Correction. The above were not reliable methods to ensure the file was copied into the data library. Checking for file_size != 0 was also not effective for large files.
Dannon, can you tell me which field we should query and what state/message which will allow us to avoid race conditions? The only solution that I can see that when the file_size != 0, you then ensure it that the file_size has not changed after a a short delay. Cheers, Rob 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 4:11 PM, Rob Leclerc <robert.lecl...@gmail.com>wrote: > 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/#!/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 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/#!/robleclerc> >>>>> 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/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> >>>> >>>> >>> >> >
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