Re: [galaxy-dev] Creating multiple datasets in a libset

30 May 2013

      Hi Niel,

I've attached my wrapper classes I'm using for the Galaxy API which allows
me to upload multiple files. This was based on the watch_folder example.
There is also a mapping mechanisms to map input and output files to their
workflow labels. See the commented section below for some hints on how to
use it

#################START##################

import config
import os
import shutil
import sys
import time
import logging

sys.path.insert( 0, os.path.dirname( __file__ ) )
from common import submit, display

logging.basicConfig(level=logging.INFO)
log = logging.getLogger('galaxy_api_utils')

class GalaxyLibrary:
    """
        Encapsulates basic functionality for creating a library and
uploading files to a library
    """
    def __init__(self, api_key, api_url, libraryname):
        self.api_key = api_key
        self.api_url = api_url
        self.libraryname = libraryname
        self.jsonstring = None
        self.libset = {}

    def get_library(self):
        """
            Get's the library created/accessed when this class was
initialized
            If the library does not exist then build it
            Returns library_id and the library_folder_id
        """
        if self.jsonstring != None:
            return self.jsonstring
        api_key = self.api_key
        api_url = self.api_url
        libraryname = self.libraryname

        libs = display(api_key, api_url + 'libraries',
return_formatted=False)
        library_id = None
        for library in libs:
            if library['name'] == libraryname:
                library_id = library['id']
        if not library_id:
            lib_create_data = {'name':libraryname}
            library = submit(api_key, api_url + 'libraries',
lib_create_data, return_formatted=False)
            library_id = library['id']
        folders = display(api_key, api_url + "libraries/%s/contents" %
library_id, return_formatted = False)
        for f in folders:
            if f['name'] == "/":
                library_folder_id = f['id']
        if not library_id or not library_folder_id:
            log.error("GalaxyLibrary:get_library    Failure to configure
library destination.")
            raise Exception('Failed to configure library destination')
        self.jsonstring = { 'library_id' : library_id, 'library_folder_id'
: library_folder_id }
        return self.jsonstring

    def upload_files(self, fullpaths):
        """
            Uploads files from a disk location to a Galaxy library
            Accepts an array of full path filenames
            Example: fullpaths = ['/home/username/file1.txt',
'/home/username/files2.txt']
        """
        if self.jsonstring == None:
            self.get_library()

        library_id = self.jsonstring['library_id']
        library_folder_id = self.jsonstring['library_folder_id']
        api_key = self.api_key
        api_url = self.api_url

        #Galaxy needs to read the pathnames as a new line delimited string
        #so we do that transformation here
        fullpaths_string = ""
        for path in fullpaths:
            fullpaths_string = fullpaths_string + path + "\n"

        fullpaths_string = fullpaths_string[:-1]
        data = {}
        data['folder_id'] = library_folder_id
        data['file_type'] = 'auto'
        data['dbkey'] = ''
        data['upload_option'] = 'upload_paths'
        data['filesystem_paths'] = fullpaths_string
        data['create_type'] = 'file'
        #Start the upload. This will return right away, but it may take
awhile
        libset = submit(api_key, api_url + "libraries/%s/contents" %
library_id, data, return_formatted = False)

        #Iterate through each dataset we just uploaded and block until all
files have been written to the Galaxy database
        for ds in libset:
            last_filesize = 0
            while True:
                #If file_size != 0 and the file_size is different after a
second iteration, then we assume the disk write is finished
                ds_id = ds['id']
                uploaded_file = display(api_key, api_url +
'libraries/%s/contents/%s' %(library_id, ds_id), return_formatted=False)
                print uploaded_file
                if uploaded_file['file_size'] != 0 and
uploaded_file['file_size'] == last_filesize:
                    break
                else:
                    last_filesize = uploaded_file['file_size']
                    time.sleep(2)
        self.libset = libset
        return libset

    def get_libset(self):
        return self.libset

    def get_file_id(self, filename):
        """
            Gets the Galaxy file id for a file that we've uploaded with
this object
        """
        libset = self.get_libset()
        for myfile in libset:
            if myfile['name'] == filename:
                return myfile['id']
        return None

class GalaxyWorkflow:
    """
        Encapsulates basic functionality to execute a workflow
    """
    def __init__(self, api_key, api_url, workflow_id):
        self.api_key = api_key
        self.api_url = api_url
        self.workflow_id = workflow_id
        self.history_name = None
        self.history_id = None

    def execute_workflow(self, workflow_id, step_id_mapping, history_name):
        """
            Variable: step_id_mapping
            Example mapping:
            step_id_mapping = { 'input_label_1' : { 'src' : 'ld', id:
<file_id_from_uploaded_lib>' }},  { 'input_label_2' : { 'src' : 'ldda', id:
<file_id_from_dataset>' }}
            where input_label_1 is the name at inputs.<step_id>.label which
you want to associate with a particular fileid
            Files uplpaded should use src':'ld' while library datasets
should be in 'src:ldda'
            history_name: should be a unique name for this run.
        """
        api_key = self.api_key
        api_url = self.api_url

        workflow = display(api_key, api_url + 'workflows/%s' %
self.workflow_id, return_formatted = False)
        wf_data = {}
        wf_data['workflow_id'] = workflow['id']
        self.history_name = "%s - %s" % (history_name, workflow['name'])
        wf_data['history'] = self.history_name
        ds_map = {}

        #We need to map to the workflow's input label names to the step id
since changes the galaxy database
        #will change the workflow step_id numbers
        for step_id, val in workflow['inputs'].iteritems():
            label = val['label']
            ds_map[step_id] =  step_id_mapping[label]
        wf_data['ds_map'] = ds_map

        #Run the workflow. This will return immediately, but it will take
awhile to run
        res = submit( api_key, api_url + 'workflows', wf_data,
return_formatted=False)
        if res:
            log.info('GalaxyWorkflow:execute_workflow    workflow executed.
Result:' + str(res))
            self.history_id = res['history']
            return GalaxyHistory(api_key, api_url, self.history_id)
        return None

class GalaxyHistory:
    """
        encapsulates basic functionality for exporting results from a
history.
    """
    def __init__(self, api_key, api_url, history_id):
        self.api_key = api_key
        self.api_url = api_url
        self.history_id = history_id

    # Export all designated 'output' files in the workflow to an export
location outside of galaxy
    # This just copies datasets located the $GALAXY_HOME/database/files/<a
sub dir> to an output director
    # dest_folder is in the format such as /Users/Robs/
    # galaxyCopyFileMap
    # We need to map the output filenames specified in the workflow to
output filenames
    # Example format:
    # galaxyCopyFileMap = { 'galaxy_output_filename1' :
'myarchivename1.ext', ''galaxy_output_filename1' : 'myarchivename2.ext' }
    def export_results(self, dest_folder, copyFileMap):
        """
            Export all designated 'output' files in the workflow to an
export location outside of galaxy
            This just copies datasets located the
$GALAXY_HOME/database/files/<a sub dir> to an output director
            dest_folder is in the format such as /Users/Robs/
            galaxyCopyFileMap
            We need to map the output filenames specified in the workflow
to output filenames
            Example format:
            galaxyCopyFileMap = { 'galaxy_output_filename1' :
'myarchivename1.ext', ''galaxy_output_filename1' : 'myarchivename2.ext' }
        """
        api_key = self.api_key
        api_url = self.api_url
        history_id = self.history_id
        if dest_folder.endswith('/') == False:
            dest_folder = dest_folder + '/'

        history_contents = display(api_key, api_url + 'histories/' +
history_id + '/contents', return_formatted=False)

        #Use the copyFileMap to copy the files designated with a specific
output label to a filename for exporting out of galaxy
        for internalfn, newfn in copyFileMap.iteritems():
            for dsh in history_contents:
                if 'name' in dsh:
                    if dsh['name'] == internalfn:
                        result_ds_url = api_url + 'histories/' + history_id
+ '/contents/' + dsh['id'];

                        #Block until all results have been written to disk
                        ds_file_size = 0
                        while True:
                            result_ds = display(api_key, result_ds_url,
return_formatted=False)
                            print result_ds
                            if result_ds["file_size"] != 0 and
result_ds["file_size"] == ds_file_size:
                                break
                            else:
                                ds_file_size = result_ds["file_size"]
                                time.sleep(2)

                        result_file_name = result_ds['file_name'];
                        fname = dest_folder + newfn
                        shutil.copy(result_file_name, fname)

# def main():
#
#     EXAMPLE:
#     workflow_id = "<your_workflow_id_here>"
#     api_key = "<your_api_key_here>"
#     api_url = "http://localhost:8080/api/"
#     library_name =  "<your_libraryname_here>"
#     history_name = library_name + '-hist'
#
#     gl = GalaxyLibrary(api_key, api_url, library_name )
#     fileset = ['/Users/Rob/input1.vcf', '/Users/Rob/input1.bed']
#     gl.upload_files(fileset);
#     libset =  gl.get_libset()
#
#     #Map workflow input labels with input files
#     step_id_mapping =  get_map(libset)
#     #Add Archived Datasets
#
#     gwf = GalaxyWorkflow(api_key, api_url, workflow_id)
#     galaxyHistory = gwf.execute_workflow(workflow_id, step_id_mapping,
history_name)
#
#     #Map the output label with a filename to export the results once the
run is completed
#     copyFileMap = {"output1":"output_file.txt"}
#     gh = GalaxyHistory(api_key, api_url, history_id)
#     gh.export_results("/Users/Rob", copyFileMap)
#
#
#
#Map a workflows input labels to the file ids of input files. Assumes
you've labeled your workflow inputs accordingly.
#def get_map(libset):
#    ds_map = {}
#    #Add dynamic data sets
#    for ds in libset:
#        if ds['name'].endswith("vcf"):
#            ds_map['INPUT_LABEL_1'] = { 'src' : 'ld', 'id' : ds['id'] }
 #The first file you uploaded
#        if ds['name'].endswith("bed"):
#            ds_map['INPUT_LABEL_2'] = { 'src' : 'ld', 'id' : ds['id'] }
 #The second file you uploaded
#    #Add Archived Datasets
#    ds_map['INPUT_LABEL_3'] = { 'src' : 'ldda', 'id' :
'<id_to_an_input_file_already_stored_in_the_data_library>'}
#    return ds_map
#
# if __name__ == '__main__':
#     main()

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 Thu, May 30, 2013 at 8:39 AM, Rob Leclerc <robert.leclerc@gmail.com>wrote:
...
Hi Neil,
Is fullpaths a *new line* delimited string?
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 May 30, 2013, at 1:09 AM, <Neil.Burdett@csiro.au> wrote:
Hi Rob,****
Thanks for the class I assume you created it in the
“example_watch_folder.py” or whatever you may have renamed it too? Can you
send me the full python script if possible ?****
** **
I modified example_watch_folder.py as followed (using your code):****
** **
if __name__ == '__main__':****
try:****
api_key = sys.argv[1]****
api_url = sys.argv[2]****
#in_folder = sys.argv[3]****
#out_folder = sys.argv[4]****
fullpaths = sys.argv[3]****
data_library = sys.argv[4]****
workflow = sys.argv[5]****
except IndexError:****
print 'usage: %s key url in_folder out_folder data_library
workflow' % os.path.basename( sys.argv[0] )****
sys.exit( 1 )****
#main(api_key, api_url, in_folder, out_folder, data_library, workflow )
****
main(api_key, api_url, fullpaths, data_library, workflow )****
** **
#def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
****
def main(api_key, api_url, fullpaths, data_library, workflow):****
...****
** **
while 1:****
#Galaxy needs to read the pathnames as a new line delimited string
****
#so we do that transformation here****
print fullpaths****
fullpaths_string = ""****
for path in fullpaths:****
fullpaths_string = fullpaths_string + path + "\n"****
****
fullpaths_string = fullpaths_string[:-1]****
data = {}****
data['folder_id'] = library_folder_id****
data['file_type'] = 'auto'****
data['dbkey'] = ''****
data['upload_option'] = 'upload_paths'****
data['filesystem_paths'] = fullpaths_string****
data['create_type'] = 'file'****
print "before libset "****
#Start the upload. This will return right away, but it may take
awhile****
libset = submit(api_key, api_url + "libraries/%s/contents" %
library_id, data, return_formatted = False)****
print "after libset "****
#Iterate through each dataset we just uploaded and block until all
files have been written to the Galaxy database****
for ds in libset:****
last_filesize = 0****
while True:****
#If file_size != 0 and the file_size is different after a
second iteration, then we assume the disk write is finished****
ds_id = ds['id']****
uploaded_file = display(api_key, api_url +
'libraries/%s/contents/%s' %(library_id, ds_id), return_formatted=False)**
**
print uploaded_file****
if uploaded_file['file_size'] != 0 and
uploaded_file['file_size'] == last_filesize:****
break****
else:****
last_filesize = uploaded_file['file_size']****
time.sleep(2)****
** **
However, when I run this I get the following output i.e. there is a new
line after each character should you not use os.path.dirname:****
** **
./milxview_watch_folder.py de5f19fcf64a47ca9b61cfc3bf41490c
http://barium-rbh/csiro/api/"/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"
"This One" f2db41e1fa331b3e
/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
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before libset
after libset
Traceback (most recent call last):
  File "./milxview_watch_folder.py", line 127, in <module>
    main(api_key, api_url, fullpaths, data_library, workflow )
  File "./milxview_watch_folder.py", line 70, in main
    ds_id = ds['id']
TypeError: string indices must be integers, not str****
** **
** **
*From:* Rob Leclerc [mailto:robert.leclerc@gmail.com<robert.leclerc@gmail.com>]
*Sent:* Wednesday, 29 May 2013 11:38 PM
*To:* Burdett, Neil (ICT Centre, Herston - RBWH)
*Cc:* galaxy-dev@lists.bx.psu.edu; Dannon Baker
*Subject:* Re: Creating multiple datasets in a libset****
** **
Hi Neil,****
** **
I've attached my class function for uploading multiple files. ****
** **
def upload_files(self, fullpaths):****
"""****
Uploads files from a disk location to a Galaxy library****
Accepts an array of full path filenames****
Example: fullpaths = ['/home/username/file1.txt',
'/home/username/files2.txt']****
"""****
if self.jsonstring == None:****
self.get_library()****
****
library_id = self.library_id****
library_folder_id = self.library_folder_id****
api_key = self.api_key****
api_url = self.api_url****
****
#Galaxy needs to read the pathnames as a new line delimited string
****
#so we do that transformation here****
fullpaths_string = ""****
for path in fullpaths:****
fullpaths_string = fullpaths_string + path + "\n"****
****
fullpaths_string = fullpaths_string[:-1]****
data = {}****
data['folder_id'] = library_folder_id****
data['file_type'] = 'auto'****
data['dbkey'] = ''****
data['upload_option'] = 'upload_paths'****
data['filesystem_paths'] = fullpaths_string****
data['create_type'] = 'file'****
#Start the upload. This will return right away, but it may take
awhile****
libset = submit(api_key, api_url + "libraries/%s/contents" %
library_id, data, return_formatted = False)****
****
#Iterate through each dataset we just uploaded and block until all
files have been written to the Galaxy database****
for ds in libset:****
last_filesize = 0****
while True:****
#If file_size != 0 and the file_size is different after a
second iteration, then we assume the disk write is finished****
ds_id = ds['id']****
uploaded_file = display(api_key, api_url +
'libraries/%s/contents/%s' %(library_id, ds_id), return_formatted=False)**
**
print uploaded_file****
if uploaded_file['file_size'] != 0 and
uploaded_file['file_size'] == last_filesize:****
break****
else:****
last_filesize = uploaded_file['file_size']****
time.sleep(2)****
self.libset = libset****
return libset****
** **
****
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 Wed, May 29, 2013 at 12:45 AM, <Neil.Burdett@csiro.au> wrote:****
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=64f32098...
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.leclerc@gmail.com>
To: Dannon Baker <dannon.baker@gmail.com>
Cc: "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] Creating multiple datasets in a libset
Message-ID:
        <CAGkd85fHSgO2YC1T+Frctyso9G5rfQb=_mLyHGSdxPM+s3=
8pg@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.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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