Re: [galaxy-dev] Verifying test output datatypes, was: Problem with change_format and conditional inputs?
Merged. Thanks again for the input! I will look into the unicode issue and respond on the other thread. -John On Sat, Mar 15, 2014 at 7:50 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Mar 14, 2014 at 9:04 PM, John Chilton jmchil...@gmail.com wrote: On Fri, Mar 14, 2014 at 10:24 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks John, I suggest making this test framework perform this check by default (the twill and API based frameworks) and seeing what - if anything - breaks as a result on the Test Tool Shed. Hey Peter, I hope it is okay, but I do not want to make this change to the Twill driven variant of tool tests, I consider that code at end of life - new development would be a waste I think. Running all tools against a modified environment that switched all tests to target the APIs would be nice, but it sounds like there is not really the infrastructure in place for doing that right now. Upon further consideration I am not sure there are really any backward compatibility concerns anyway - or at least no more so than anything else when switching over to the API driven tests. I'll let the pull request sit open for a few days and then merge it as is. Note that one area of fuzziness is subclasses, e.g. if the tool output was labelled fastqsanger, but the test just said fastq, I would say the test was broken. On the other hand, if the test used a specific datatype like fastqsanger but the tool produced a dataset tagged with a more generic datatype like fastq I think that is a again a real failure. 100% agreed on both points. I believe the implementation proposed in pull request #347 reflects this resolution of the fuzziness. Thanks and have a great weekend, -John That sounds like a plan :) Hmm. I wonder if it would be trivial to tweak our TravisCI setup to run the functional tests twice, once with the old twill framework and once with the new API based framework? Seems doable (but would up the run time quite a bit). 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] Verifying test output datatypes, was: Problem with change_format and conditional inputs?
On Fri, Mar 14, 2014 at 9:04 PM, John Chilton jmchil...@gmail.com wrote: On Fri, Mar 14, 2014 at 10:24 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks John, I suggest making this test framework perform this check by default (the twill and API based frameworks) and seeing what - if anything - breaks as a result on the Test Tool Shed. Hey Peter, I hope it is okay, but I do not want to make this change to the Twill driven variant of tool tests, I consider that code at end of life - new development would be a waste I think. Running all tools against a modified environment that switched all tests to target the APIs would be nice, but it sounds like there is not really the infrastructure in place for doing that right now. Upon further consideration I am not sure there are really any backward compatibility concerns anyway - or at least no more so than anything else when switching over to the API driven tests. I'll let the pull request sit open for a few days and then merge it as is. Note that one area of fuzziness is subclasses, e.g. if the tool output was labelled fastqsanger, but the test just said fastq, I would say the test was broken. On the other hand, if the test used a specific datatype like fastqsanger but the tool produced a dataset tagged with a more generic datatype like fastq I think that is a again a real failure. 100% agreed on both points. I believe the implementation proposed in pull request #347 reflects this resolution of the fuzziness. Thanks and have a great weekend, -John That sounds like a plan :) Hmm. I wonder if it would be trivial to tweak our TravisCI setup to run the functional tests twice, once with the old twill framework and once with the new API based framework? Seems doable (but would up the run time quite a bit). 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] Verifying test output datatypes, was: Problem with change_format and conditional inputs?
On Sat, Mar 15, 2014 at 12:50 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Mar 14, 2014 at 9:04 PM, John Chilton jmchil...@gmail.com wrote: On Fri, Mar 14, 2014 at 10:24 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks John, I suggest making this test framework perform this check by default (the twill and API based frameworks) and seeing what - if anything - breaks as a result on the Test Tool Shed. Hey Peter, I hope it is okay, but I do not want to make this change to the Twill driven variant of tool tests, I consider that code at end of life - new development would be a waste I think. Running all tools against a modified environment that switched all tests to target the APIs would be nice, but it sounds like there is not really the infrastructure in place for doing that right now. Upon further consideration I am not sure there are really any backward compatibility concerns anyway - or at least no more so than anything else when switching over to the API driven tests. I'll let the pull request sit open for a few days and then merge it as is. Note that one area of fuzziness is subclasses, e.g. if the tool output was labelled fastqsanger, but the test just said fastq, I would say the test was broken. On the other hand, if the test used a specific datatype like fastqsanger but the tool produced a dataset tagged with a more generic datatype like fastq I think that is a again a real failure. 100% agreed on both points. I believe the implementation proposed in pull request #347 reflects this resolution of the fuzziness. Thanks and have a great weekend, -John That sounds like a plan :) Hmm. I wonder if it would be trivial to tweak our TravisCI setup to run the functional tests twice, once with the old twill framework and once with the new API based framework? Seems doable (but would up the run time quite a bit). I've just seen your other email, the new environment variable GALAXY_TEST_DEFAULT_INTERACTOR would make this easy. http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-March/018673.html http://dev.list.galaxyproject.org/Tool-Testing-Enhancements-tt4663799.html 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] Verifying test output datatypes, was: Problem with change_format and conditional inputs?
On Fri, Mar 14, 2014 at 10:24 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks John, I suggest making this test framework perform this check by default (the twill and API based frameworks) and seeing what - if anything - breaks as a result on the Test Tool Shed. Hey Peter, I hope it is okay, but I do not want to make this change to the Twill driven variant of tool tests, I consider that code at end of life - new development would be a waste I think. Running all tools against a modified environment that switched all tests to target the APIs would be nice, but it sounds like there is not really the infrastructure in place for doing that right now. Upon further consideration I am not sure there are really any backward compatibility concerns anyway - or at least no more so than anything else when switching over to the API driven tests. I'll let the pull request sit open for a few days and then merge it as is. Note that one area of fuzziness is subclasses, e.g. if the tool output was labelled fastqsanger, but the test just said fastq, I would say the test was broken. On the other hand, if the test used a specific datatype like fastqsanger but the tool produced a dataset tagged with a more generic datatype like fastq I think that is a again a real failure. 100% agreed on both points. I believe the implementation proposed in pull request #347 reflects this resolution of the fuzziness. Thanks and have a great weekend, -John Peter On Fri, Mar 14, 2014 at 3:15 PM, John Chilton jmchil...@gmail.com wrote: Grepping around the code I think this is the only way a ftype attribute on an output affects the evaluation of test data. if attributes.get( 'ftype', None ) == 'bam': local_fh, temp_name = self._bam_to_sam( local_name, temp_name ) local_name = local_fh.name I am not sure it was ever meant as a strict test. I worry about breaking backward compatibility but it is easy enough to implement this as an actual check when using newer API driven tests. I have opened a pull request for this functionality here: https://bitbucket.org/galaxy/galaxy-central/pull-request/347/check-ftype-attribute-if-defined-on-test/diff Thoughts? -John On Tue, Mar 11, 2014 at 10:30 AM, Peter Cock p.j.a.c...@googlemail.com wrote: That seems to work - thanks Björn :) This seems to have exposed a bug in the test framework, e.g. test param name=query value=rhodopsin_nucs.fasta ftype=fasta / param name=db_opts_selector value=file / param name=subject value=three_human_mRNA.fasta ftype=fasta / param name=database value= / param name=evalue_cutoff value=1e-40 / param name=out_format value=5 / param name=adv_opts_selector value=basic / output name=output1 file=blastn_rhodopsin_vs_three_human.xml ftype=blastxml / /test This was saying the output should have been blastxml, but until I just fixed it the output was being tagged as tabular (although run_functional_tests.sh did check the content it didn't check the datatype matched). Dave - do think this is a reasonable enhancement? 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/