These names have meaning in CollectedDatasetMatch:

designation means designation if that exists else name
name means name
dbkey means dbkey
ext means ext
visible means visible


On 21 October 2015 at 08:44, Steve Cassidy <steve.cass...@mq.edu.au> wrote:

> Thanks, yes that works, though I'm not really sure what the difference is
> between __name__ and __designation__. They both seem to have the same
> effect in my example.
>
> Thanks for your help.
>
> Steve
>
>
> On 21 October 2015 at 16:49, Peter van Heusden <p...@sanbi.ac.za> wrote:
>
>> Since you're using a directory, you can use one of the built in patterns:
>>
>> DEFAULT_EXTRA_FILENAME_PATTERN = 
>> r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
>>
>> NAMED_PATTERNS = {
>>     "__default__": DEFAULT_EXTRA_FILENAME_PATTERN,
>>     "__name__": r"(?P<name>.*)",
>>     "__designation__": r"(?P<designation>.*)",
>>     "__name_and_ext__": r"(?P<name>.*)\.(?P<ext>[^\.]+)?",
>>     "__designation_and_ext__": r"(?P<designation>.*)\.(?P<ext>[^\._]+)?",
>> }
>>
>> In terms of docs, I don't know what the future is - the Galaxy wiki or 
>> http://galaxy.readthedocs.org/en/master/
>>
>>
>> On 21 October 2015 at 04:26, Steve Cassidy <steve.cass...@mq.edu.au>
>> wrote:
>>
>>> Ah, thankyou, yes, I can now get results by using patterns to match the
>>> output.  I used your example but prepend 'simple' to the filename and then
>>> searches for that with:
>>>
>>> <discover_datasets pattern="simple(?P&lt;name&gt;.*)" />
>>> this solves the problem for the sample script but not generally since in
>>> general I can't predict the filenames that will be generated - this is a
>>> tool for downloading data from a repository which could be text, audio or
>>> video data.
>>>
>>> If I don't use the 'simple' prefix and omit the file extension I still
>>> get my data but I also get three other files which are temporary scripts
>>> generated by galaxy and placed in the working directory.  So, back to
>>> trying to put things in a subdirectory. It turns out that the issue I was
>>> having was as you pointed out earlier, the directory attribute to
>>> discover_datasets doesn't allow variables, so I need to write to a fixed
>>> directory name:
>>>
>>> <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="SampleDataset
>>> " />
>>> This now works!
>>>
>>> I had thought that I'd need to use a unique directory name but since
>>> galaxy runs each job in a separate directory, this isn't required.  My real
>>> tool now works too after following the same pattern.
>>>
>>> Thanks for your help.  I'll see if I can write this up in a blog post.
>>>
>>> Steve
>>>
>>>
>>>
>>> On 21 October 2015 at 00:06, Peter van Heusden <p...@sanbi.ac.za> wrote:
>>>
>>>> I poked around at your tool XML and the code a bit and the problem is
>>>> directory="$job_name". Galaxy expects to collect files from the job's
>>>> working directory - basically the current working directory the job runs
>>>> in. The directory= argument doesn't have variables expanded as far as I can
>>>> tell. In any event it is used in walk_over_extra_files() that is in
>>>> lib/galaxy/tools/parameters/output_collect.py - if you look there you see
>>>> that it is simply appended to the job's working directory.
>>>>
>>>> So if you use:
>>>>
>>>>             <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" />
>>>>
>>>> (note the &lt; and &gt; - this is effectively the regexp
>>>> r"(?P<name>.*)\.txt" with the < and > escaped out)
>>>>
>>>> And alter the code so that it just writes files to the current
>>>> directory, then you'll pick up the files one.txt, two,txt and three.txt.
>>>>
>>>> Peter
>>>>
>>>> On 20 October 2015 at 12:28, Steve Cassidy <steve.cass...@mq.edu.au>
>>>> wrote:
>>>>
>>>>> Sorry, it was just an example of a tool that works - the file that it
>>>>> writes out is put into that directory, so I assume that's where my files
>>>>> should end up too.
>>>>>
>>>>> Steve
>>>>>
>>>>> On 20 October 2015 at 21:12, Peter van Heusden <p...@sanbi.ac.za>
>>>>> wrote:
>>>>>
>>>>>> Sorry, I don't understand - what does the Upload File tool have to do
>>>>>> with this?
>>>>>>
>>>>>> On 20 October 2015 at 11:49, Steve Cassidy <steve.cass...@mq.edu.au>
>>>>>> wrote:
>>>>>>
>>>>>>> Yes, I'm sure that's where the problem lies. Writing out to the
>>>>>>> current directory doesn't work.  The files get written to
>>>>>>> 'job_working_directory/000/1/' but if I run the Upload File tool the 
>>>>>>> result
>>>>>>> is placed in 'files/000/'.  I think I need to work out where to write 
>>>>>>> the
>>>>>>> files, I found some references to $__new_file_path__ but that doesn't 
>>>>>>> seem
>>>>>>> to help.
>>>>>>>
>>>>>>> Steve
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 20 October 2015 at 19:57, Peter van Heusden <p...@sanbi.ac.za>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> I suspect that the problem might be in the <discover_datasets>
>>>>>>>> then. I'm not an export on this, but "__name_and_ext__" turns into the
>>>>>>>> regexp r"(?P<name>.*)\.(?P<ext>[^\.]+)?" in
>>>>>>>> lib/galaxy/tools/parameters/output_collect.py, and is used by the
>>>>>>>> DatasetCollector (line 358). This looks like it should match the 
>>>>>>>> filenames
>>>>>>>> you're creating, but I'm not 100% sure how that code works. One thing I
>>>>>>>> notice is the "directory" argument. If you write jobs to the current
>>>>>>>> directory instead of "output_path" can you get it to work?
>>>>>>>>
>>>>>>>> Peter
>>>>>>>>
>>>>>>>> On 20 October 2015 at 09:52, Steve Cassidy <steve.cass...@mq.edu.au
>>>>>>>> > wrote:
>>>>>>>>
>>>>>>>>> Thanks Peter,
>>>>>>>>>   I did see that proviso somewhere but no, refreshing doesn't help.
>>>>>>>>>
>>>>>>>>> That page was one of those that I referred to getting to this
>>>>>>>>> point.
>>>>>>>>>
>>>>>>>>> Steve
>>>>>>>>>
>>>>>>>>> On 20 October 2015 at 18:33, Peter van Heusden <p...@sanbi.ac.za>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Just a quick check - did you refresh your history to confirm that
>>>>>>>>>> the dataset *is* empty? We had the same thing at SANBI but it turns 
>>>>>>>>>> out
>>>>>>>>>> that Galaxy creates an empty output collection and then only 
>>>>>>>>>> populates it
>>>>>>>>>> sometime after job completion (this is a know UI bug).
>>>>>>>>>>
>>>>>>>>>> See:
>>>>>>>>>> http://pvh.wp.sanbi.ac.za/2015/09/18/adventures-in-galaxy-output-collections/
>>>>>>>>>>
>>>>>>>>>> On 20 October 2015 at 08:48, Steve Cassidy <
>>>>>>>>>> steve.cass...@mq.edu.au> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi all,
>>>>>>>>>>>   I'm trying to understand how to write a tool that generates a
>>>>>>>>>>> dataset rather than a single output file.  I've tried following all 
>>>>>>>>>>> of the
>>>>>>>>>>> examples but I'm stuck, so I thought I would distil down the 
>>>>>>>>>>> simplest
>>>>>>>>>>> example I could write and ask for help here.
>>>>>>>>>>>
>>>>>>>>>>> So here's my example:
>>>>>>>>>>>
>>>>>>>>>>> https://gist.github.com/stevecassidy/0fa45ad5853faacb5f55
>>>>>>>>>>>
>>>>>>>>>>> it's a simple python script that writes three files to a
>>>>>>>>>>> directory named for the single input parameter.
>>>>>>>>>>>
>>>>>>>>>>> I think one of the problems I'm having is knowing where to write
>>>>>>>>>>> the output to. I've run this under planemo serve and the job runs, 
>>>>>>>>>>> creating
>>>>>>>>>>> the output directory within the 
>>>>>>>>>>> 'job_working_directory/000/1/SampleDataset'
>>>>>>>>>>> directory, however my dataset doesn't contain anything so clearly my
>>>>>>>>>>> outputs directive isn't working:
>>>>>>>>>>>
>>>>>>>>>>>     <outputs>
>>>>>>>>>>>         <collection type="list" label="$job_name" name="output1">
>>>>>>>>>>>             <discover_datasets pattern="__name_and_ext__"
>>>>>>>>>>> directory="$job_name" />
>>>>>>>>>>>         </collection>
>>>>>>>>>>>     </outputs>
>>>>>>>>>>>
>>>>>>>>>>> ($job_name is the name of the directory that is being written
>>>>>>>>>>> to, SampleDataset in this case)
>>>>>>>>>>>
>>>>>>>>>>> Any help in getting this example working would be appreciated.
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Steve
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Department of Computing, Macquarie University
>>>>>>>>>>> http://web.science.mq.edu.au/~cassidy/
>>>>>>>>>>>
>>>>>>>>>>> ___________________________________________________________
>>>>>>>>>>> Please keep all replies on the list by using "reply all"
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>>>>>>>>>>>
>>>>>>>>>>> To search Galaxy mailing lists use the unified search at:
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>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ___________________________________________________________
>>>>>>>>>> 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:
>>>>>>>>>>   https://lists.galaxyproject.org/
>>>>>>>>>>
>>>>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>>>>>   http://galaxyproject.org/search/mailinglists/
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Department of Computing, Macquarie University
>>>>>>>>> http://web.science.mq.edu.au/~cassidy/
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ___________________________________________________________
>>>>>>>> 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:
>>>>>>>>   https://lists.galaxyproject.org/
>>>>>>>>
>>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>>>   http://galaxyproject.org/search/mailinglists/
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Department of Computing, Macquarie University
>>>>>>> http://web.science.mq.edu.au/~cassidy/
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Department of Computing, Macquarie University
>>>>> http://web.science.mq.edu.au/~cassidy/
>>>>>
>>>>
>>>>
>>>> ___________________________________________________________
>>>> 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:
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>>>>
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>>>>
>>>
>>>
>>>
>>> --
>>> Department of Computing, Macquarie University
>>> http://web.science.mq.edu.au/~cassidy/
>>>
>>
>>
>
>
> --
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy/
>
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