Update to latest tool factory external.

Author: jmchilton

planemo_ext/tool_factory_2/getlocalrpackages.py

@@ -1,52 +1,39 @@
 import os
 import subprocess
-import sys
 
 
 def find_packages(prefix="package_r_"):
     """
     """
-    #locate env.sh | grep -i package_r_
-    #/data/extended/galaxyJune14_2014/tool_dependency/readline/6.2/devteam/package_r_2_15_0/8ab0d08a3da1/env.sh
-    #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/5f1b8d22140a/env.sh
-    #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/d9964efbfbe3/env.sh
-    #/data/home/rlazarus/galtest/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/63cdb9b2234c/env.sh
+    # locate env.sh | grep -i package_r_
+    # /data/extended/galaxyJune14_2014/tool_dependency/readline/6.2/devteam/package_r_2_15_0/8ab0d08a3da1/env.sh
+    # /data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/5f1b8d22140a/env.sh
+    # /data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/d9964efbfbe3/env.sh
+    # /data/home/rlazarus/galtest/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/63cdb9b2234c/env.sh
     eprefix = prefix
     if prefix.find('/') != -1:
-        eprefix = prefix.replace('/','\/') # for grep
+        eprefix = prefix.replace('/', '\/')  # for grep
     path = '.'
-    # fails on nitesh's recent mac - locate not working 
+    # fails on nitesh's recent mac - locate not working
     # cl = ['locate env.sh | grep -i %s' % eprefix,]
-    cl = ['find %s -iname "env.sh" | grep -i %s' % (path,eprefix),]
-    p = subprocess.Popen(cl, stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
+    cl = ['find %s -iname "env.sh" | grep -i %s' % (path, eprefix), ]
+    p = subprocess.Popen(cl, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
     out, err = p.communicate()
     fpaths = out.split('\n')
     fpaths = [x for x in fpaths if len(x) > 1]
     fver = [x.split(os.path.sep)[-4:-1] for x in fpaths]
     # >>> foo.split(os.path.sep)[-4:-1]
     # ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
     if len(fpaths) > 0:
-        res = [['%s rev %s owner %s' % (x[1],x[2],x[0]),fpaths[i],False] for i,x in enumerate(fver)]
-        res[0][2] = True # selected if more than one
-        res.insert(0,['Use default (system) interpreter','system',False])
+        res = [['%s rev %s owner %s' % (x[1], x[2], x[0]), fpaths[i], False] for i, x in enumerate(fver)]
+        res[0][2] = True  # selected if more than one
+        res.insert(0, ['Use default (system) interpreter', 'system', False])
     else:
-        res = [['Use default (system) interpreter','system',True],
-        ['**WARNING** NO package env.sh files found - is the "find" system command working? Are any interpreters installed?','system',False]]
+        res = [['Use default (system) interpreter', 'system', True],
+               ['**WARNING** NO package env.sh files found - is the "find" system command working? Are any interpreters installed?', 'system', False]]
     # return a triplet - user_sees,value,selected - all unselected if False
     return res
 
-def testapi():
-    host_url = 'http://localhost:8080'
-    new_path = [ os.path.join( os.getcwd(), "lib" ) ]
-    new_path.extend( sys.path[1:] ) # remove scripts/ from the path
-    sys.path = new_path
-    from galaxy import config
-    aconfig = config.Configuration( )
-    M_A_K = aconfig.master_api_key
-    tooldeps = aconfig.tool_dependency_dir
-    gi = GalaxyInstance(url=host_url, key=M_A_K)
-
 
 if __name__ == "__main__":
     print(find_packages())
-