Re: [galaxy-dev] Planemo 0.19.0 testing tools that produce dataset collections

2015-11-05 Thread Von Kuster, Greg 
Nicola, thanks a bunch!  Your eyes are phenomenal!

Greg

> On Nov 4, 2015, at 8:09 PM, Nicola Soranzo  wrote:
> 
> Hi Greg,
> in the inputs the param has name "input_gff", while in the test you are using 
> name "input".
> 
> Cheers, 
> Nicola 
> 
>  Von Kuster, Greg ha scritto 
> 
>> Hello Galaxy devs,
>> 
>> I’m developing a tool that uses a multi-select list to accept any number of 
>> input datasets.  The tool works fine when executing it within Galaxy, but 
>> when running it through planemo testing, it never passes, so I’m wondering 
>> if there are known issues with planemo testing tools that produce dataset 
>> collections.
>> 
>> I’ve spent some time adding debugging log statements into the Galaxy 
>> framework for planemo test runs, but haven’t uncovered anything obvious.  So 
>> if there are no known issues with planemo testing dataset_collections, I’m 
>> wondering if my tool config syntax is incorrect.
>> 
>> Does anyone see anything obvious?  Any insight is much appreciated!
>> 
>> Here is the command line.  Notice that I do not define any outputs since I 
>> am using a dataset collection.  Is this causing a problem for planemo?
>> 
>>   
>>   python $__tool_directory__/genetrack.py
>>   --input_format $input_format_cond.input_format
>>   #if str($input_format_cond.input_format) == "genetracktool":
>>   #for $i in $input_format_cond.input_genetracktool:
>>--input "${i}" "${i.hid}" "${i.name}"
>>   #end for
>>   #elif str($input_format_cond.input_format) == "gff":
>>   #for $i in $input_format_cond.input_gff:
>>--input "${i}" "${i.hid}" "${i.name}"
>>   #end for
>>   #end if
>>   --sigma $sigma
>>   --exclusion $exclusion
>>   --up_width $up_width
>>   --down_width $down_width
>>   --filter $filter
>>   --chromosome $chromosome
>>   --chunk_size $chunk_size
>>   --output_format $output_format
>>   
>> 
>> The input  dataset parameter looks like this:
>> 
>> > label="Predict peaks on" />
>> 
>> The tool produces a list of outputs, so I’ve defined a collection like this:
>> 
>>   
>>   
>>   > directory="output" ext="gff" visible="false" />
>>   
>>   
>> 
>> I’m using planemo, version 0.19.0.
>> 
>> Here is one of the tools’ functional test definitions.
>> 
>>   
>>   > ftype="gff" />
>>   
>>   
>>   
>>   
>>   
>>   
>>   
>>   
>>   
>>   
>>   > ftype="gff" />
>>   
>>   
>> 
>> Here is the log from running the test with planemo.
>> 
>> Genetrack ( genetrack ) > Test-3 ... 
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,292 
>> Starting new HTTP connection (1): localhost
>> galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,295 Session 
>> authenticated using Galaxy master api key
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,303 "GET 
>> /api/users?key=test_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,305 
>> Starting new HTTP connection (1): localhost
>> galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,308 Session 
>> authenticated using Galaxy master api key
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,326 "POST 
>> /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,328 
>> Starting new HTTP connection (1): localhost
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,418 "POST 
>> /api/histories HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,421 
>> Starting new HTTP connection (1): localhost
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,475 "POST 
>> /api/tools HTTP/1.1" 400 None
>> ERROR
>> 
>> ==
>> ERROR: Genetrack ( genetrack ) > Test-1
>> --
>> Traceback (most recent call last):
>> File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
>> line 289, in test_tool
>>   self.do_it( td )
>> File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
>> line 58, in do_it
>>   raise e
>> RunToolException: Error creating a job for these tool inputs - Unknown error 
>> occurred while processing request.
>>  >> begin captured logging << 
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
>> (1): localhost
>> galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
>> api key
>> requests.packages.urllib3.connectionpool: DEBUG: "GET 
>> /api/users?key=test_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
>> (1): localhost
>>

[galaxy-dev] Planemo 0.19.0 testing tools that produce dataset collections

2015-11-04 Thread Von Kuster, Greg 
Hello Galaxy devs,

I’m developing a tool that uses a multi-select list to accept any number of 
input datasets.  The tool works fine when executing it within Galaxy, but when 
running it through planemo testing, it never passes, so I’m wondering if there 
are known issues with planemo testing tools that produce dataset collections.

I’ve spent some time adding debugging log statements into the Galaxy framework 
for planemo test runs, but haven’t uncovered anything obvious.  So if there are 
no known issues with planemo testing dataset_collections, I’m wondering if my 
tool config syntax is incorrect.

Does anyone see anything obvious?  Any insight is much appreciated!

Here is the command line.  Notice that I do not define any outputs since I am 
using a dataset collection.  Is this causing a problem for planemo?


python $__tool_directory__/genetrack.py
--input_format $input_format_cond.input_format
#if str($input_format_cond.input_format) == "genetracktool":
#for $i in $input_format_cond.input_genetracktool:
 --input "${i}" "${i.hid}" "${i.name}"
#end for
#elif str($input_format_cond.input_format) == "gff":
#for $i in $input_format_cond.input_gff:
 --input "${i}" "${i.hid}" "${i.name}"
#end for
#end if
--sigma $sigma
--exclusion $exclusion
--up_width $up_width
--down_width $down_width
--filter $filter
--chromosome $chromosome
--chunk_size $chunk_size
--output_format $output_format


The input  dataset parameter looks like this:



The tool produces a list of outputs, so I’ve defined a collection like this:







I’m using planemo, version 0.19.0.

Here is one of the tools’ functional test definitions.

















Here is the log from running the test with planemo.

Genetrack ( genetrack ) > Test-3 ... requests.packages.urllib3.connectionpool 
INFO 2015-11-04 15:22:03,292 Starting new HTTP connection (1): localhost
galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,295 Session authenticated 
using Galaxy master api key
requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,303 "GET 
/api/users?key=test_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,305 Starting 
new HTTP connection (1): localhost
galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,308 Session authenticated 
using Galaxy master api key
requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,326 "POST 
/api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,328 Starting 
new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,418 "POST 
/api/histories HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,421 Starting 
new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,475 "POST 
/api/tools HTTP/1.1" 400 None
ERROR

==
ERROR: Genetrack ( genetrack ) > Test-1
--
Traceback (most recent call last):
  File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
line 289, in test_tool
self.do_it( td )
  File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
line 58, in do_it
raise e
RunToolException: Error creating a job for these tool inputs - Unknown error 
occurred while processing request.
 >> begin captured logging << 
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
(1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
api key
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key 
HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
(1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
api key
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1" 200 
None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
(1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
api key
requests.packages.urllib3.connectionpool: DEBUG: "POST 
/api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
(1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 
200 None
requests.packages.urllib3.connectionpool: INFO: