on errors 2024-02-08 15:33:33 +01:00
Wolfgang Maier 387c9f0c87 Start modernizing data_source.py script 
- Drop support for very old format of specifying execution params in a
  tabular file instead of a json one
- Use O_TRUNC to discard previous file contents instead of opening for
  writing, then closing
- Do not silently ignore non-integer values for max_file_size
 2024-02-08 15:23:03 +01:00
mvdbeek f9e3380a48 Drop unreachable compression extension stripping 
Not going to do further work on upload1, so not fixing this.
 2024-02-01 10:32:03 +01:00
mvdbeek 33ccacf77a Fix upload1 tool 2023-12-01 19:57:38 +01:00
Yakubov, Sergey c30a4c06c2 Replace file_name property with get_file_name function 2023-11-08 17:17:14 -05:00
Nicola Soranzo d258e5791e Fix new E721 errors from ruff 0.0.290 2023-09-20 01:43:40 +01:00
mvdbeek 0bac18d0bb Drop old run_as_real_user check 2023-06-06 18:52:32 +02:00
Nicola Soranzo 64af46c4ae Fix new B018 errors raised by ruff 0.0.260 2023-04-13 16:53:01 +01:00
Nicola Soranzo 30f60493c3 Format Python code with black 23.1.0 
with manual fixes to 3 files to make them compatible with black 22.12.0 .

We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
 2023-02-01 23:51:03 +00:00
Nicola Soranzo 3bca59b8e9 Remove uses of six library 
Remove unused file `tools/data_source/hbvar_filter.py` .
 2022-06-10 10:32:00 +01:00
John Chilton 37892dcabc Refactor sniff.stream_url_to_file to galaxy.files.uris. 
The value of this can be seen for instance in unpack_tar_gz_archive - which should have nothing to do with datatypes and now doesn't need to load the whole datatypes module.

Use this in workflows API to allow downloading workflow files from configured URIs.
 2022-05-21 17:22:41 -04:00
mvdbeek 4ca0d63c3b Merge branch 'release_22.01' into dev 2022-05-04 17:10:29 +02:00
mvdbeek da1dd283f3 Add @TOOL_VERSION@ token for NCBI Datasets Genomes 2022-05-04 16:34:09 +02:00
mvdbeek 5c014d2048 Bump ncb-datasets-cli dependency to 13.14.0 
Fixes

```
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x10 pc=0x8a3fea]

goroutine 1 [running]:
main/datasets/datasets.downloadData(0xc000010380, 0x0, 0x0, 0x0, 0x7ffe36956316, 0x62, 0xffffffffffffffff, 0x0, 0x0)
	src/datasets/datasets/Download.go:41 +0xea
main/datasets/datasets.downloadAssembly(0xc000069100, 0x7ffe36956316, 0x62, 0x8ef4a0, 0xc000010298)
	src/datasets/datasets/DownloadGenome.go:63 +0x294
main/datasets/datasets.glob..func1(0xd9d080, 0xc000074730, 0x0, 0x5, 0x0, 0x0)
	src/datasets/datasets/Download.go:106 +0x2a7
github.com/spf13/cobra.(*Command).execute(0xd9d080, 0xc0000746e0, 0x5, 0x5, 0xd9d080, 0xc0000746e0)
	external/com_github_spf13_cobra/command.go:842 +0x472
github.com/spf13/cobra.(*Command).ExecuteC(0xd9cde0, 0x4686c5, 0xc000000180, 0x200000003)
	external/com_github_spf13_cobra/command.go:950 +0x375
github.com/spf13/cobra.(*Command).Execute(...)
	external/com_github_spf13_cobra/command.go:887
main/datasets/datasets.Execute()
	src/datasets/datasets/root.go:444 +0x31
main.main()
	src/cmd/datasets/main.go:10 +0x25
```
 2022-05-03 17:13:16 +02:00
Dannon Baker 03351d2a9f Apply black to tools as well 2022-02-03 09:12:13 -05:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
Nicola Soranzo 30337fbd94 Merge branch 'release_21.09' into dev 2021-11-23 13:30:36 +00:00
Marius van den Beek 90c2f31cb4 Don't add ca-ceritificates to tool requirements 
ca-certificates is now part of the ncbi-datasets-cli conda package
 2021-11-18 17:17:19 +01:00
Marius van den BeekandHelena f1986a481f Export just once 
Thanks!

Co-authored-by: Helena <hxr@hx42.org>
 2021-11-17 15:28:07 +01:00
mvdbeek 47120ca48f Fix containerized NCBI Datasets Genomes data source tool 2021-11-12 20:17:34 +01:00
John Chilton 4fe7109ab1 Track transformations applied during uploads. 2021-11-12 10:21:55 -05:00
John Chilton 8643daf1dd Attempt to type more upload related things. 2021-11-05 11:58:53 -04:00
mvdbeek 63e25b20f4 Set profile version of ncbi_datasets so it can run containerized 2021-10-31 16:28:38 +01:00
mvdbeek a10645d664 Use ncbi_genome_dataset.zip format 2021-09-13 12:05:53 +02:00
mvdbeek 947832541b Use version_command tag, single quotes for paths 2021-09-09 19:15:19 +02:00
Brad Holmes 8b77edbb53 Implement NCBI Datasets Genome Dataset server 2021-09-09 12:28:02 -04:00
Brad Holmes 0186289a63 Improve wording and target URL for NCBI Datasets Genomes link tool 2021-09-08 11:00:39 -04:00
mvdbeek 44ee10e93d Add json_param as possible parameter type 2021-08-31 16:49:54 +02:00
mvdbeek 278b1422fd Replace taxon with generic file parameter 2021-08-31 16:45:56 +02:00
mvdbeek 58e530e65a Use separate dehydrated.zip datatype subclass 2021-08-31 16:45:56 +02:00
mvdbeek e552f79b49 Add dependency on ncbi-datasets-cli 2021-08-31 16:45:55 +02:00
mvdbeek e0855b7d9a Add simple NCBI datasets source tool 2021-08-31 16:45:55 +02:00
mvdbeek 11363a013e Merge branch 'release_21.05' into dev 2021-06-24 12:22:55 +02:00
mvdbeek 4dabdf4282 Add socket timeout for urlopen 2021-06-20 14:04:23 +02:00
mvdbeek 9d45e2b0db Remove unused legacy controller things 2021-06-19 16:28:56 +02:00
John Chilton 2a0474730b Rev mypy. 2021-04-23 14:49:53 -04:00
mvdbeek f85086f6d5 Assert file:// urls are not being downloaded without explicit handling 
And allow file_sources in add_composite_file to_path
 2021-04-20 16:24:41 +02:00
Matthias Bernt cfd0f02c56 add and use a new util foo is_url 2021-04-12 16:13:52 +02:00
Nicola Soranzo d26b3d9848 Fix all E203, E741 and W504 flake8 errors 2021-01-18 10:35:41 +00:00
Nicola Soranzo 452aba9ee3 Fix remaining issues reported by bugbear; add it to flake8 reqs 2021-01-16 05:58:15 +00:00
Marius van den Beek af4d041dc9 Merge pull request #10592 from hexylena/edam-tool-panel 
EDAM tool panel
 2021-01-08 18:56:28 +01:00
Nicola Soranzo 970c23015e Remove commented lines 2021-01-07 20:42:27 +00:00
M Bernt ea88a8a5a3 allow empty file uploads 2021-01-07 19:38:53 +01:00
Helena Rasche 646b133bb3 Add EDAM topics to unannotated tools 2020-10-30 17:59:45 +01:00