def post(self, request, *args, **kwargs):
from_old_template = False
if 'isa_tab_url' in request.POST:
# TODO: I think isa_tab_url is already a full url,
# making this redundant.
full_isa_tab_url = get_full_url(request.POST['isa_tab_url'])
from_old_template = True
else:
request_body = request.body
if not request_body:
err_msg = "Neither form data nor a request body has been sent."
logger.error(err_msg)
return HttpResponseBadRequest(err_msg)
try:
body = json.loads(request_body)
except Exception as e:
err_msg = "Request body is no valid JSON"
logger.error("%s: %s" % (err_msg, e))
return HttpResponseBadRequest("%s." % err_msg)
if "data_set_uuid" in body:
data_set_uuid = body["data_set_uuid"]
else:
err_msg = "Request body doesn't contain data_set_uuid."
logger.error(err_msg)
return HttpResponseBadRequest(err_msg)
try:
full_isa_tab_url = DataSet.objects.get(
uuid=data_set_uuid).get_isa_archive().get_datafile_url()
except (DataSet.DoesNotExist, DataSet.MultipleObjectsReturned,
Exception) as e:
err_msg = "Something went wrong"
logger.error("%s: %s" % (err_msg, e))
return HttpResponseBadRequest("%s." % err_msg)
if from_old_template:
# Redirect to process_isa_tab view
response = HttpResponseRedirect(
get_full_url(reverse('process_isa_tab')))
else:
# Redirect to process_isa_tab view with arg 'ajax' if request is
# not coming from old Django Template
response = HttpResponseRedirect(
get_full_url(reverse('process_isa_tab', args=['ajax'])))
# set cookie
response.set_cookie('isa_tab_url', full_isa_tab_url)
return response
def post(self, request, *args, **kwargs):
from_old_template = False
if 'isa_tab_url' in request.POST:
full_isa_tab_url = get_full_url(request.POST['isa_tab_url'])
from_old_template = True
else:
request_body = request.body
if not request_body:
err_msg = "Neither form data nor a request body has been sent."
logger.error(err_msg)
return HttpResponseBadRequest(err_msg)
try:
body = json.loads(request_body)
except Exception as e:
err_msg = "Request body is no valid JSON"
logger.error("%s: %s" % (err_msg, e))
return HttpResponseBadRequest("%s." % err_msg)
if "data_set_uuid" in body:
data_set_uuid = body["data_set_uuid"]
else:
err_msg = "Request body doesn't contain data_set_uuid."
logger.error(err_msg)
return HttpResponseBadRequest(err_msg)
try:
full_isa_tab_url = get_full_url(DataSet.objects.get(
uuid=data_set_uuid).get_isa_archive().get_datafile_url())
except (DataSet.DoesNotExist, DataSet.MultipleObjectsReturned,
Exception) as e:
err_msg = "Something went wrong"
logger.error("%s: %s" % (err_msg, e))
return HttpResponseBadRequest("%s." % err_msg)
if from_old_template:
# Redirect to process_isa_tab view
response = HttpResponseRedirect(
reverse('process_isa_tab')
)
else:
# Redirect to process_isa_tab view with arg 'ajax' if request is
# not coming from old Django Template
response = HttpResponseRedirect(
reverse('process_isa_tab', args=['ajax'])
)
# set cookie
response.set_cookie('isa_tab_url', full_isa_tab_url)
return response
def get_file_name(nodeuuid, sampFile=None, is_file_uuid=False):
"""Helper function for getting a file_name from a filestore uuid
:param fileuuid: Filestore uuid
:type fileuuid: String
"""
# if uuid is a file_store uuid (associated w/ analysis results)
if is_file_uuid:
temp_fs = FileStoreItem.objects.get(uuid=nodeuuid)
else:
# getting the current file_uuid from the given node_uuid
curr_file_uuid = Node.objects.get(uuid=nodeuuid).file_uuid
# checking to see if it has a file_server item
temp_fs = get_aux_file_item(curr_file_uuid)
# If no associated file_server auxiliary file then use main data file for
# IGV
if temp_fs is None:
# getting file information based on file_uuids
temp_fs = FileStoreItem.objects.get(uuid=curr_file_uuid)
temp_name = temp_fs.datafile.name.split('/')
temp_name = temp_name[len(temp_name) - 1]
# full path to selected UUID File
temp_url = get_full_url(temp_fs.get_datafile_url())
# IGV SEG FILE HACK
if sampFile:
if temp_name.startswith("metaData"):
new_name = temp_name.split("_")
if len(new_name) > 1:
temp_name = new_name[0]
return temp_name, temp_url
def addIGVSamples(fields, results_samp, annot_samples=None):
"""creates phenotype file for IGV
:param samples: Solr results for samples to be included
:type samples: Array.
:param annot_samples: includes annotation files included with solr results
:type annot_samples: Array
"""
# creates human readable indexes of fields to iterate over
fields_dict = {}
for i in fields:
find_index = i.find("_Characteristics_")
if find_index > -1:
new_key = i.split("_Characteristics_")[0]
fields_dict[i] = new_key
# Creating temp file to enter into file_store
tempsampname = tempfile.NamedTemporaryFile(delete=False)
# writing header to sample file
tempsampname.write("#sampleTable" + "\n")
# writing column names to sample file
col_names = "Linking_id"
for k, v in fields_dict.iteritems():
col_names = col_names + '\t' + v
tempsampname.write(col_names + "\n")
# iterating over sample files
pheno_results = get_sample_lines(fields_dict, results_samp)
tempsampname.write(pheno_results)
# if annotations are not null
if annot_samples:
pheno_annot = get_sample_lines(fields_dict, annot_samples)
tempsampname.write(pheno_annot)
# closing temp file
tempsampname.close()
# getting file_store_uuid
filestore_uuid = create(tempsampname.name, permanent=True, filetype="txt")
filestore_item = import_file(filestore_uuid, permanent=True, refresh=True)
# file to rename
temp_file = filestore_item.datafile.name.split('/')
temp_file = temp_file[len(temp_file) - 1] + '.txt'
# rename file by way of file_store
filestore_item = rename(filestore_uuid, temp_file)
# getting file information based on file_uuids
curr_fs = FileStoreItem.objects.get(uuid=filestore_uuid)
# full path to selected UUID File
curr_url = get_full_url(curr_fs.get_datafile_url())
# delete temp file
os.unlink(tempsampname.name)
return curr_url
def test_get_full_url_remote_file(self):
"""Check if the source URL is returned for files that have not been
imported
"""
# create FileStoreItem instances without any disk operations
item_from_url = FileStoreItem.objects.create(source=self.url_source,
sharename=self.sharename)
self.assertEqual(get_full_url(item_from_url.get_datafile_url()),
item_from_url.source)
def test_get_full_url_remote_file(self):
"""Check if the source URL is returned for files that have not been
imported
"""
# create FileStoreItem instances without any disk operations
item_from_url = FileStoreItem.objects.create(source=self.url_source,
sharename=self.sharename)
self.assertEqual(get_full_url(item_from_url.get_datafile_url()),
item_from_url.source)
def logout(request):
token = request.session.get('webinar_access_token')
if token is not None:
requests.post(get_full_url(request, 'revoke-token'),
data={
'token': token,
})
request.session.pop('webinar_access_token', None)
return redirect('index')
def test_get_full_url_local_file(self):
"""Check if the full URL is properly returned for files that exist
in Refinery
"""
# create FileStoreItem instances without any disk operations
local_file = FileStoreItem.objects.create(datafile=SimpleUploadedFile(
self.filename, 'Coffee is delicious!'),
source=self.path_source,
sharename=self.sharename)
self.assertEqual(
get_full_url(local_file.get_datafile_url()),
'{}://{}{}'.format(settings.REFINERY_URL_SCHEME,
Site.objects.get_current().domain,
local_file.datafile.url))
def post(self, request, *args, **kwargs):
serializer_class = self.get_serializer_class()
serializer = serializer_class(data=request.data,
context={'request': request})
serializer.is_valid(raise_exception=True)
shortcut = serializer.validated_data['shortcut']
full_url = get_full_url(shortcut)
if full_url:
return JsonResponse({
'status': 'ok',
'full_url': full_url
},
status=status.HTTP_200_OK)
return HttpResponseBadRequest()
def index(request):
# create callback url
callback_url = get_full_url(request, 'callback')
# get access token from session
token = request.session.get('webinar_access_token')
context = {
'registered':
bool(token is not None),
'auth_url':
(f'{settings.OAUTH_SERVER_URL}/o/authorize?response_type=code'
f'&client_id={settings.CLIENT_ID}&redirect_uri={callback_url}'),
'form':
ResourceForm()
}
return render(request, 'front/index.html', context)
def token(request):
"""
Gets token with auth code. Input should be in the format:
{"code": "code"}
"""
redir_url = get_full_url(request, 'callback')
resp = requests.post(
f'{OAUTH_SERVER_URL}/o/token/',
data={
'grant_type': 'authorization_code',
'redirect_uri': redir_url,
'code': request.data['code'],
'client_id': CLIENT_ID,
'client_secret': CLIENT_SECRET,
},
)
return Response(resp.json())
def callback(request):
# clear stored auth code
request.session.pop('webinar_auth_code', None)
# get auth code sent from Authorization server
code = request.GET.get('code')
if code is not None:
# save it in the session
request.session['webinar_auth_code'] = code
resp = requests.post(get_full_url(request, 'get-token'),
data={
'code': code,
})
resp_data = resp.json()
if 'access_token' in resp_data:
# delete auth code, as it is no longer needed
request.session.pop('webinar_auth_code', None)
request.session['webinar_access_token'] = resp_data['access_token']
return redirect('index')
def _import_analysis_in_galaxy(ret_list, library_id, connection):
"""Take workflow configuration and import files into galaxy
assign galaxy_ids to ret_list
"""
logger.debug("Uploading analysis input files to Galaxy")
for fileset in ret_list:
for k, v in fileset.iteritems():
cur_item = fileset[k]
# getting the current file_uuid from the given node_uuid
try:
curr_file_uuid = Node.objects.get(
uuid=cur_item['node_uuid']).file_uuid
except Node.DoesNotExist:
logger.error("Couldn't fetch Node")
return None
try:
current_filestore_item = FileStoreItem.objects.get_item(
uuid=curr_file_uuid)
except FileStoreItem.DoesNotExist:
logger.error("Couldn't fetch FileStoreItem")
return None
# Create url based on filestore_item's location (local file or
# external file)
file_url = get_full_url(current_filestore_item.get_datafile_url())
try:
file_id = connection.libraries.upload_file_from_url(
library_id, file_url)[0]['id']
except (galaxy.client.ConnectionError, IOError) as exc:
logger.error(
"Failed adding file '%s' to Galaxy "
"library '%s': %s", curr_file_uuid, library_id, exc)
raise
cur_item["id"] = file_id
return ret_list
def import_analysis_in_galaxy(ret_list, library_id, connection):
"""Take workflow configuration and import files into galaxy
assign galaxy_ids to ret_list
"""
logger.debug("Uploading analysis input files to Galaxy")
for fileset in ret_list:
for k, v in fileset.iteritems():
cur_item = fileset[k]
# getting the current file_uuid from the given node_uuid
try:
curr_file_uuid = Node.objects.get(
uuid=cur_item['node_uuid']).file_uuid
except Node.DoesNotExist:
logger.error("Couldn't fetch Node!")
return None
try:
current_filestore_item = FileStoreItem.objects.get_item(
uuid=curr_file_uuid)
except FileStoreItem.DoesNotExist:
logger.error("Couldn't fetch FileStoreItem!")
return None
# Create url based on filestore_item's location (local file or
# external file)
file_url = get_full_url(current_filestore_item.get_datafile_url())
try:
file_id = connection.libraries.upload_file_from_url(
library_id, file_url)[0]['id']
except (galaxy.client.ConnectionError, IOError) as exc:
logger.error("Failed adding file '%s' to Galaxy "
"library '%s': %s",
curr_file_uuid, library_id, exc)
raise
cur_item["id"] = file_id
return ret_list
def test_get_full_url_local_file(self):
"""Check if the full URL is properly returned for files that exist
in Refinery
"""
# create FileStoreItem instances without any disk operations
local_file = FileStoreItem.objects.create(source=self.path_source,
sharename=self.sharename)
local_file.datafile = self.test_file
local_file.save()
self.assertEqual(
get_full_url(local_file.get_datafile_url()),
'{}://{}{}'.format(
settings.REFINERY_URL_SCHEME,
Site.objects.get_current().domain,
local_file.datafile.url
)
)
def create_temp_filename_and_url(temp_fs, samp_file):
"""Helper function for creating a temporary filename and file url from a
given FileStore Item and sample file
:param temp_fs: Filestore uuid
:type temp_fs: FileStoreItem
:param samp_file: T/F value for # IGV SEG FILE HACK
:type samp_file: Bool
:returns: temp_name, temp_url
"""
temp_name = temp_fs.datafile.name.split('/')
temp_name = temp_name[len(temp_name) - 1]
# full path to selected UUID File
temp_url = get_full_url(temp_fs.get_datafile_url())
# IGV SEG FILE HACK
if samp_file:
if temp_name.startswith("metaData"):
new_name = temp_name.split("_")
if len(new_name) > 1:
temp_name = new_name[0]
return temp_name, temp_url
def create_temp_filename_and_url(temp_fs, samp_file):
"""Helper function for creating a temporary filename and file url from a
given FileStore Item and sample file
:param temp_fs: Filestore uuid
:type temp_fs: FileStoreItem
:param samp_file: T/F value for # IGV SEG FILE HACK
:type samp_file: Bool
:returns: temp_name, temp_url
"""
temp_name = temp_fs.datafile.name.split("/")
temp_name = temp_name[len(temp_name) - 1]
# full path to selected UUID File
temp_url = get_full_url(temp_fs.get_datafile_url())
# IGV SEG FILE HACK
if samp_file:
if temp_name.startswith("metaData"):
new_name = temp_name.split("_")
if len(new_name) > 1:
temp_name = new_name[0]
return temp_name, temp_url
def get(self, request, shortcut):
full_url = get_full_url(shortcut)
if full_url:
return HttpResponseRedirect(full_url)
return HttpResponseBadRequest()
def create_igv_session(genome, uuids, is_file_uuid=False):
""" Creates session file for selected file uuids, returns newly created
filestore uuid
:param is_file_uuid:
:param genome: Genome to be used in session file i.e. hg18, dm3
:type genome: string.
:param uuids: Array of UUIDs to be used
:type uuids: array.
:param uuids: Host URL i.e. 127.0.0.1:8000
:type uuids: string
"""
# Create IGV Session file and put into Filestore
"""
http://www.postneo.com/projects/pyxml/
<?xml version="1.0" encoding="UTF-8"?>
<Global genome="hg18" locus="EGFR" version="3">
<Resources>
<Resource name="RNA Genes"
path="http://www.broadinstitute.org/igvdata/tcga/gbm/GBM_batch1-8_level3_exp.txt.recentered.080820.gct.tdf"/>
<Resource name="RNA Genes"
path="http://www.broadinstitute.org/igvdata/annotations/hg18/rna_genes.bed"/>
<Resource name="sno/miRNA"
path="http://www.broadinstitute.org/igvdata/tcga/gbm/Sample_info.txt"/>
</Resources>
</Global>
"""
logger.debug("visualization_manager.create_igv_session called")
# Create the minidom document
doc = Document()
# Create the <wml> base element
xml = doc.createElement("Global")
xml.setAttribute("genome", genome)
xml.setAttribute("locus", "All")
xml.setAttribute("version", "4")
doc.appendChild(xml)
# Add Resources
xml_resources = doc.createElement("Resources")
xml.appendChild(xml_resources)
# get paths to url
for samp in uuids:
# gets filestore item
curr_name, curr_url = get_file_name(samp, is_file_uuid=is_file_uuid)
logger.debug('New resource: ' + curr_name + ' - ' + curr_url)
# What to do if fs does not exist?
if curr_name:
# creates Resource element
res = doc.createElement("Resource")
res.setAttribute("name", curr_name)
res.setAttribute("path", curr_url)
xml_resources.appendChild(res)
# Creating temp file to enter into file_store
tempfilename = tempfile.NamedTemporaryFile(delete=False)
tempfilename.write(doc.toprettyxml(indent=" "))
tempfilename.close()
# getting file_store_uuid
filestore_uuid = create(tempfilename.name, filetype="xml")
filestore_item = import_file(filestore_uuid, refresh=True)
# file to rename
temp_name = filestore_item.datafile.name.split('/')
temp_name = temp_name[len(temp_name) - 1] + '.xml'
# rename file by way of file_store
filestore_item = rename(filestore_uuid, temp_name)
# delete temp file
os.unlink(tempfilename.name)
# Url for session file
fs_url = get_full_url(filestore_item.get_datafile_url())
# IGV url for automatic launch of Java Webstart
igv_url = "http://www.broadinstitute.org/igv/projects/current/igv.php" \
"?sessionURL=" + fs_url
return igv_url
def add_igv_samples(fields, results_samp, annot_samples=None):
"""creates phenotype file for IGV
:param samples: Solr results for samples to be included
:type samples: Array.
:param annot_samples: includes annotation files included with solr results
:type annot_samples: Array
"""
# creates human readable indexes of fields to iterate over
fields_dict = {}
for i in fields:
find_index = i.find("_Characteristics_")
if find_index > -1:
new_key = i.split("_Characteristics_")[0]
fields_dict[i] = new_key
# Creating temp file to enter into file_store
temp_sample_name = tempfile.NamedTemporaryFile(delete=False)
# writing header to sample file
temp_sample_name.write("#sampleTable" + "\n")
# writing column names to sample file
col_names = "Linking_id"
for k, v in fields_dict.iteritems():
col_names = col_names + '\t' + v
temp_sample_name.write(col_names + "\n")
# iterating over sample files
pheno_results = get_sample_lines(fields_dict, results_samp)
try:
temp_sample_name.write(pheno_results)
except UnicodeEncodeError as e:
logger.error("Could not write results to file: %s. "
"Trying again with the content to write encoded "
"properly." % e)
temp_sample_name.write(pheno_results.encode("utf-8"))
# if annotations are not null
if annot_samples:
pheno_annot = get_sample_lines(fields_dict, annot_samples)
temp_sample_name.write(pheno_annot)
# closing temp file
temp_sample_name.close()
# getting file_store_uuid
filestore_uuid = create(temp_sample_name.name, filetype="txt")
filestore_item = import_file(filestore_uuid, refresh=True)
# file to rename
temp_file = filestore_item.datafile.name.split('/')
temp_file = temp_file[len(temp_file) - 1] + '.txt'
# rename file by way of file_store
filestore_item = rename(filestore_uuid, temp_file)
# getting file information based on file_uuids
curr_fs = FileStoreItem.objects.get(uuid=filestore_uuid)
# full path to selected UUID File
curr_url = get_full_url(curr_fs.get_datafile_url())
# delete temp file
os.unlink(temp_sample_name.name)
return curr_url
def createIGVsessionAnnot(genome, uuids, annot_uuids=None, samp_file=None):
"""Creates session file for selected file uuids, returns newly created
filestore uuid
:param genome: Genome to be used in session file i.e. hg18, dm3
:type genome: string.
:param uuids: Array of UUIDs to be used
:type uuids: array.
:param uuids: Host URL i.e. 127.0.0.1:8000
:type uuids: string
"""
# Create IGV Session file and put into Filestore
"""
http://www.postneo.com/projects/pyxml/
<?xml version="1.0" encoding="UTF-8"?>
<Global genome="hg18" locus="EGFR" version="3">
<Resources>
<Resource name="RNA Genes"
path="http://www.broadinstitute.org/igvdata/tcga/gbm/GBM_batch1-8_level3_exp.txt.recentered.080820.gct.tdf"/>
<Resource name="RNA Genes"
path="http://www.broadinstitute.org/igvdata/annotations/hg18/rna_genes.bed"/>
<Resource name="sno/miRNA"
path="http://www.broadinstitute.org/igvdata/tcga/gbm/Sample_info.txt"/>
</Resources>
</Global>
"""
# Create the minidom document
doc = Document()
# Create the <wml> base element
xml = doc.createElement("Global")
xml.setAttribute("genome", genome)
xml.setAttribute("locus", "All")
xml.setAttribute("version", "4")
doc.appendChild(xml)
# Add Resources
xml_resources = doc.createElement("Resources")
xml.appendChild(xml_resources)
# adding selected samples to xml file
addIGVResource(uuids["node_uuid"], xml_resources, doc)
if annot_uuids:
# adding selected samples to xml file
addIGVResource(annot_uuids["node_uuid"], xml_resources, doc)
# adds sample information file to IGV session file
if samp_file:
# <Resource name="Sample Information"
# path="http://igv.broadinstitute.org/data/hg18/tcga/gbm/gbmsubtypes/sampleTable.txt.gz"/>
# creates Resource element
res = doc.createElement("Resource")
res.setAttribute("name", "Sample Information")
res.setAttribute("path", samp_file)
xml_resources.appendChild(res)
# <HiddenAttributes>
# <Attribute name="DATA FILE"/>
# <Attribute name="Linking_id"/>
# <Attribute name="DATA TYPE"/>
# </HiddenAttributes>
# Adding parameters to hide basic unnecessary sample info
hidden_attr = doc.createElement("HiddenAttributes")
xml.appendChild(hidden_attr)
attr = doc.createElement("Attribute")
attr.setAttribute("name", "DATA FILE")
hidden_attr.appendChild(attr)
attr = doc.createElement("Attribute")
attr.setAttribute("name", "Linking_id")
hidden_attr.appendChild(attr)
attr = doc.createElement("Attribute")
attr.setAttribute("name", "DATA TYPE")
hidden_attr.appendChild(attr)
# Creating temp file to enter into file_store
tempfilename = tempfile.NamedTemporaryFile(delete=False)
tempfilename.write(doc.toprettyxml(indent=" "))
tempfilename.close()
# getting file_store_uuid
filestore_uuid = create(tempfilename.name, permanent=True, filetype="xml")
filestore_item = import_file(filestore_uuid, permanent=True, refresh=True)
# file to rename
temp_name = filestore_item.datafile.name.split('/')
temp_name = temp_name[len(temp_name) - 1] + '.xml'
# rename file by way of file_store
filestore_item = rename(filestore_uuid, temp_name)
# delete temp file
os.unlink(tempfilename.name)
# Url for session file
sessionfile_url = get_full_url(filestore_item.get_datafile_url())
# IGV url for automatic launch of Java Webstart
igv_url = "http://www.broadinstitute.org/igv/projects/current/igv.php" \
"?sessionURL=" + sessionfile_url
return igv_url
def createIGVsession(genome, uuids, is_file_uuid=False):
""" Creates session file for selected file uuids, returns newly created
filestore uuid
:param genome: Genome to be used in session file i.e. hg18, dm3
:type genome: string.
:param uuids: Array of UUIDs to be used
:type uuids: array.
:param uuids: Host URL i.e. 127.0.0.1:8000
:type uuids: string
"""
# Create IGV Session file and put into Filestore
"""
http://www.postneo.com/projects/pyxml/
<?xml version="1.0" encoding="UTF-8"?>
<Global genome="hg18" locus="EGFR" version="3">
<Resources>
<Resource name="RNA Genes"
path="http://www.broadinstitute.org/igvdata/tcga/gbm/GBM_batch1-8_level3_exp.txt.recentered.080820.gct.tdf"/>
<Resource name="RNA Genes"
path="http://www.broadinstitute.org/igvdata/annotations/hg18/rna_genes.bed"/>
<Resource name="sno/miRNA"
path="http://www.broadinstitute.org/igvdata/tcga/gbm/Sample_info.txt"/>
</Resources>
</Global>
"""
logger.debug("visualization_manager.createIGVsession called")
# Create the minidom document
doc = Document()
# Create the <wml> base element
xml = doc.createElement("Global")
xml.setAttribute("genome", genome)
xml.setAttribute("locus", "All")
xml.setAttribute("version", "4")
doc.appendChild(xml)
# Add Resources
xml_resources = doc.createElement("Resources")
xml.appendChild(xml_resources)
# get paths to url
for samp in uuids:
# gets filestore item
curr_name, curr_url = get_file_name(samp, is_file_uuid=is_file_uuid)
logger.debug('New resource: ' + curr_name + ' - ' + curr_url)
# What to do if fs does not exist?
if (curr_name):
# creates Resource element
res = doc.createElement("Resource")
res.setAttribute("name", curr_name)
res.setAttribute("path", curr_url)
xml_resources.appendChild(res)
# Creating temp file to enter into file_store
tempfilename = tempfile.NamedTemporaryFile(delete=False)
tempfilename.write(doc.toprettyxml(indent=" "))
tempfilename.close()
# getting file_store_uuid
filestore_uuid = create(tempfilename.name, permanent=True, filetype="xml")
filestore_item = import_file(filestore_uuid, permanent=True, refresh=True)
# file to rename
temp_name = filestore_item.datafile.name.split('/')
temp_name = temp_name[len(temp_name) - 1] + '.xml'
# rename file by way of file_store
filestore_item = rename(filestore_uuid, temp_name)
# delete temp file
os.unlink(tempfilename.name)
# Url for session file
fs_url = get_full_url(filestore_item.get_datafile_url())
# IGV url for automatic launch of Java Webstart
igv_url = "http://www.broadinstitute.org/igv/projects/current/igv.php" \
"?sessionURL=" + fs_url
return igv_url
def create_igv_session_annot(genome, uuids, annot_uuids=None, samp_file=None):
"""Creates session file for selected file uuids, returns newly created
filestore uuid
:param genome: Genome to be used in session file i.e. hg18, dm3
:type genome: string.
:param uuids: Array of UUIDs to be used
:type uuids: array.
:param uuids: Host URL i.e. 127.0.0.1:8000
:type uuids: string
"""
# Create IGV Session file and put into Filestore
"""
http://www.postneo.com/projects/pyxml/
<?xml version="1.0" encoding="UTF-8"?>
<Global genome="hg18" locus="EGFR" version="3">
<Resources>
<Resource name="RNA Genes"
path="http://www.broadinstitute.org/igvdata/tcga/gbm/GBM_batch1-8_level3_exp.txt.recentered.080820.gct.tdf"/>
<Resource name="RNA Genes"
path="http://www.broadinstitute.org/igvdata/annotations/hg18/rna_genes.bed"/>
<Resource name="sno/miRNA"
path="http://www.broadinstitute.org/igvdata/tcga/gbm/Sample_info.txt"/>
</Resources>
</Global>
"""
# Create the minidom document
doc = Document()
# Create the <wml> base element
xml = doc.createElement("Global")
xml.setAttribute("genome", genome)
xml.setAttribute("locus", "All")
xml.setAttribute("version", "4")
doc.appendChild(xml)
# Add Resources
xml_resources = doc.createElement("Resources")
xml.appendChild(xml_resources)
# adding selected samples to xml file
add_igv_resource(uuids["node_uuid"], xml_resources, doc)
if annot_uuids:
# adding selected samples to xml file
add_igv_resource(annot_uuids["node_uuid"], xml_resources, doc)
# adds sample information file to IGV session file
if samp_file:
# <Resource name="Sample Information"
# path="http://igv.broadinstitute.org/data/hg18/tcga/gbm/gbmsubtypes/sampleTable.txt.gz"/>
# creates Resource element
res = doc.createElement("Resource")
res.setAttribute("name", "Sample Information")
res.setAttribute("path", samp_file)
xml_resources.appendChild(res)
# <HiddenAttributes>
# <Attribute name="DATA FILE"/>
# <Attribute name="Linking_id"/>
# <Attribute name="DATA TYPE"/>
# </HiddenAttributes>
# Adding parameters to hide basic unnecessary sample info
hidden_attr = doc.createElement("HiddenAttributes")
xml.appendChild(hidden_attr)
attr = doc.createElement("Attribute")
attr.setAttribute("name", "DATA FILE")
hidden_attr.appendChild(attr)
attr = doc.createElement("Attribute")
attr.setAttribute("name", "Linking_id")
hidden_attr.appendChild(attr)
attr = doc.createElement("Attribute")
attr.setAttribute("name", "DATA TYPE")
hidden_attr.appendChild(attr)
# Creating temp file to enter into file_store
tempfilename = tempfile.NamedTemporaryFile(delete=False)
tempfilename.write(doc.toprettyxml(indent=" "))
tempfilename.close()
# getting file_store_uuid
filestore_uuid = create(tempfilename.name, filetype="xml")
filestore_item = import_file(filestore_uuid, refresh=True)
# file to rename
temp_name = filestore_item.datafile.name.split('/')
temp_name = temp_name[len(temp_name) - 1] + '.xml'
# rename file by way of file_store
filestore_item = rename(filestore_uuid, temp_name)
# delete temp file
os.unlink(tempfilename.name)
# Url for session file
sessionfile_url = get_full_url(filestore_item.get_datafile_url())
# IGV url for automatic launch of Java Webstart
igv_url = "http://www.broadinstitute.org/igv/projects/current/igv.php" \
"?sessionURL=" + sessionfile_url
return igv_url
def add_igv_samples(fields, results_samp, annot_samples=None):
"""creates phenotype file for IGV
:param samples: Solr results for samples to be included
:type samples: Array.
:param annot_samples: includes annotation files included with solr results
:type annot_samples: Array
"""
# creates human readable indexes of fields to iterate over
fields_dict = {}
for i in fields:
find_index = i.find("_Characteristics_")
if find_index > -1:
new_key = i.split("_Characteristics_")[0]
fields_dict[i] = new_key
# Creating temp file to enter into file_store
temp_sample_name = tempfile.NamedTemporaryFile(delete=False)
# writing header to sample file
temp_sample_name.write("#sampleTable" + "\n")
# writing column names to sample file
col_names = "Linking_id"
for k, v in fields_dict.iteritems():
col_names = col_names + "\t" + v
temp_sample_name.write(col_names + "\n")
# iterating over sample files
pheno_results = get_sample_lines(fields_dict, results_samp)
try:
temp_sample_name.write(pheno_results)
except UnicodeEncodeError as e:
logger.error(
"Could not write results to file: %s. " "Trying again with the content to write encoded " "properly.", e
)
temp_sample_name.write(pheno_results.encode("utf-8"))
# if annotations are not null
if annot_samples:
pheno_annot = get_sample_lines(fields_dict, annot_samples)
temp_sample_name.write(pheno_annot)
# closing temp file
temp_sample_name.close()
# getting file_store_uuid
filestore_uuid = create(temp_sample_name.name, filetype="txt")
filestore_item = import_file(filestore_uuid, refresh=True)
# file to rename
temp_file = filestore_item.datafile.name.split("/")
temp_file = temp_file[len(temp_file) - 1] + ".txt"
# rename file by way of file_store
filestore_item = rename(filestore_uuid, temp_file)
# getting file information based on file_uuids
curr_fs = FileStoreItem.objects.get(uuid=filestore_uuid)
# full path to selected UUID File
curr_url = get_full_url(curr_fs.get_datafile_url())
# delete temp file
os.unlink(temp_sample_name.name)
return curr_url