Further, when I look in the ~galaxy-dist/database/files/000 I can see both
files have been uploaded but only the second file has a history associated to it
Thanks
Neil
-----Original Message-----
From: Burdett, Neil (ICT Centre, Herston - RBWH)
Sent: Wednesday, 29 May 2013 2:45 PM
To: galaxy-dev@lists.bx.psu.edu; 'Dannon Baker'; 'robert.lecl...@gmail.com'
Subject: Re: Creating multiple datasets in a libset
Hi Guys,
Did you manage to get multiple datasets working? I can't seem to
upload multiple files. Only the last file appears in the history. I changed my
code as mentioned in the thread below in "example_watch_folder.py" to add
multiple files separated by a new line and increased the sleep time:
for fname in os.listdir(in_folder):
fullpath = os.path.join(in_folder, fname)
print ' fullpath is [%s] ' % fullpath
if os.path.isfile(fullpath):
data = {}
data['folder_id'] = library_folder_id
data['file_type'] = 'auto'
data['dbkey'] = ''
data['upload_option'] = 'upload_paths'
data['filesystem_paths'] =
"/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T1_Screening.nii.gz\n
/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz"
print ' data is [%s] ' % str(data['filesystem_paths'])
data['create_type'] = 'file'
libset = submit(api_key, api_url + "libraries/%s/contents" %
library_id, data, return_formatted = False)
#TODO Handle this better, but the datatype isn't always
# set for the followup workflow execution without this
# pause.
time.sleep(65)
However, I get the following crash:
./example_watch_folder.py 64f3209856a3cf4f2d034a1ad5bf851c
http://barium-rbh/csiro/api/ /home/galaxy/galaxy-drop/input
/home/galaxy/galaxy-drop/output "This One" f2db41e1fa331b3e
fullpath is [/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz]
data is [/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T1_Screening.nii.gz
/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz]
url is :
http://barium-rbh/csiro/api/libraries/33b43b4e7093c91f/contents?key=64f3209856a3cf4f2d034a1ad5bf851c
data is : {'file_type': 'auto', 'dbkey': '', 'create_type': 'file',
'folder_id': 'F33b43b4e7093c91f', 'upload_option': 'upload_paths',
'filesystem_paths':
'/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T1_Screening.nii.gz\n
/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz'}
url is :
http://barium-rbh/csiro/api/workflows?key=64f3209856a3cf4f2d034a1ad5bf851c
data is : {'workflow_id': 'f2db41e1fa331b3e', 'ds_map': {'14': {'src': 'ld',
'id': 'ff5476bcf6c921fa'}}, 'history': '141_S_0851_MRI_T2_Screening.nii.gz -
apiFullCTE'}
{'outputs': ['daecbdd824e1c349', '358eb58cd5463e0d', 'c0279aab05812500'],
'history': '3cc0effd29705aa3'} url is :
http://barium-rbh/csiro/api/workflows?key=64f3209856a3cf4f2d034a1ad5bf851c
data is : {'workflow_id': 'f2db41e1fa331b3e', 'ds_map': {'14': {'src': 'ld',
'id': '79966582feb6c081'}}, 'history': '141_S_0851_MRI_T2_Screening.nii.gz -
apiFullCTE'}
{'outputs': ['19c51286b777bc04', '0f71f1fc170d4ab9', '256444f6e7017e58'],
'history': 'b701da857886499b'} Traceback (most recent call last):
File "./example_watch_folder.py", line 89, in <module>
main(api_key, api_url, in_folder, out_folder, data_library, workflow )
File "./example_watch_folder.py", line 75, in main
shutil.move(fullpath, os.path.join(out_folder, fname))
File "/usr/lib/python2.7/shutil.py", line 299, in move
copy2(src, real_dst)
File "/usr/lib/python2.7/shutil.py", line 128, in copy2
copyfile(src, dst)
File "/usr/lib/python2.7/shutil.py", line 82, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz'
It says there is no such file, but this file has already been copied from the
input to the output directory. Any help much appreciated
Neil
------------------------------
Message: 2
Date: Mon, 29 Apr 2013 16:11:39 -0400
From: Rob Leclerc <robert.lecl...@gmail.com>
To: Dannon Baker <dannon.ba...@gmail.com>
Cc: "galaxy-...@bx.psu.edu" <galaxy-...@bx.psu.edu>
Subject: Re: [galaxy-dev] Creating multiple datasets in a libset
Message-ID:
<CAGkd85fHSgO2YC1T+Frctyso9G5rfQb=_mLyHGSdxPM+s3=8...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi Dannon,
I've written some code to (i) query a dataset to ensure that it's been uploaded
after a submit and (ii) to ensure a resulting dataset has been written to the
file.
*#Block until all datasets have been uploaded* libset = submit(api_key, api_url
+ "libraries/%s/contents" % library_id, data, return_formatted = False) for ds
in libset:
while True:
uploaded_file = display(api_key, api_url + 'libraries/%s/contents/%s'
%(library_id, ds['id']), return_formatted=False)
if uploaded_file['misc_info'] == None:
time.sleep(1)
else:
break
*#Block until all result datasets have been saved to the filesystem*
result_ds_url = api_url + 'histories/' + history_id + '/contents/' + dsh['id'];
while True:
result_ds = display(api_key, result_ds_url, return_formatted=False)
if result_ds["state"] == 'ok':
break
else:
time.sleep(1)
Rob Leclerc, PhD
<http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc>
P: (US) +1-(917)-873-3037
P: (Shanghai) +86-1-(861)-612-5469
Personal Email: rob.lecl...@aya.yale.edu
On Mon, Apr 29, 2013 at 11:18 AM, Dannon Baker <dannon.ba...@gmail.com>wrote:
> Yep, that example filesystem_paths you suggest should work fine. The
> sleep() bit was a complete hack from the start, for simplicity in
> demonstrating a very basic pipeline, but what you probably want to do
> for a real implementation is query the dataset in question via the
> API, verify that the datatype/etc have been set, and only after that
> execute the workflow; instead of relying on sleep.
>
>
> On Mon, Apr 29, 2013 at 9:24 AM, Rob Leclerc <robert.lecl...@gmail.com>wrote:
>
>> Hi Dannon,
>>
>> Thanks for the response. Sorry to be pedantic, but just to make sure
>> that I understand the interpretation of this field on the other side
>> of the API, I would need to have something like the following:
>>
>> data['filesystem_paths'] = "/home/me/file1.vcf \n /home/me/file2.vcf
>> /n /home/me/file3.vcf"
>>
>> I assume I should also increase the time.sleep() to reflect the
>> uploading of extra files?
>>
>> Cheers,
>>
>> Rob
>>
>> Rob Leclerc, PhD
>> <http://www.linkedin.com/in/robleclerc><https://twitter.com/#!/roblec
>> lerc>
>> P: (US) +1-(917)-873-3037
>> P: (Shanghai) +86-1-(861)-612-5469
>> Personal Email: rob.lecl...@aya.yale.edu
>>
>>
>> On Mon, Apr 29, 2013 at 9:15 AM, Dannon Baker <dannon.ba...@gmail.com>wrote:
>>
>>> Hey Rob,
>>>
>>> That example_watch_folder.py does just submit exactly one at a time,
>>> executes the workflow, and then does the next all in separate transactions.
>>> If you wanted to upload multiple filepaths at once, you'd just
>>> append more to the ''filesystem_paths' field (newline separated paths).
>>>
>>> -Dannon
>>>
>>>
>>> On Fri, Apr 26, 2013 at 11:54 PM, Rob Leclerc
>>> <robert.lecl...@gmail.com>wrote:
>>>
>>>> I'm looking at example_watch_folder.py and it's not clear from the
>>>> example how you submit multiple datasets to a library. In the
>>>> example, the first submit returns a libset [] with only a single
>>>> entry and then proceeds to iterate through each dataset in the libset in
>>>> the following section:
>>>>
>>>> data = {}
>>>>
>>>> data['folder_id'] = library_folder_id
>>>>
>>>> data['file_type'] = 'auto'
>>>>
>>>> data['dbkey'] = ''
>>>>
>>>> data['upload_option'] = 'upload_paths'
>>>>
>>>>
>>>>
>>>> *data['filesystem_paths'] = fullpath*
>>>>
>>>> data['create_type'] = 'file'
>>>>
>>>> libset = submit(api_key, api_url + "libraries/%s/contents" %
>>>> library_id, data, return_formatted = False)
>>>>
>>>> time.sleep(5)
>>>>
>>>> for ds in libset:
>>>>
>>>> if 'id' in ds:
>>>>
>>>> wf_data = {}
>>>>
>>>> wf_data['workflow_id'] = workflow['id']
>>>>
>>>> wf_data['history'] = "%s - %s" % (fname,
>>>> workflow['name'])
>>>>
>>>> wf_data['ds_map'] = {}
>>>>
>>>> for step_id, ds_in in workflow['inputs'
>>>> ].iteritems():
>>>>
>>>> wf_data['ds_map'][step_id] =
>>>> {'src':'ld', 'id':ds['id']}
>>>>
>>>> res = submit( api_key, api_url +
>>>> 'workflows', wf_data, return_formatted=False)
>>>>
>>>>
>>>>
>>>> Rob Leclerc, PhD
>>>> <http://www.linkedin.com/in/robleclerc><https://twitter.com/#!/robl
>>>> eclerc>
>>>> P: (US) +1-(917)-873-3037
>>>> P: (Shanghai) +86-1-(861)-612-5469
>>>> Personal Email: rob.lecl...@aya.yale.edu
>>>>
>>>> ___________________________________________________________
>>>> 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/
>>>>
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>>>> http://galaxyproject.org/search/mailinglists/
>>>>
>>>
>>>
>>
>
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