Pre Connect 2021

README.md

@@ -1,5 +1,5 @@
 # fasp-scripts
- Scripts and clients for GA4GH Federated Analysis Systems Project
+ Notebooks and clients for GA4GH Federated Analysis Systems Project
 
 [TOC]
 
@@ -78,6 +78,10 @@ Wrapper to make a WES call. Currently does an MD5 checksum and the plenary GWAS
 
 Client to call Seven Bridges WES Servers. The specific features addressed include authentication, setting a project to work within and the use of apps stored in the Seven Bridges environment. For testing and demo purposes this client encapsulates running samtools. 
 
+#### elixir_wes_client.py
+
+Client to call Elixir WES Servers. The specific features addressed include authentication, setting a project to work within and the use of apps stored in the Seven Bridges environment. For testing and demo purposes this client encapsulates running samtools. 
+
 #### WESClient.py
 
 Superclass for WES clients. Has generic capability to run WES requiring full configuration of the request body and possibly knowledge of the specific WES server being called.

fasp/runner/fasp_runner.py

@@ -104,7 +104,7 @@ def runQuery(self, query, note):
 			via = 'sh'
 			#pipeline_id = 'paste here'
 
-			time = datetime.datetime.now().strftime("%m/%d/%Y, %H:%M:%S")
+			time = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
 			if self.live:
 				self.pipelineLogger.logRun(time, via, note,  pipeline_id, outfile, str(fileSize),
 					self.searchClient, self.drsClient, self.workClient)

fasp/workflow/elixir_wesclient.py

@@ -9,8 +9,11 @@ class ElixirWESClient(WESClient):
 	Client for ELIXIR WES Service
 	"""
 
-	def __init__(self, client_credentials_path, debug=False):
-		super(ElixirWESClient, self).__init__('https://wes-eu.egci-endpoints.imsi.athenarc.gr/ga4gh/wes/v1')
+	def __init__(self, api_base_url, client_credentials_path=None, debug=False):
+		self.api_base = api_base_url
+		if client_credentials_path == None:
+			client_credentials_path = '~/.keys/elixir_wes_credentials.json'
+		super(ElixirWESClient, self).__init__(api_base_url)
 		full_credentials_path = os.path.expanduser(client_credentials_path)
 		with open(full_credentials_path) as f:
 			self.credentials = json.load(f)
@@ -41,7 +44,7 @@ def runWorkflow(self, path, outFile):
 
 
 if __name__ == "__main__":
-	myClient = ElixirWESClient('~/.keys/elixir_wes_credentials.json', debug=True)
+	myClient = ElixirWESClient(debug=True)
 
 	res = myClient.runWorkflow('http://62.217.82.57/test.txt')
 	#res = myClient.getRuns()