Fix two bugs with `split_file_to_collection` #1358

simonbray · 2023-11-23T18:45:10Z

Allow chunksize to be greater than the number of records in the input file without raising the following error:

Traceback (most recent call last):
  File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py", line 281, in <module>
    main()
  File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py", line 52, in main
    split_by_record(args, in_file, out_dir, top, ftype)
  File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py", line 169, in split_by_record
    new_file = open(newfile_names[new_file_counter], "a")
IndexError: list index out of range

Allow an empty file to be split without raising the following error:

Traceback (most recent call last):
  File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py", line 281, in <module>
    main()
  File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py", line 52, in main
    split_by_record(args, in_file, out_dir, top, ftype)
  File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py", line 141, in split_by_record
    if sep_at_end and not last_line_matched:
UnboundLocalError: local variable 'last_line_matched' referenced before assignment

* allow chunksize to be greater than the number of records in the input file without failing * allow an empty file to be split without an error

* fix two bugs * allow chunksize to be greater than the number of records in the input file without failing * allow an empty file to be split without an error * bump version number

* woundhealing tool * added gitlab citation * fixing typo * remove unwanted file * add .shed.yml * added location tag in tests * clean test data * update shed.yml * Fix two bugs with `split_file_to_collection` (#1358) * fix two bugs * allow chunksize to be greater than the number of records in the input file without failing * allow an empty file to be split without an error * bump version number * Update Nanopolish to v0.14 (#1359) * fix lint error + version upgrade * Explicit untar of .tar.xz * Adapt tests to multithreading and code refactoring * Add RBPBench tool wrapper (#1360) * add wrapper files * add macros * modify select_rbps command * add fasta_indexes.loc * fix data_table and genome fasta path * new conda version with wrapper script * new conda version with wrapper script * remove python_template_version --------- Co-authored-by: Pavankumar Videm <[email protected]> * update rbpbench tool-data conf (#1362) * Add palette options to convert (#1364) * tool to query ftplinks from bioimage archive (#1345) * added tool to query ftplink from bia * multiple values * add help * add .shed.yml;remove multiple from param * remove wrong file * updates to the tool * Update biaftplink.xml * Update .shed.yml * Update biaftplink.xml --------- Co-authored-by: Yi Sun <[email protected]> Co-authored-by: Björn Grüning <[email protected]> * update v08 to fix meme version check error (#1366) * add mavedb data source tool (#1367) * add mavedb data source tool * Rename shed.yml to .shed.yml * change category * remove duplicate category * change tool ID to mavedb_importer * Update tools/mave_tools/mavedb/.shed.yml * Update mavedb.xml --------- Co-authored-by: Björn Grüning <[email protected]> * Change query params according mavedb requirements (#1368) * add mavedb data source tool * Rename shed.yml to .shed.yml * change category * remove duplicate category * change tool ID to mavedb_importer * Update tools/mave_tools/mavedb/.shed.yml * Update mavedb.xml * change param names for mavedb requirements * remove comment --------- Co-authored-by: Björn Grüning <[email protected]> Co-authored-by: Björn Grüning <[email protected]> * update to v081 (#1369) * gm updates (#1373) * gm updates * fix linting * Update compare.xml * Integrate another bioMLmodel (biomd0000001076) (#1371) * Add tool BIOMD0000001076 * update tool desc * update tool desc * add version * update * update test * remove print * add creator * update tool * update doi * Update tools/biomodelsML/biomodels_BIOMD0000001076.xml Co-authored-by: Björn Grüning <[email protected]> * remove xlsx * test bibtext to fix test * revert to type=doi * remove creator tag * update profile * update embedded script name --------- Co-authored-by: Björn Grüning <[email protected]> * fix typo in param documentation (#1374) * bump intarna 3.4.0 (#1378) * Updating tools/cpat from version 3.0.4 to 3.0.5 (#1379) Co-authored-by: planemo-autoupdate <[email protected]> * Updating tools/image_processing/graphicsmagick from version 1.3.40 to 1.3.42 (#1380) Co-authored-by: planemo-autoupdate <[email protected]> * Cool to hic (#1382) * adding first tested and working generated tool from https://github.com/fubar2/nftoolmaker It actually does work. Sort of. Hope this is useful to someone. * fixes suggested by bgruening for the PR - all adjustments will now apply to all future generated tools :) * add yara mapper ToolFactory - NOT from nf-core. Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq * small test files still work :) * single quotes for $runme - disappeared mysteriously :( * adding panaroo * Finally fixed the '$runme' suggestion and got the sanitisers not to. * fix profile="22.05" - need to update galaxyxml to fix this and the stdio replacement... * cool_to_hic tool * add cool_to_hic * cleanup other branch * fix bogus gfastats fix * fix gfastats * and again * fix yaml * fix so allows cool/mcool/scool - untested as I got no data... * need test data. * fixes from review * fix bogus help transition * Update .shed.yml * some small cleanups * Update .shed.yml * lets call it juicebox_hic --------- Co-authored-by: Björn Grüning <[email protected]> * Add juicebox_hic format and citation (#1383) * adding first tested and working generated tool from https://github.com/fubar2/nftoolmaker It actually does work. Sort of. Hope this is useful to someone. * fixes suggested by bgruening for the PR - all adjustments will now apply to all future generated tools :) * add yara mapper ToolFactory - NOT from nf-core. Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq * small test files still work :) * single quotes for $runme - disappeared mysteriously :( * adding panaroo * Finally fixed the '$runme' suggestion and got the sanitisers not to. * fix profile="22.05" - need to update galaxyxml to fix this and the stdio replacement... * add citation and link to github add juicebox_hic as the name of the output * fix branch again * update CI * Add TAPscan (#1357) * add tapscan tool * update shed file for this repo * add edam topic and creator * compress domains file * AGAT - Add new feature (functional annotation) (#1377) * add new feature * small modifications * some modification * small changes * small modifications * small modification * small modification --------- Co-authored-by: Bjoern Gruening <[email protected]> * update CI * update CI * Tapscan update (#1388) * add new updated tapscan files * update wrapper and test data * change fiji-mopholibj version * small cleanups * Update woundhealing.xml --------- Co-authored-by: Yi Sun <[email protected]> Co-authored-by: Simon Bray <[email protected]> Co-authored-by: Tunc Kayikcioglu <[email protected]> Co-authored-by: Michael Uhl <[email protected]> Co-authored-by: Pavankumar Videm <[email protected]> Co-authored-by: Helena <[email protected]> Co-authored-by: Björn Grüning <[email protected]> Co-authored-by: Polina Polunina <[email protected]> Co-authored-by: Björn Grüning <[email protected]> Co-authored-by: Anup Kumar <[email protected]> Co-authored-by: Linelle <[email protected]> Co-authored-by: Martin Raden <[email protected]> Co-authored-by: gxydevbot <[email protected]> Co-authored-by: planemo-autoupdate <[email protected]> Co-authored-by: Ross Lazarus <[email protected]> Co-authored-by: Saskia Hiltemann <[email protected]> Co-authored-by: Rlibouban <[email protected]>

simonbray added 2 commits November 23, 2023 18:41

fix two bugs

1649575

* allow chunksize to be greater than the number of records in the input file without failing * allow an empty file to be split without an error

bump version number

9ddb5f1

bgruening approved these changes Nov 23, 2023

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bgruening merged commit 37305ce into master Nov 23, 2023
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bgruening deleted the simonbray-patch-1 branch November 23, 2023 19:48

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Fix two bugs with `split_file_to_collection` #1358

Fix two bugs with `split_file_to_collection` #1358

simonbray commented Nov 23, 2023

Fix two bugs with split_file_to_collection #1358

Fix two bugs with split_file_to_collection #1358

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simonbray commented Nov 23, 2023

Fix two bugs with `split_file_to_collection` #1358

Fix two bugs with `split_file_to_collection` #1358