def get_workflow_status(user):
# go through every galaxy instance
gits = GalaxyInstanceTracking.objects.filter(
galaxyuser__internal_user=user)
dj_wfs = Workflow.objects.all()
# loop through instances
status = []
for git in gits:
## loop through workflows for that instance
gi, gu = get_gi_gu(user, git)
wc = WorkflowClient(gi)
hc = HistoryClient(gi)
wfs = wc.get_workflows()
for wf in wfs:
wfd = wc.show_workflow(wf['id'])
winvoke = wc.get_invocations(wf['id'])
for wi in winvoke:
wid = wc.show_invocation(wf['id'], wi['id'])
h_l = hc.get_histories(wid['history_id'], deleted=True)
if h_l:
h = h_l[0]
else:
continue
sd = get_status_d(wid)
sd['name'] = wfd['name']
hd = hc.show_history(h['id'])
sd['history_name'] = h['name']
datetime_object = datetime.strptime(hd['update_time'],
'%Y-%m-%dT%H:%M:%S.%f')
# sd['history_url'] = '{}{}'.format(git.url, hd['url'])
sd['update_time'] = datetime_object.strftime(
'%Y-%m-%d %H:%M:%S')
sd['update_time_unix'] = unixtime(datetime_object)
sd['galaxy_instance'] = git.name
status.append(sd)
status = sorted(status, key=lambda k: k['update_time_unix'], reverse=True)
return status
def main():
galaxyInstance = GalaxyInstance(url=GALAXY_URL, key=API_KEY)
toolClient = ToolClient(galaxyInstance)
historyClient = HistoryClient(galaxyInstance)
workflowsClient = WorkflowClient(galaxyInstance)
libraryClient = LibraryClient(galaxyInstance)
datasetClient = DatasetClient(galaxyInstance)
histories = historyClient.get_histories(deleted=False)
for hist in histories:
hist_id = hist['id']
countSecondary = historyClient.show_matching_datasets(
hist_id, name_filter=name_filter)
if len(countSecondary) != 0:
#print(countSecondary)
file_path = dir_name + '/' + hist[
'name'] + '_' + name_filter + '.' + ext
#print(file_path)
#print(countSecondary[0]['dataset_id'])
datasetClient.download_dataset(countSecondary[0]['id'],
file_path=file_path,
use_default_filename=False)
sys.exit()
def get_history_status(user, hist_id=None):
# go through every galaxy instance
gits = GalaxyInstanceTracking.objects.filter(
galaxyuser__internal_user=user)
# loop through instances
status = []
for git in gits:
## loop through workflows for that instance
gi, gu = get_gi_gu(user, git)
hc = HistoryClient(gi)
hists = hc.get_histories()
# loop through and create a list of dictionaries for our django table
for hist in hists:
sd = {}
# add useful info
if hist_id and hist['id'] != hist_id:
continue
history_info = hc.show_history(hist['id'])
# add status info
sd_bioblend = hc.get_status(hist['id'])
state_details = sd_bioblend['state_details']
sd.update(state_details)
sd['estimated_progress'] = sd_bioblend['percent_complete']
datetime_object = datetime.strptime(history_info['update_time'],
'%Y-%m-%dT%H:%M:%S.%f')
sd['update_time'] = datetime_object.strftime('%Y-%m-%d %H:%M:%S')
sd['update_time_unix'] = unixtime(datetime_object)
sd['galaxy_instance'] = git.name
sd['name'] = hist['name']
hsq = History.objects.filter(galaxy_id=hist['id'],
galaxyinstancetracking=git)
if hsq:
hs = hsq[0]
hs.name = hist['name']
hs.update_time = datetime_object.strftime('%Y-%m-%d %H:%M:%S')
hs.empty = state_details['empty']
hs.error = state_details['error']
hs.failed_metadata = state_details['failed_metadata']
hs.new = state_details['new']
hs.ok = state_details['ok']
hs.paused = state_details['paused']
hs.running = state_details['running']
hs.queued = state_details['queued']
hs.setting_metadata = state_details['setting_metadata']
hs.upload = state_details['upload']
hs.estimated_progress = sd_bioblend['percent_complete']
else:
hs = History(
galaxyinstancetracking=git,
name=hist['name'],
update_time=datetime_object.strftime('%Y-%m-%d %H:%M:%S'),
empty=state_details['empty'],
error=state_details['error'],
failed_metadata=state_details['failed_metadata'],
new=state_details['new'],
ok=state_details['ok'],
paused=state_details['paused'],
running=state_details['running'],
queued=state_details['queued'],
setting_metadata=state_details['setting_metadata'],
upload=state_details['upload'],
galaxy_id=hist['id'],
estimated_progress=sd_bioblend['percent_complete'])
hs.save()
sd['history_data_bioblend_list'] = '/galaxy/history_data_bioblend_list/{}'.format(
hs.pk)
status.append(sd)
status = sorted(status, key=lambda k: k['update_time_unix'], reverse=True)
return status
#!/usr/bin/python import sys; import galaxy_key; from bioblend.galaxy import GalaxyInstance from bioblend.galaxy.libraries import LibraryClient from bioblend.galaxy.histories import HistoryClient #Create a file called galaxy_key and add your key there gi = GalaxyInstance(url=galaxy_key.galaxy_host, key=galaxy_key.galaxy_key); hc = HistoryClient(gi); my_history = hc.get_histories()[0]; my_history_id = my_history['id']; dataset = hc.show_matching_datasets(my_history_id, 'sum_vector')[0]; dataset_provenance = hc.show_dataset_provenance(my_history_id, dataset['id']); print(dataset_provenance);
def getGalaxyData(accession, dataType, species, foldChangeOnly):
api_key = 'ENTER_API_KEY'
galaxy_host = 'http://localhost:8080'
gi = GalaxyInstance(url=galaxy_host, key=api_key)
history_client = HistoryClient(gi)
dataDirectory = "Sybil/Shiny/data/" + accession
if not os.path.exists(dataDirectory):
os.makedirs(dataDirectory)
wwwDirectory = "Shiny/www/microarrayQC.html/" + accession
if not os.path.exists(wwwDirectory):
os.makedirs(wwwDirectory)
wwwDirectoryPlots = "Shiny/www/plots/" + accession
if not os.path.exists(wwwDirectoryPlots):
os.makedirs(wwwDirectoryPlots)
#get the most recent history
history = history_client.get_histories(name=accession)[0]
#get the experiment level data
getPCA(history, history_client, dataDirectory, galaxy_host)
getChrDirTable(history, history_client, dataDirectory, galaxy_host)
if dataType == "Microarray":
getQC(history, history_client, wwwDirectory, galaxy_host)
comparisons = getComparisonsTable(history, history_client, dataDirectory,
galaxy_host)
number_of_comparisons = -1
for line in open(comparisons):
if not line.isspace():
number_of_comparisons += 1
if foldChangeOnly == "FALSE":
pvalues = ["1", "0.05"]
foldchanges = ["1", "1.5", "2"]
thresholds = list(itertools.product(pvalues, foldchanges))
thresholds.pop(0)
else:
pvalues = ["1"]
foldchanges = ["1.5", "2"]
thresholds = list(itertools.product(pvalues, foldchanges))
for i in reversed(range(number_of_comparisons)):
getFoldChange(i, history, history_client, dataDirectory, galaxy_host)
for index, values in reversed(
list(
enumerate(
list(
itertools.product(range(number_of_comparisons),
thresholds))))):
(comparison, (pvalue, foldchange)) = values
print(index)
print(values)
getStringNetworks(index, comparison, history, history_client,
dataDirectory, galaxy_host)
getBioGridNetworks(index, comparison, history, history_client,
dataDirectory, galaxy_host)
getPathways(index, comparison, pvalue, foldchange, history,
history_client, dataDirectory, galaxy_host)
getDrugEnrichment(index, comparison, pvalue, foldchange, history,
history_client, dataDirectory, galaxy_host)
getGOEnrichment(index, comparison, pvalue, foldchange, history,
history_client, dataDirectory, wwwDirectoryPlots,
galaxy_host)
if species in ["Human", "Mouse"]:
getTFs(index, comparison, pvalue, foldchange, history,
history_client, dataDirectory, galaxy_host)