Hey Rob, I haven't touched in quite some time, but from the comments it indicates that the sleep was because the datatype hadn't been detected and set yet, so that's what I'd check for -- specifically result_ds['data_type'] being something sensible (I have no idea what it is by default off the top of my head). Let me know if this doesn't work and I can take a closer look. -Dannon On Mon, Apr 29, 2013 at 7:37 PM, Rob Leclerc <robert.leclerc@gmail.com>wrote:
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.leclerc@aya.yale.edu
On Mon, Apr 29, 2013 at 4:11 PM, Rob Leclerc <robert.leclerc@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.leclerc@aya.yale.edu
On Mon, Apr 29, 2013 at 11:18 AM, Dannon Baker <dannon.baker@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.leclerc@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.leclerc@aya.yale.edu
On Mon, Apr 29, 2013 at 9:15 AM, Dannon Baker <dannon.baker@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.leclerc@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.leclerc@aya.yale.edu
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