Re: [galaxy-dev] Tool unit tests using composite datatypes
On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote: On Thu, Apr 25, 2013 at 9:36 AM, Peter Cock wrote: ... As noted in my last email, for some reason when running the test case, the input FASTA file is being included on the command line TWICE. Curiously the -hash_index argument has been omitted. Linked maybe? Peter, I have fixed the double listing of the FASTA file. Putting min=1 on a repeat statement would result in two repeat instances when using functional tests without this bug fix. https://bitbucket.org/galaxy/galaxy-central/commits/5e534cc8da856ad598d63b8b9f03fe20629df05f Thank you - such a little thing once you'd traced its cause. It is likely also the problem with your mira tests? This should help for the MIRA4 tests too :) The hash_index missing was caused because to the param value you put in the test tag should be true or false, not the truevalue/falsevalue attributes as far as I can tell - those are used only by cheetah I guess. Adding the hash_index parameter creates and additional 5 files - including ones you listed in your test case. I think I tried that too (true/false), but it was a while ago now. Hitting multiple test framework issues at the same time made debugging this hard. With these change, I was able to write working functional tests for your tool using the template you outlined in the Trello card. The .pin file doesn't match, I think there is something time-based in there so I had to set two lines of diff. Yes, I agree the PIN file varies run to run, so the diff trick looks good. Also, since this e-mail, you now have two parameters named file, that doesn't go over well yet - so I renamed mask|file to mask|mask_file. The makeblastdb wrapper on the main Tool Shed don't yet have the masking file parameter, but does already on the Test Tool Shed - so I'd prefer not to change this: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus http://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus In principle the pipe-based fully specified parameter name would work here too, to resolve the potential ambiguity? (That is a separate Trello Card for handling potentially ambiguous parameters in the test framework): https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-functional-tests ... These changes should work right out of central, does not utilize my API driven variant on github. I discovered no problems with auto_primary versus basic composite types here, just the things listed above. Not for me though, even if I rename the masking file param to avoid the ambiguous file parameters, commits here: https://github.com/peterjc/galaxy_blast/commit/2043cc813c2e138d93f8a940ea711ad7538a50c7 https://github.com/peterjc/galaxy_blast/commit/f4f74cd065921b069499a5fcc4209b299a403c96 and continuing on this branch: https://github.com/peterjc/galaxy_blast/tree/test_makeblastdb https://github.com/peterjc/galaxy_blast/commit/e828543539ab0a0ca8f8b16dbdce132812605282 That gave: $ ./run_functional_tests.sh -id ncbi_makeblastdb ... galaxy.jobs.runners.local DEBUG 2013-11-18 11:25:38,449 execution finished: export GALAXY_SLOTS=1; makeblastdb -version /tmp/tmpF81TF5/tmpghF4ik/new_files_path_lVhJ4E/GALAXY_VERSION_STRING_2; makeblastdb -out /tmp/tmpF81TF5/tmpghF4ik/database/files/000/dataset_2_files/blastdb -hash_index -in /tmp/tmpF81TF5/tmpghF4ik/database/files/000/dataset_1.dat /tmp/tmpF81TF5/tmpghF4ik/database/files/000/dataset_1.dat -title Just 4 human proteins -dbtype prot ... Composite file (blastdb.phr) of History item 2 different than expected, difference (using diff): Binary data detected, not displaying diff ... FAILED (failures=1) ... I find that changing the order of the extra_files tags in the test seems to alter the failure - which supports my hunch that something is scrambling the order of the extra files, so that it fails to compare the generated blastdb.phr with the provided four_human_proteins.fasta.phd e.g. Here it seems to compare to the (place holder) text I generate when viewing a database in the Galaxy interface: https://github.com/peterjc/galaxy_blast/commit/e828543539ab0a0ca8f8b16dbdce132812605282 $ ./run_functional_tests.sh -id ncbi_makeblastdb ... galaxy.jobs.runners.local DEBUG 2013-11-18 12:23:24,812 execution finished: export GALAXY_SLOTS=1; python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmph0YlBO/tmpRK7bhO/new_files_path_0SO6J0/tmpkPWlQd /tmp/tmph0YlBO/tmpRK7bhO/new_files_path_0SO6J0/tmpr_xBCK 1:/tmp/tmph0YlBO/tmpRK7bhO/job_working_directory_Qh_YcY/000/1/dataset_1_files:/tmp/tmph0YlBO/tmpRK7bhO/database/files/000/dataset_1.dat ... Composite file (blastdb.phd) of History item 2 different than expected, difference (using diff): --- local_file +++ history_data @@ -1,4 +1,1 @@ -7184492 -29249033410 -36665887501 -5392473183 +This is a BLAST protein database. ... FAILED (failures=1) ... If it works for you then perhaps the filesystem is a
Re: [galaxy-dev] Tool unit tests using composite datatypes
On Mon, Nov 18, 2013 at 12:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote: With these change, I was able to write working functional tests for your tool using the template you outlined in the Trello card. ... I discovered no problems with auto_primary versus basic composite types here, just the things listed above. Not for me though, even if I rename the masking file param to avoid the ambiguous file parameters ... I find that changing the order of the extra_files tags in the test seems to alter the failure - which supports my hunch that something is scrambling the order of the extra files, so that it fails to compare the generated blastdb.phr with the provided four_human_proteins.fasta.phd John's replies via Twitter: https://twitter.com/jmchilton/status/402436500131807232 @pjacock Hard to argue with @travisci but your makeblastdb test works unmodified on my box and I can reorder the extras. I'm still looking.. https://twitter.com/jmchilton/status/402446372231581696 @pjacock Got it, you are overriding display_data in blast DB datatypes. This breaks much! Is how the test framework/API/etc access datasets. There may be trouble ahead... the current display_data override is to give some meaningful output to the user when they click the eye ball icon for a BLAST database - rather than something unhelpful and scary like a blank page. A more slick option would be to override display_data to run blastdbcmd live, but that means a run time dependency of the datatype definition on (a specific version of) the BLAST+ binaries - which could be problematic. I had considered capturing the makeblastdb stdout to a file as blastdb.log and having that as the (human viewable) primary file of a composite datatype - but that would cause trouble if and when I manage to support user uploaded BLAST databases. 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] Tool unit tests using composite datatypes
On Mon, Nov 18, 2013 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Nov 18, 2013 at 12:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote: With these change, I was able to write working functional tests for your tool using the template you outlined in the Trello card. ... I discovered no problems with auto_primary versus basic composite types here, just the things listed above. Not for me though, even if I rename the masking file param to avoid the ambiguous file parameters ... I find that changing the order of the extra_files tags in the test seems to alter the failure - which supports my hunch that something is scrambling the order of the extra files, so that it fails to compare the generated blastdb.phr with the provided four_human_proteins.fasta.phd John's replies via Twitter: https://twitter.com/jmchilton/status/402436500131807232 @pjacock Hard to argue with @travisci but your makeblastdb test works unmodified on my box and I can reorder the extras. I'm still looking.. https://twitter.com/jmchilton/status/402446372231581696 @pjacock Got it, you are overriding display_data in blast DB datatypes. This breaks much! Is how the test framework/API/etc access datasets. There may be trouble ahead... the current display_data override is to give some meaningful output to the user when they click the eye ball icon for a BLAST database - rather than something unhelpful and scary like a blank page. I didn't implement any of this composite dataset stuff so I am just guessing on best practices here, but is the right thing to do here switch from 'basic' to 'auto_primary_file' ? Just generate a file that just includes the content you want to display and set that as the primary file - I think this might be better practice than overriding display_data. If you want that file to a log if it is available that is fine, if files are uploaded an optional log could be available and you can provide a default fallback if unavailable in generate_primary_file/regenerate_primary_file. If you do insist on overriding display data, than you should at least allow fallback to what the super class would do if (filename and filename != 'index'). -John A more slick option would be to override display_data to run blastdbcmd live, but that means a run time dependency of the datatype definition on (a specific version of) the BLAST+ binaries - which could be problematic. I had considered capturing the makeblastdb stdout to a file as blastdb.log and having that as the (human viewable) primary file of a composite datatype - but that would cause trouble if and when I manage to support user uploaded BLAST databases. 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] Tool unit tests using composite datatypes
On Mon, Nov 18, 2013 at 4:02 PM, John Chilton chil...@msi.umn.edu wrote: On Mon, Nov 18, 2013 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Nov 18, 2013 at 12:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote: With these change, I was able to write working functional tests for your tool using the template you outlined in the Trello card. ... I discovered no problems with auto_primary versus basic composite types here, just the things listed above. Not for me though, even if I rename the masking file param to avoid the ambiguous file parameters ... I find that changing the order of the extra_files tags in the test seems to alter the failure - which supports my hunch that something is scrambling the order of the extra files, so that it fails to compare the generated blastdb.phr with the provided four_human_proteins.fasta.phd John's replies via Twitter: https://twitter.com/jmchilton/status/402436500131807232 @pjacock Hard to argue with @travisci but your makeblastdb test works unmodified on my box and I can reorder the extras. I'm still looking.. https://twitter.com/jmchilton/status/402446372231581696 @pjacock Got it, you are overriding display_data in blast DB datatypes. This breaks much! Is how the test framework/API/etc access datasets. There may be trouble ahead... the current display_data override is to give some meaningful output to the user when they click the eye ball icon for a BLAST database - rather than something unhelpful and scary like a blank page. I didn't implement any of this composite dataset stuff so I am just guessing on best practices here, but is the right thing to do here switch from 'basic' to 'auto_primary_file' ? Just generate a file that just includes the content you want to display and set that as the primary file - I think this might be better practice than overriding display_data. If you want that file to a log if it is available that is fine, if files are uploaded an optional log could be available and you can provide a default fallback if unavailable in generate_primary_file/regenerate_primary_file. If you do insist on overriding display data, than you should at least allow fallback to what the super class would do if (filename and filename != 'index'). I see, so my (dummy) primary file could just a small text file saying This is a BLAST protein database. or similar - and that would let me reproduce the current behaviour? The only possible downside I can see right now is wondering what happens to existing histories containing old BLAST databases created with the current code... but that will sort itself out eventually with some user inconvenience. Who is the composite file architect (for their thoughts)? Regards, 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] Tool unit tests using composite datatypes
On Thu, Apr 25, 2013 at 9:36 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Apr 5, 2013 at 3:08 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Apr 4, 2013 at 7:19 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Peter, What is the test error given when you do have a value defined for name in output? Can you try using 'empty_file.dat'? e.g. output name=out_file file=empty_file.dat or output name=out_file file=empty_file.dat compare=contains etc Hi Daniel, That seems to help (plus fixing a typo in one of my child file extensions). However there is something else amiss, but my Galaxy is a little out of date: ... I will have to checkout the latest Galaxy code and retest in case this is something already fixed... OK, I've updated to the latest galaxy-central default branch. Here's the slightly revised test for ncbi_makeblastdb.xml, tests test !-- makeblastdb -in four_human_proteins.fasta -dbtype prot -hash_index -title Just 4 human proteins -out four_human_proteins.fasta -- param name=dbtype value=prot/ param name=file value=four_human_proteins.fasta/ param name=title value=Just 4 human proteins/ param name=parse_seqids value=/ param name=hash_index value=-hash_index/ output name=out_file file=empty_file.dat ftype=blastdbp extra_files type=file value=four_human_proteins.fasta.phd name=blastdb.pdb/ extra_files type=file value=four_human_proteins.fasta.phi name=blastdb.phi/ extra_files type=file value=four_human_proteins.fasta.phr name=blastdb.phr/ extra_files type=file value=four_human_proteins.fasta.pin name=blastdb.pin/ extra_files type=file value=four_human_proteins.fasta.pog name=blastdb.pog/ extra_files type=file value=four_human_proteins.fasta.psd name=blastdb.psd/ extra_files type=file value=four_human_proteins.fasta.psi name=blastdb.psi/ extra_files type=file value=four_human_proteins.fasta.psq name=blastdb.psq/ /output /test /tests Here's some of the Galaxy log when I run this example manually through the web interface: galaxy.jobs.handler INFO 2013-04-25 15:17:43,820 (43) Job dispatched galaxy.jobs.runners.local DEBUG 2013-04-25 15:17:44,377 (43) executing: makeblastdb -version /mnt/galaxy/galaxy-central/database/tmp/GALAXY_VERSION_STRING_43; makeblastdb -out /mnt/galaxy/galaxy-central/database/files/000/dataset_46_files/blastdb -hash_index -in /mnt/galaxy/galaxy-central/database/files/000/dataset_45.dat -title Just 4 human proteins -dbtype prot galaxy.jobs DEBUG 2013-04-25 15:17:44,436 (43) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-04-25 15:17:44,751 execution finished: makeblastdb -version /mnt/galaxy/galaxy-central/database/tmp/GALAXY_VERSION_STRING_43; makeblastdb -out /mnt/galaxy/galaxy-central/database/files/000/dataset_46_files/blastdb -hash_index -in /mnt/galaxy/galaxy-central/database/files/000/dataset_45.dat -title Just 4 human proteins -dbtype prot galaxy.jobs DEBUG 2013-04-25 15:17:45,456 job 43 ended Now a snippets from the test run (unedited version at end of email). $ ./run_functional_tests.sh -id ncbi_makeblastdb ... galaxy.jobs.handler DEBUG 2013-04-25 15:12:44,214 (2) Dispatching to local runner galaxy.jobs DEBUG 2013-04-25 15:12:45,599 (2) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-04-25 15:12:45,711 (2) Job dispatched galaxy.jobs.runners.local DEBUG 2013-04-25 15:12:46,345 (2) executing: makeblastdb -version /tmp/tmpovUM3w/database/tmp/GALAXY_VERSION_STRING_2; makeblastdb -out /tmp/tmpovUM3w/database/files/000/dataset_2_files/blastdb -in /tmp/tmpovUM3w/database/files/000/dataset_1.dat /tmp/tmpovUM3w/database/files/000/dataset_1.dat -title Just 4 human proteins -dbtype prot galaxy.jobs DEBUG 2013-04-25 15:12:46,409 (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-04-25 15:12:46,897 execution finished: makeblastdb -version /tmp/tmpovUM3w/database/tmp/GALAXY_VERSION_STRING_2; makeblastdb -out /tmp/tmpovUM3w/database/files/000/dataset_2_files/blastdb -in /tmp/tmpovUM3w/database/files/000/dataset_1.dat /tmp/tmpovUM3w/database/files/000/dataset_1.dat -title Just 4 human proteins -dbtype prot galaxy.jobs DEBUG 2013-04-25 15:12:47,502 job 2 ended ... As noted in my last email, for some reason when running the test case, the input FASTA file is being included on the command line TWICE. Curiously the -hash_index argument has been omitted. Linked maybe? Peter, I have fixed the double listing of the FASTA file. Putting min=1 on a repeat statement would result in two repeat instances when using functional tests without this bug fix.
Re: [galaxy-dev] Tool unit tests using composite datatypes
On Tue, Apr 30, 2013 at 4:30 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Apr 25, 2013 at 3:36 PM, Peter Cock p.j.a.c...@googlemail.com wrote: OK, I've updated to the latest galaxy-central default branch. Here's the slightly revised test for ncbi_makeblastdb.xml, ... In the absence of any fresh feedback, I've filed an issue on Trello for this to make sure it gets tracked: https://trello.com/card/basic-composite-datatypes-not-working-as-test-outputs/506338ce32ae458f6d15e4b3/819 Composite datatypes like HTML seem to work (with a primary file). Basic composite datatypes seem not to work (with no primary file). Regards, Peter Hi guys, Has anything changed in this area of the test framework since April? 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] Tool unit tests using composite datatypes
On Thu, Apr 25, 2013 at 3:36 PM, Peter Cock p.j.a.c...@googlemail.com wrote: OK, I've updated to the latest galaxy-central default branch. Here's the slightly revised test for ncbi_makeblastdb.xml, ... In the absence of any fresh feedback, I've filed an issue on Trello for this to make sure it gets tracked: https://trello.com/card/basic-composite-datatypes-not-working-as-test-outputs/506338ce32ae458f6d15e4b3/819 Composite datatypes like HTML seem to work (with a primary file). Basic composite datatypes seem not to work (with no primary file). Regards, 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] Tool unit tests using composite datatypes
On Fri, Apr 5, 2013 at 3:08 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Apr 4, 2013 at 7:19 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
What is the test error given when you do have a value defined for name in
output?
Can you try using 'empty_file.dat'?
e.g.
output name=out_file file=empty_file.dat
or
output name=out_file file=empty_file.dat compare=contains
etc
Hi Daniel,
That seems to help (plus fixing a typo in one of my child file extensions).
However there is something else amiss, but my Galaxy is a little out of date:
...
I will have to checkout the latest Galaxy code and retest in case this
is something already fixed...
OK, I've updated to the latest galaxy-central default branch. Here's
the slightly revised test for ncbi_makeblastdb.xml,
tests
test
!-- makeblastdb -in four_human_proteins.fasta -dbtype prot
-hash_index -title Just 4 human proteins -out
four_human_proteins.fasta --
param name=dbtype value=prot/
param name=file value=four_human_proteins.fasta/
param name=title value=Just 4 human proteins/
param name=parse_seqids value=/
param name=hash_index value=-hash_index/
output name=out_file file=empty_file.dat ftype=blastdbp
extra_files type=file
value=four_human_proteins.fasta.phd name=blastdb.pdb/
extra_files type=file
value=four_human_proteins.fasta.phi name=blastdb.phi/
extra_files type=file
value=four_human_proteins.fasta.phr name=blastdb.phr/
extra_files type=file
value=four_human_proteins.fasta.pin name=blastdb.pin/
extra_files type=file
value=four_human_proteins.fasta.pog name=blastdb.pog/
extra_files type=file
value=four_human_proteins.fasta.psd name=blastdb.psd/
extra_files type=file
value=four_human_proteins.fasta.psi name=blastdb.psi/
extra_files type=file
value=four_human_proteins.fasta.psq name=blastdb.psq/
/output
/test
/tests
Here's some of the Galaxy log when I run this example manually through the
web interface:
galaxy.jobs.handler INFO 2013-04-25 15:17:43,820 (43) Job dispatched
galaxy.jobs.runners.local DEBUG 2013-04-25 15:17:44,377 (43)
executing: makeblastdb -version
/mnt/galaxy/galaxy-central/database/tmp/GALAXY_VERSION_STRING_43;
makeblastdb -out
/mnt/galaxy/galaxy-central/database/files/000/dataset_46_files/blastdb
-hash_index -in
/mnt/galaxy/galaxy-central/database/files/000/dataset_45.dat -title
Just 4 human proteins -dbtype prot
galaxy.jobs DEBUG 2013-04-25 15:17:44,436 (43) Persisting job
destination (destination id: local:///)
galaxy.jobs.runners.local DEBUG 2013-04-25 15:17:44,751 execution
finished: makeblastdb -version
/mnt/galaxy/galaxy-central/database/tmp/GALAXY_VERSION_STRING_43;
makeblastdb -out
/mnt/galaxy/galaxy-central/database/files/000/dataset_46_files/blastdb
-hash_index -in
/mnt/galaxy/galaxy-central/database/files/000/dataset_45.dat -title
Just 4 human proteins -dbtype prot
galaxy.jobs DEBUG 2013-04-25 15:17:45,456 job 43 ended
Now a snippets from the test run (unedited version at end of email).
$ ./run_functional_tests.sh -id ncbi_makeblastdb
...
galaxy.jobs.handler DEBUG 2013-04-25 15:12:44,214 (2) Dispatching to
local runner
galaxy.jobs DEBUG 2013-04-25 15:12:45,599 (2) Persisting job
destination (destination id: local:///)
galaxy.jobs.handler INFO 2013-04-25 15:12:45,711 (2) Job dispatched
galaxy.jobs.runners.local DEBUG 2013-04-25 15:12:46,345 (2) executing:
makeblastdb -version
/tmp/tmpovUM3w/database/tmp/GALAXY_VERSION_STRING_2; makeblastdb -out
/tmp/tmpovUM3w/database/files/000/dataset_2_files/blastdb -in
/tmp/tmpovUM3w/database/files/000/dataset_1.dat
/tmp/tmpovUM3w/database/files/000/dataset_1.dat -title Just 4
human proteins -dbtype prot
galaxy.jobs DEBUG 2013-04-25 15:12:46,409 (2) Persisting job
destination (destination id: local:///)
galaxy.jobs.runners.local DEBUG 2013-04-25 15:12:46,897 execution
finished: makeblastdb -version
/tmp/tmpovUM3w/database/tmp/GALAXY_VERSION_STRING_2; makeblastdb -out
/tmp/tmpovUM3w/database/files/000/dataset_2_files/blastdb -in
/tmp/tmpovUM3w/database/files/000/dataset_1.dat
/tmp/tmpovUM3w/database/files/000/dataset_1.dat -title Just 4
human proteins -dbtype prot
galaxy.jobs DEBUG 2013-04-25 15:12:47,502 job 2 ended
...
As noted in my last email, for some reason when running the test case,
the input FASTA file is being included on the command line TWICE.
Curiously the -hash_index argument has been omitted. Linked maybe?
And then once this has run, as before, the file comparison is hard to
fathom (it is not comparing the correct files to each other).
The example rgClean.xml which Dave Bouvier pointed me at uses
a composite datatypes with a central file ('pbed' which is a subclass
of 'html') while the other examples I've found are 'html'.
i.e. composite_type='auto_primary_file'
It does seem likely at this point that I could be the first
Re: [galaxy-dev] Tool unit tests using composite datatypes
On Thu, Apr 4, 2013 at 7:19 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Peter, What is the test error given when you do have a value defined for name in output? Can you try using 'empty_file.dat'? e.g. output name=out_file file=empty_file.dat or output name=out_file file=empty_file.dat compare=contains etc Hi Daniel, That seems to help (plus fixing a typo in one of my child file extensions). However there is something else amiss, but my Galaxy is a little out of date: begin captured logging galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9486/ galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9486/ galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9486/user/logout galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9486/ galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 galaxy.jobs.manager: DEBUG: (1) Job assigned to handler 'main' galaxy.jobs: DEBUG: (1) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/1 galaxy.jobs.handler: DEBUG: dispatching job 1 to local runner galaxy.jobs.handler: INFO: (1) Job dispatched galaxy.jobs.runners.local: DEBUG: Local runner: starting job 1 galaxy.jobs.runners.local: DEBUG: executing: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpOBsw3s/database/tmp/tmpshAqc4 /tmp/tmpOBsw3s/database/tmp/tmpjPyydZ 1:/mnt/galaxy/galaxy-central/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpOBsw3s/database/files/000/dataset_1.dat galaxy.jobs.runners.local: DEBUG: execution finished: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpOBsw3s/database/tmp/tmpshAqc4 /tmp/tmpOBsw3s/database/tmp/tmpjPyydZ 1:/mnt/galaxy/galaxy-central/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpOBsw3s/database/files/000/dataset_1.dat galaxy.jobs: DEBUG: Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs: DEBUG: job 1 ended galaxy.jobs.manager: DEBUG: (2) Job assigned to handler 'main' galaxy.jobs: DEBUG: (2) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/2 galaxy.jobs.handler: DEBUG: dispatching job 2 to local runner galaxy.jobs.handler: INFO: (2) Job dispatched galaxy.jobs.runners.local: DEBUG: Local runner: starting job 2 galaxy.jobs.runners.local: DEBUG: executing: makeblastdb -version /tmp/tmpOBsw3s/database/tmp/GALAXY_VERSION_STRING_2; makeblastdb -out /tmp/tmpOBsw3s/database/files/000/dataset_2_files/blastdb -in /tmp/tmpOBsw3s/database/files/000/dataset_1.dat /tmp/tmpOBsw3s/database/files/000/dataset_1.dat -title Just 4 human proteins -dbtype prot galaxy.jobs.runners.local: DEBUG: execution finished: makeblastdb -version /tmp/tmpOBsw3s/database/tmp/GALAXY_VERSION_STRING_2; makeblastdb -out /tmp/tmpOBsw3s/database/files/000/dataset_2_files/blastdb -in /tmp/tmpOBsw3s/database/files/000/dataset_1.dat /tmp/tmpOBsw3s/database/files/000/dataset_1.dat -title Just 4 human proteins -dbtype prot galaxy.tools: DEBUG: Error opening galaxy.json file: [Errno 2] No such file or directory: '/mnt/galaxy/galaxy-central/database/job_working_directory/000/2/galaxy.json' galaxy.jobs: DEBUG: job 2 ended base.twilltestcase: INFO: ## files diff /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd (51 bytes, 4 lines) and /tmp/tmpOBsw3s/database/tmp/tmpPaxnAGblastdb.phd (33 bytes, 1 lines) base.twilltestcase: INFO: ## file /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd line 1 is '718449\x022\n' base.twilltestcase: INFO: ## file /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd line 2 is '2924903341\x020\n' base.twilltestcase: INFO: ## file /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd line 3 is '3666588750\x021\n' base.twilltestcase: INFO: ## file /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd line 4 is '539247318\x023\n' base.twilltestcase: INFO: ## file /tmp/tmpOBsw3s/database/tmp/tmpPaxnAGblastdb.phd line 1 is 'This is a BLAST protein database.' base.twilltestcase: INFO: ## sibling files to /tmp/tmpOBsw3s/database/tmp/tmpPaxnAGblastdb.phd in same directory: base.twilltestcase: INFO: ## sibling file: tmpUMWHqD base.twilltestcase: INFO: ## sibling file: twilltestcase-MDnhZ1.html base.twilltestcase: INFO: ## sibling file: twilltestcase-_vAVc9.html base.twilltestcase: INFO: ## sibling file: tmpyiy0Kvempty_file.dat base.twilltestcase: INFO: ## sibling file: twilltestcase-MHWm9w.html base.twilltestcase: INFO: ## sibling file: tmpPaxnAGblastdb.phd base.twilltestcase: INFO: ## sibling file: twilltestcase-dVKyqw.html base.twilltestcase: INFO: ## sibling file: tmpshAqc4
Re: [galaxy-dev] Tool unit tests using composite datatypes
On Wed, Apr 3, 2013 at 2:48 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Apr 3, 2013 at 2:37 PM, Dave Bouvier d...@bx.psu.edu wrote: For the outputs, rgClean.xml provides an example of comparing a composite output dataset with the expected test data. Here there is a tag extra_files used within the output tag. Many thanks Dave - those should be enough to get me started, and maybe I can update the wiki once I'm happy with how this works... I'm trying this for makeblastdb which produces a single output, a composite datatype which is a BLAST database. The examples I found all seemed to be composite datatypes with a central file (e.g. HTML plus images), i.e. composite_type='auto_primary_file' In the case of the BLAST databases, this is a composite datatype without a primary file, aka composite_type='basic'. Leaving the param without a file gives: Exception: Test output does not have a 'file' Using a empty value doesn't work, Traceback (most recent call last): File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File /mnt/galaxy/galaxy-central/test/base/twilltestcase.py, line 828, in verify_dataset_correctness self.files_diff( local_name, temp_name, attributes=attributes ) File /mnt/galaxy/galaxy-central/test/base/twilltestcase.py, line 66, in files_diff local_file = open( file1, 'U' ).readlines() IOError: [Errno 21] Is a directory: '/mnt/galaxy/galaxy-central/test-data' Using /dev/null gets a bit further but something is confusing the comparisons. My current experimental test looks like this: tests test param name=dbtype value=prot/ param name=file value=four_human_proteins.fasta/ param name=title value=Just 4 human proteins/ param name=parse_seqids value=/ param name=hash_index value=-hash_index/ output name=out_file file=/dev/null ftype=blastdbp extra_files type=file value=four_human_proteins.fasta.phd name=blastdb.pdb/ extra_files type=file value=four_human_proteins.fasta.phi name=blastdb.phi/ extra_files type=file value=four_human_proteins.fasta.phr name=blastdb.phr/ extra_files type=file value=four_human_proteins.fasta.pin name=blastdb.pin/ extra_files type=file value=four_human_proteins.fasta.pog name=blastdb.pog/ extra_files type=file value=four_human_proteins.fasta.psd name=blastdb.psd/ extra_files type=file value=four_human_proteins.fasta.psi name=blastdb.psi/ extra_files type=file value=four_human_proteins.fasta.psq name=blastdb.psq/ /output /test /tests Any advice? 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] Tool unit tests using composite datatypes
Hi Peter, What is the test error given when you do have a value defined for name in output? Can you try using 'empty_file.dat'? e.g. output name=out_file file=empty_file.dat or output name=out_file file=empty_file.dat compare=contains etc Thanks for using Galaxy, Dan On Apr 4, 2013, at 1:34 PM, Peter Cock wrote: On Wed, Apr 3, 2013 at 2:48 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Apr 3, 2013 at 2:37 PM, Dave Bouvier d...@bx.psu.edu wrote: For the outputs, rgClean.xml provides an example of comparing a composite output dataset with the expected test data. Here there is a tag extra_files used within the output tag. Many thanks Dave - those should be enough to get me started, and maybe I can update the wiki once I'm happy with how this works... I'm trying this for makeblastdb which produces a single output, a composite datatype which is a BLAST database. The examples I found all seemed to be composite datatypes with a central file (e.g. HTML plus images), i.e. composite_type='auto_primary_file' In the case of the BLAST databases, this is a composite datatype without a primary file, aka composite_type='basic'. Leaving the param without a file gives: Exception: Test output does not have a 'file' Using a empty value doesn't work, Traceback (most recent call last): File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File /mnt/galaxy/galaxy-central/test/base/twilltestcase.py, line 828, in verify_dataset_correctness self.files_diff( local_name, temp_name, attributes=attributes ) File /mnt/galaxy/galaxy-central/test/base/twilltestcase.py, line 66, in files_diff local_file = open( file1, 'U' ).readlines() IOError: [Errno 21] Is a directory: '/mnt/galaxy/galaxy-central/test-data' Using /dev/null gets a bit further but something is confusing the comparisons. My current experimental test looks like this: tests test param name=dbtype value=prot/ param name=file value=four_human_proteins.fasta/ param name=title value=Just 4 human proteins/ param name=parse_seqids value=/ param name=hash_index value=-hash_index/ output name=out_file file=/dev/null ftype=blastdbp extra_files type=file value=four_human_proteins.fasta.phd name=blastdb.pdb/ extra_files type=file value=four_human_proteins.fasta.phi name=blastdb.phi/ extra_files type=file value=four_human_proteins.fasta.phr name=blastdb.phr/ extra_files type=file value=four_human_proteins.fasta.pin name=blastdb.pin/ extra_files type=file value=four_human_proteins.fasta.pog name=blastdb.pog/ extra_files type=file value=four_human_proteins.fasta.psd name=blastdb.psd/ extra_files type=file value=four_human_proteins.fasta.psi name=blastdb.psi/ extra_files type=file value=four_human_proteins.fasta.psq name=blastdb.psq/ /output /test /tests Any advice? 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/ ___ 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] Tool unit tests using composite datatypes
Hello all, I'd like to be able to write some simple test entries for some of the BLAST+ tools using composite datatypes as input or output (i.e. small BLAST databases). This doesn't seem to be mentioned or hinted at on the wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action=showredirect=Admin%2FTools%2FTool+Config+Syntax#A.3Ctest.3E_tag_set Is it possible to use a composite datatype as a test input? If so how? Normal datatypes are loaded into the test history using using the upload tool - does that mean I first need to extend the relevant datatypes to allow them to be uploaded? Example: Run blastp using a small query FASTA file and a small database, check the output (eg tabular). Is it possible to use a composite datatype as a test output? If so how? Example: Run makeblastdb using a small FASTA file, and check the output (a small BLAST database). 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] Tool unit tests using composite datatypes
Peter, Yes, it is definitely possible to use a composite datatype in functional tests, and a number of tools in the Galaxy distribution do so. For examples on how to define composite inputs, you can look at the tools in tools/rgenetics/, such as rgGLM.xml or rgHaploView.xml. For the outputs, rgClean.xml provides an example of comparing a composite output dataset with the expected test data. --Dave B. On 4/3/13 09:24:34.000, Peter Cock wrote: Hello all, I'd like to be able to write some simple test entries for some of the BLAST+ tools using composite datatypes as input or output (i.e. small BLAST databases). This doesn't seem to be mentioned or hinted at on the wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action=showredirect=Admin%2FTools%2FTool+Config+Syntax#A.3Ctest.3E_tag_set Is it possible to use a composite datatype as a test input? If so how? Normal datatypes are loaded into the test history using using the upload tool - does that mean I first need to extend the relevant datatypes to allow them to be uploaded? Example: Run blastp using a small query FASTA file and a small database, check the output (eg tabular). Is it possible to use a composite datatype as a test output? If so how? Example: Run makeblastdb using a small FASTA file, and check the output (a small BLAST database). 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/ ___ 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] Tool unit tests using composite datatypes
On Wed, Apr 3, 2013 at 2:37 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, Yes, it is definitely possible to use a composite datatype in functional tests, and a number of tools in the Galaxy distribution do so. Hooray - I was hoping this functionality already existed but was just undocumented. For examples on how to define composite inputs, you can look at the tools in tools/rgenetics/, such as rgGLM.xml or rgHaploView.xml. Got it - I see that uses the tag composite_data within the param tag. For the outputs, rgClean.xml provides an example of comparing a composite output dataset with the expected test data. Here there is a tag extra_files used within the output tag. Many thanks Dave - those should be enough to get me started, and maybe I can update the wiki once I'm happy with how this works... Cheers, 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/
