Re: [galaxy-dev] Galaxy code: data libraries
I think the relevant piece of code is in templates/webapps/galaxy/ibrary/common/common.mako. The lines %if not link_data_only or link_data_only == 'copy_files': Copy files into Galaxy Link to files without copying into Galaxy %else: Copy files into Galaxy Link to files without copying into Galaxy %endif could probably be modified a few different ways. I have not really tried this but if you really do want to eliminate copying all together you can probably just replace it with: Link to files without copying into Galaxy Alternatively, you could probably modify the default to be linking by replacing this with: %if link_data_only and link_data_only == 'copy_files': Link to files without copying into Galaxy Copy files into Galaxy %else: Link to files without copying into Galaxy Copy files into Galaxy %endif Hope this helps! -John On Thu, Nov 28, 2013 at 6:56 AM, Misharl mon wrote: > Hi eveybody, > > Is there a way in the code of Galaxy, to force the users to use "link to > files without copying in Galaxy" by hiding the "copy files into Galaxy" > option in the interface, when they add datasets in their library? We want to > avoid users to click on "copy files into Galaxy" by mistake. > > > Thanks in advance to all > > Mish > > > > > > > > Hi everybody, > > > In my lab, after upgrading our Galaxy instance to the latest version, we > have a problem with displaying tabular files. > > Any idea from where the problem can come? > > Thanks in advance to all. > > Mish > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > > > ___ Please keep all > replies on the list by using "reply all" in your mail client. To manage your > subscriptions to this and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified > search at: http://galaxyproject.org/search/mailinglists/ > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] character set encoding metadata
Excellent talk! I watched it earlier in the week - I feel like it has already made me a better programmer. That said, I am not sure I have any real great answers for you. The least disruptive thing you could do is add a new metadata element to the Text datatype (hopefully most text based datatypes are sub-typing that). Intuitively this makes sense to because this attribute is only valid for text-based datatypes not all datasets or hdas. How to set that is not entirely clear to me though - for any given datatype you could override or modify set_meta to do this - but I don't know how I would get that input from the user into the set_meta procedure. Depending on your use cases - this next suggestion might not be viable - but the easiest and most robust thing to do is probably not track what character-set something is but instead assume it is all UTF-8 (ISO-8859-1 and ASCII files are already right). Then modify the upload form(s) to have new option to convert incoming input files from a supplied character set into UTF-8. Then in tools/data-source/upload.py check for this new character set parameter and use a tool such as recode or icov to do this conversion during the upload/dataset creation process. I am making no promises, but if you were hoping to get these changes included in Galaxy this is what I would be most willing to consider. Getting Galaxy to track, process, and serve a bunch of different character sets would be a real challenge - allowing for the assumption that it is all just UTF-8 though however is much easier. It is a variant on the advice given in the video you sent along as well, instead of converting everything to unicode as soon as possible though, you would be converting everything to UTF-8 as soon as possible. Hope this helps. -John On Sun, Nov 24, 2013 at 5:22 PM, Robert Baertsch wrote: > Does galaxy have an official place to store the character set for a text file? > > I'm thinking of modifying the upload tool to prompt for the character set, > since it cannot be sniffed. > > It should go in the hda/ldda metadata hash or extended_metadata for the > dataset. > > Any opinions? > > BTW: everyone should watch this talk on unicode. > > http://bit.ly/unipain > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
Hi Peter, On Nov 28, 2013, at 12:56 PM, Peter Cock wrote: > On Thu, Nov 28, 2013 at 5:30 PM, Peter Cock wrote: >> >> Thank you - that alerted me to a missing set of out output files for a >> recently added test, hopefully addressed in this revision: >> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045 >> >> But its not all good news - another test is now listed as failing, but with >> missing test results: >> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f >> > > Another little oddity, the three test results for mira_bait.xml are missing > (although it correctly tells me mira_4_0_mapping and mira_4_0_de_novo > have no tests): > > http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler/302d13490b23 Here is what I am seeing for the missing tests. Is this information ot correct? If not, what is incorrect? Automated tool test results Test runs 2013-11-28 13:02:42 Automated test environment Time tested: 2013-11-28 13:02:42 System: Architecture: Python version: Galaxy revision: Galaxy database version: Tool shed revision: 11549:5aede225ebef Tool shed database version: 21 Tool shed mercurial version: 2.2.3 Tools missing tests or test data Tool id: mira_4_0_mapping Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2 Missing components: Functional test definitions missing for mira_4_0_mapping. Tool id: mira_4_0_de_novo Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo/0.0.2 Missing components: Functional test definitions missing for mira_4_0_de_novo. 2013-11-28 11:29:49 Automated test environment Time tested: 2013-11-28 11:29:49 System: Architecture: Python version: Galaxy revision: Galaxy database version: Tool shed revision: 11549:5aede225ebef Tool shed database version: 21 Tool shed mercurial version: 2.2.3 Tools missing tests or test data Tool id: mira_4_0_mapping Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2 Missing components: Functional test definitions missing for mira_4_0_mapping. Tool id: mira_4_0_de_novo Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo/0.0.2 Missing components: Functional test definitions missing for mira_4_0_de_novo. > > Peter > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy-dev Digest, Vol 89, Issue 32
Hi folks,
Has someone seen this behaviour? I'm trying to do a once-over maintenance
cleanup of our galaxy installs. The galaxy account is getting emailed nightly
with an error which is happening when it gets to delete_datasets.sh cron task,
basically:
AttributeError: 'NoneType' object has no attribute 'dataset_id'
1) Now I found this thread:
http://dev.list.galaxyproject.org/Error-when-running-cleanup-datasets-py-td4656392.html
- and implemented that solution which removed some of the preceding log error
info, but this related error remains:
sh ... /production2/galaxy-dist/scripts/cleanup_datasets/delete_datasets.sh
Traceback (most recent call last):
File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in
if __name__ == "__main__": main()
File "./scripts/cleanup_datasets/cleanup_datasets.py", line 126, in main
delete_datasets( app, cutoff_time, options.remove_from_disk, info_only
= options.info_only, force_retry = options.force_retry )
File "./scripts/cleanup_datasets/cleanup_datasets.py", line 301, in
delete_datasets
dataset_ids.append( ldda.dataset_id )
AttributeError: 'NoneType' object has no attribute 'dataset_id'
In the delete_datasets.log it shows that this is last log line before error
occurs:
# Processing LibraryDataset id: 14201
2) So to recap, in step 1 I found:
galaxydb_prod2=> select * from library_dataset where
library_dataset_dataset_association_id is null;
id | library_dataset_dataset_association_id | folder_id | order_id |
create_time |update_time | name | info |
deleted | purged
---++---+--+++---+--+-+
14201 || 544 | 18 |
2012-11-01 17:26:23.877817 | 2012-11-01 17:26:35.787611 | NC_006625.fna |
| f | f
(1 row)
And so I ran the recommended query, "update library_dataset set folder_id =
null where id=14201;" and that seemed to have a positive effect.
For what its worth,
galaxydb_prod2=> select * from library_dataset_dataset_association where
id = 14201
galaxydb_prod2-> ;
id | library_dataset_id | dataset_id |create_time |
update_time| copied_from_history_dataset_association_id |
copied_from_library_dataset_dataset_association_id | name | info |
blurb | peek | extension | metadata | parent_id | designation | deleted
| visible | user_id | message | state | tool_version
---++++--+++---+--+---+--+---+--+---+-+-+-+-+-+---+--
14201 | 14201 | 14706 | 2012-11-01 17:26:28.593081 |
2012-11-01 17:26:30.8649 ||
| NC_006625.fna | |
| | auto | {"dbkey": ["?"]} | | | f | t
| 1 | | |
(1 row)
The last thing I'd say is that this 'NC_006625.fna' item doesn't show up in the
website front-end's sole Data Library list of folders and sub-items, nor does
it show in the deleted list. It seems orphaned but I'd rather someone had
confident advice on this one. My novice attempt at surgery would probably lead
to lots of blood on the table.
Help much appreciated!
Damion
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed
On Thu, Nov 28, 2013 at 5:30 PM, Peter Cock wrote: > > Thank you - that alerted me to a missing set of out output files for a > recently added test, hopefully addressed in this revision: > http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045 > > But its not all good news - another test is now listed as failing, but with > missing test results: > http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f > Another little oddity, the three test results for mira_bait.xml are missing (although it correctly tells me mira_4_0_mapping and mira_4_0_de_novo have no tests): http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler/302d13490b23 Peter ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
On Thu, Nov 28, 2013 at 5:16 PM, Greg Von Kuster wrote: > Hello Peter, > > On Nov 28, 2013, at 4:56 AM, Peter Cock wrote: > > Hi Greg, > > Things look much better today on the Test Tool Shed, with > most of my tools under "Latest revision: all tool tests pass" > again - or as expected a few under "Latest revision: missing > tool tests" due to not yet having full test coverage. > > I've only spotted one glitch so far, missing test results for: > http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4 > > > The above repository was not displaying the missing test components due to > a problem in the previous test runs which I fixed yesterday. The problem > resulted in test result data that could not be displayed. > Perhaps a fall back error message would be useful here (e.g. "Test failed but unable to display data"), which would be better than the "missing" test results? > When I introduced the new feature for stroing and displaying multiple test > runs, I decided to not eliminate the bad data, but just to let enough test > runs proceed that the bad data would eventually be eliminated. I forced > new test runs, and now things should be displaying as expected. Here is > the display for the above repository for the latest run this morning: > > Thank you - that alerted me to a missing set of out output files for a recently added test, hopefully addressed in this revision: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045 But its not all good news - another test is now listed as failing, but with missing test results: http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f Thanks, Peter ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
Hello Peter, On Nov 28, 2013, at 4:56 AM, Peter Cock wrote: > On Wed, Nov 27, 2013 at 9:02 PM, Greg Von Kuster wrote: >> >> Hello Peter, >> >> I've done a significant amount of re-engineering of the >> Tool Shed's install and test framework over the past 2 >> weeks, so the results you are seeing are probably a >> reflection of some broken peices during the time frame >> in which I was making changes. I believe I have most >> of the things ironed out in 11545:32205f911e74 which >> is now running on the test tool shed. >> >> We will be performing some test runs of thie new >> framework over the long weekend, so more correct >> test results should hopefully be showing up for yours >> and other repositories. >> > > Hi Greg, > > Things look much better today on the Test Tool Shed, with > most of my tools under "Latest revision: all tool tests pass" > again - or as expected a few under "Latest revision: missing > tool tests" due to not yet having full test coverage. > > I've only spotted one glitch so far, missing test results for: > http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4 The above repository was not displaying the missing test components due to a problem in the previous test runs which I fixed yesterday. The problem resulted in test result data that could not be displayed. When I introduced the new feature for stroing and displaying multiple test runs, I decided to not eliminate the bad data, but just to let enough test runs proceed that the bad data would eventually be eliminated. I forced new test runs, and now things should be displaying as expected. Here is the display for the above repository for the latest run this morning: Automated tool test results Automated test environment Time tested: 2013-11-28 11:29:38 System: Architecture: Python version: Galaxy revision: Galaxy database version: Tool shed revision: 11549:5aede225ebef Tool shed database version: 21 Tool shed mercurial version: 2.2.3 Tools missing tests or test data Tool id: ncbi_rpstblastn_wrapper Tool version: 0.0.22 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.0.22 Missing components: Functional test definitions missing for ncbi_rpstblastn_wrapper. Tool id: ncbi_blastdbcmd_info Tool version: 0.0.22 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastdbcmd_info/0.0.22 Missing components: Functional test definitions missing for ncbi_blastdbcmd_info. Tool id: ncbi_makeblastdb Tool version: 0.0.22 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_makeblastdb/0.0.22 Missing components: One or more test files are missing for tool ncbi_makeblastdb: four_human_proteins.fasta.log Tool id: ncbi_blastdbcmd_wrapper Tool version: 0.0.22 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.0.22 Missing components: Functional test definitions missing for ncbi_blastdbcmd_wrapper. Tool id: ncbi_rpsblast_wrapper Tool version: 0.0.22 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.0.22 Missing components: Functional test definitions missing for ncbi_rpsblast_wrapper. > > I saw a recent commit on galaxy-central addressing a test > time display - that may have explained why yesterday > the Test Tool Shed was claiming the test results were > from four days ago. Yes, there is a flag that can be set for testing a repository that eliminates it from being tested by the install and test framework. This flag had been inappropriately set on many repositories, including the one to which you are referring. That problem has been corrected, so testing should be more stable. > >> I've also enhanced the "Tool test results" components to store a >> configurable number of test runs instead of just 1. The test tool >> shed is configured to store 5 test runs. So from here on you'll >> begin to see multiple containers in the Tool test results container >> - something like this: > > That sounds useful when the framework itself is changing > rapidly, or if there is anything stochastic in a test failure. > > Presumably this shows the last 5 tests against the current > tool revision? It displays the last 5 test runs against any installable revision that is tested. We are currently restricting testing to the latest installable revision, so the 5 test runs will be displayed for that revision only. > > Thank Greg, and enjoy Thanksgiving, Thanks Peter, your too! > > Peter ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailingli
[galaxy-dev] Including descriptions etc in extended BLAST+ tabular output
Hello all, FAO: Administrators of local Galaxy instances using the NCBI BLAST+ wrappers. Over on the galaxy_blast repository I have been updating the NCBI BLAST+ wrappers (including unit tests) to work with the current release, NCBI BLAST+ 2.2.28 (aka BLAST 2.2.28+): https://github.com/peterjc/galaxy_blast The initial set of changes is now on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus This includes a workaround for a known regression in the makeblastdb tool dealing with duplicated identifiers: https://github.com/peterjc/galaxy_blast/commit/349e31c6cec4429c5523fde5975e28e399e0dfb1 In terms of end-user features, the big improvement in the BLAST+ 2.2.28 release was the ability to get the BLAST match descriptions in the tabular output, and other fields: http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html staxids means Subject Taxonomy ID(s), separated by a ';' sscinames means Subject Scientific Name(s), separated by a ';' scomnames means Subject Common Name(s), separated by a ';' sblastnames means Subject Blast Name(s), separated by a ';' (in alphabetical order) sskingdoms means Subject Super Kingdom(s), separated by a ';' (in alphabetical order) stitle means Subject Title salltitles means All Subject Title(s), separated by a '<>' sstrand means Subject Strand qcovs means Query Coverage Per Subject qcovhsp means Query Coverage Per HSP On this branch I am including the new salltitles field as the 25th column in the extended BLAST tabular output offered within the Galaxy interface: https://github.com/peterjc/galaxy_blast/tree/c25 However, I'm not so sure about the taxonomy fields. Since (thus far) they are not available via the XML, I am leaning to introducing a third tabular mode, e.g. * Standard 12 columns (can convert from XML) * Extended 25 columns (can convert from XML) * Extended also with taxonomy (cannot currently convert from XML) Instead, we could offer a pick-you-own columns route (in all the primary BLAST tools, handled via macros)?: * Standard 12 columns (can convert from XML) * Extended 25 columns (can convert from XML) * Pick your own columns from the full NCBI list (depending on columns, can convert from XML) This is inspired by JJ's changes to the BLAST XML to tabular conversion tool for Galaxy-P, https://github.com/jmchilton/galaxy_blast/commit/d79afc03522768323494818a40aac10513a6fa09 I would be much keener on the pick-you-own columns option if it was possible for the tool to record arbitrary column names for a tabular file in Galaxy's metadata (I can't find a trello card, but I'm sure I've asked about this before). Any thoughts or comments? eg Hurry up and just release this branch adding the hit descriptions as column 25 - we want that now ;) [*] Regards, Peter [*] For our local instance, the taxonomy stuff will be useful, but right now I would prioritise the description, which we currently get via the BLAST XML using this tool: https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Active Directory
Hi there, I have a server set up of galaxy. I would like to have a system setup where people can login via their active directory name and then use their mounted share drive to download processed data from the galaxy server. I saw that it is possible via apache to login through the AD, but will the AD also mount the share drives? If yes, is there a wrapper that allows to download Galaxy Histories onto the shared drive? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy code: data libraries
Hi eveybody, Is there a way in the code of Galaxy, to force the users to use "link to files without copying in Galaxy" by hiding the "copy files into Galaxy" option in the interface, when they add datasets in their library? We want to avoid users to click on "copy files into Galaxy" by mistake. Thanks in advance to all Mish Hi everybody, In my lab, after upgrading our Galaxy instance to the latest version, we have a problem with displaying tabular files. Any idea from where the problem can come? Thanks in advance to all. Mish ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Uploading files from password protected URL's
Thanks a lot for the answer ! kind regards, Nicolas Cybulski ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Add a tool to galaxy
hello all, We have a transcript classification tool named CNCI, that published on NAR August 6 2013, and the title of this article is "Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts". The source code is writen by python, and can be download at : http://www.bioinfo.org/software/cnci/ . We would like to add CNCI to galaxy cloudman, and help more researchers in transcriptome analysis community . If have any question please contact me! Looking forward to hearing from you soon. Yours sincerely, 85b03c90e6791b654377c3898449790a.png Description: Binary data ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
On Wed, Nov 27, 2013 at 9:02 PM, Greg Von Kuster wrote: > > Hello Peter, > > I've done a significant amount of re-engineering of the > Tool Shed's install and test framework over the past 2 > weeks, so the results you are seeing are probably a > reflection of some broken peices during the time frame > in which I was making changes. I believe I have most > of the things ironed out in 11545:32205f911e74 which > is now running on the test tool shed. > > We will be performing some test runs of thie new > framework over the long weekend, so more correct > test results should hopefully be showing up for yours > and other repositories. > Hi Greg, Things look much better today on the Test Tool Shed, with most of my tools under "Latest revision: all tool tests pass" again - or as expected a few under "Latest revision: missing tool tests" due to not yet having full test coverage. I've only spotted one glitch so far, missing test results for: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4 I saw a recent commit on galaxy-central addressing a test time display - that may have explained why yesterday the Test Tool Shed was claiming the test results were from four days ago. > I've also enhanced the "Tool test results" components to store a > configurable number of test runs instead of just 1. The test tool > shed is configured to store 5 test runs. So from here on you'll > begin to see multiple containers in the Tool test results container > - something like this: That sounds useful when the framework itself is changing rapidly, or if there is anything stochastic in a test failure. Presumably this shows the last 5 tests against the current tool revision? Thank Greg, and enjoy Thanksgiving, Peter ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
