From 683982921142ec6d753239522ee9fdcbfd0f0170 Mon Sep 17 00:00:00 2001
From: Richard Park <rpark@bu.edu>
Date: Fri, 3 Aug 2012 02:09:05 -0400
Subject: [PATCH] Cleaned up codebase for attempting adding api additions to
 the galaxy main branch

---
 ...e_workflow_rpark.py => workflow_delete.py} |  9 +++--
 scripts/api/workflow_execute_parameters.py    | 35 ++++++-------------
 2 files changed, 17 insertions(+), 27 deletions(-)
 rename scripts/api/{workflow_delete_workflow_rpark.py => workflow_delete.py} (59%)

diff --git a/scripts/api/workflow_delete_workflow_rpark.py b/scripts/api/workflow_delete.py
similarity index 59%
rename from scripts/api/workflow_delete_workflow_rpark.py
rename to scripts/api/workflow_delete.py
index 734e12ca8f5..3b6d5a872bc 100644
--- a/scripts/api/workflow_delete_workflow_rpark.py
+++ b/scripts/api/workflow_delete.py
@@ -1,7 +1,12 @@
 #!/usr/bin/env python
 """
-# Author: RPARK
-API script for deleting workflows 
+# ---------------------------------------------- #
+# PARKLAB, Author: RPARK
+API example script for deleting workflows 
+# ---------------------------------------------- #
+
+Example calls:
+python workflow_delete.py <api_key> <galaxy_url>/api/workflows/<workflow id> True
 """
 
 import os, sys
diff --git a/scripts/api/workflow_execute_parameters.py b/scripts/api/workflow_execute_parameters.py
index 47a87980e16..7ce37db885e 100644
--- a/scripts/api/workflow_execute_parameters.py
+++ b/scripts/api/workflow_execute_parameters.py
@@ -1,23 +1,13 @@
 #!/usr/bin/env python
 """
+# ---------------------------------------------- #
+# PARKLAB, Author: RPARK
+# ---------------------------------------------- #
+
 Execute workflows from the command line.
 Example calls:
-python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'Test API History' '38=ldda=0qr350234d2d192f'
-python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'hist_id=a912e9e5d84530d4' '38=hda=03501d7626bd192f'
-"""
-
-"""
-python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'hist_id=a912e9e5d84530d4' '38=hda=03501d7626bd192f' 'param=tool=name=value' 
-
-'param=tool=name=value'
-
-Example 
-python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bwa' 
-
-python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=arachne' 'param=bowtie_wrapper=suppressHeader=True'
-
-python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bowtie' 'param=bowtie_wrapper=suppressHeader=True' 'param=peakcalling_spp=window_size=1000' 
-
+python workflow_execute.py <api_key> <galaxy_url>/api/workflows <workflow_id> 'hist_id=<history_id>' '38=hda=<file_id>' 'param=tool=name=value' 
+python workflow_execute_parameters.py <api_key> http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bowtie' 'param=bowtie_wrapper=suppressHeader=True' 'param=peakcalling_spp=window_size=1000' 
 """
 
 import os, sys
@@ -34,7 +24,6 @@ def main():
         data['ds_map'] = {}
 
         #########################################################
-        ### MY EDITS ############################################
         ### Trying to pass in parameter for my own dictionary ###
         data['parameters'] = {};
 
@@ -51,14 +40,10 @@ def main():
             except ValueError:
                 print("VALUE ERROR:");
                 wtype, wtool, wparam, wvalue = v.split('=');
-                data['parameters'][wtool] = {'param':wparam, 'value':wvalue}
-
-
-        #########################################################
-        ### MY EDITS ############################################
-        ### Trying to pass in parameter for my own dictionary ###
-        #data['parameters']['bowtie'] = {'param':'stepSize', 'value':100}
-        #data['parameters']['sam_to_bam'] = {'param':'genome', 'value':'hg18'}
+                try:
+                    data['parameters'][wtool] = {'param':wparam, 'value':wvalue}
+                except ValueError:
+                    print("TOOL ID ERROR:");
 
     except IndexError:
         print 'usage: %s key url workflow_id history step=src=dataset_id' % os.path.basename(sys.argv[0])