# HG changeset patch
# User fubar
# Date 1421281031 18000
# Node ID ce5ec1d989fd72777342944add7ae18f8d64362e
# Parent  9d58cc32a12dca7cc617382e20af6fd5d42c185a
Uploaded

diff -r 9d58cc32a12d -r ce5ec1d989fd getlocalrpackages.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getlocalrpackages.py	Wed Jan 14 19:17:11 2015 -0500
@@ -0,0 +1,31 @@
+import os
+import subprocess
+
+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
+    eprefix = prefix
+    if prefix.find('/') <> -1:
+        eprefix = prefix.replace('/','\/') # for grep
+    cl = ['locate env.sh | grep -i %s' % 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']
+    res = [['%s rev %s owner %s' % (x[1],x[2],x[0]),fpaths[i],False] for i,x in enumerate(fver)]
+    res.insert(0,['Use default (system) interpreter','system',False])
+    if len(res) > 1:
+        res[1][2] = True # selected if more than one
+    # return a triplet - user_sees,value,selected - all unselected if False
+    return res
+
+if __name__ == "__main__":
+   print find_packages()
diff -r 9d58cc32a12d -r ce5ec1d989fd rgToolFactory2.py
--- a/rgToolFactory2.py	Mon Jan 12 05:27:52 2015 -0500
+++ b/rgToolFactory2.py	Wed Jan 14 19:17:11 2015 -0500
@@ -172,7 +172,20 @@
             citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
     return citation_tuples
 
-
+def shell_source(script):
+    """need a way to source a Galaxy tool interpreter env.sh so we can use that dependency
+    package 
+    see http://pythonwise.blogspot.fr/2010/04/sourcing-shell-script.html
+    Sometime you want to emulate the action of "source" in bash,
+    settings some environment variables. Here is a way to do it.
+    Note that we have to finesse the automagic exports using nulls as newlines for env"""
+    pipe = subprocess.Popen("env -i ; . %s ; env -0" % script, stdout=subprocess.PIPE, shell=True)
+    output = pipe.communicate()[0]
+    outl = output.split('\0')
+    outl = [x for x in outl if len(x.split("=")) == 2]
+    newenv = dict((line.split("=", 1) for line in outl))
+    os.environ.update(newenv)
+    
 class ScriptRunner:
     """class is a wrapper for an arbitrary script
     """
@@ -218,10 +231,7 @@
         self.test1Inputs = [] # now a list
         a = self.cl.append
         a(opts.interpreter)
-        if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
-            a(self.sfile)
-        else:
-            a('-') # stdin
+        a(self.sfile)
         # if multiple inputs - positional or need to distinguish them with cl params
         if opts.input_tab:
             tests = []
@@ -391,7 +401,8 @@
     %(citations)s
     <citation type="doi">10.1093/bioinformatics/bts573</citation>
 </citations>
-</tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
+</tool>"""
+# needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
 
         newCommand="""
         %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
@@ -433,8 +444,8 @@
         xdict['additionalInputs'] = ''
         if self.opts.additional_parameters:
             if self.opts.edit_additional_parameters: # add to new tool form with default value set to original value
-                xdict['additionalInputs'] = '\n'.join(['<param name="%s" value="%s" label="%s" help="%s" type="%s"/>' % (x.split(',')[0],html_escape(x.split(',')[1]),html_escape(x.split(',')[2]),
-                    html_escape(x.split(',')[3]), x.split(',')[4]) for x in self.opts.additional_parameters])
+                xdict['additionalInputs'] = '\n'.join(['<param name="%s" value="%s" label="%s" help="%s" type="%s"/>' % \
+                (x.split(',')[0],html_escape(x.split(',')[1]),html_escape(x.split(',')[2]),html_escape(x.split(',')[3]), x.split(',')[4]) for x in self.opts.additional_parameters])
             xdict['additionalParams'] = '\n'.join(['<param name="%s" value="%s" />' % (x.split(',')[0],html_escape(x.split(',')[1])) for x in self.opts.additional_parameters])
         xdict['requirements'] = ''
         if self.opts.make_HTML:
@@ -774,10 +785,13 @@
         self.html = html
 
 
+
     def run(self):
         """
         scripts must be small enough not to fill the pipe!
         """
+        if self.opts.envshpath <> 'system':
+            shell_source(self.opts.envshpath)
         if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
           retval = self.runBash()
         else:
@@ -786,11 +800,9 @@
                 sto = open(self.tlog,'w')
                 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
                 sto.flush()
-                p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
+                p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,cwd=self.opts.output_dir)
             else:
-                p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
-            p.stdin.write(self.script)
-            p.stdin.close()
+                p = subprocess.Popen(self.cl,shell=False)
             retval = p.wait()
             if self.opts.output_dir:
                 sto.close()
@@ -851,6 +863,7 @@
     a('--citations',default=None)
     a('--additional_parameters', dest='additional_parameters', action='append', default=[])
     a('--edit_additional_parameters', action="store_true", default=False)
+    a('--envshpath',default="system")   
     opts, args = op.parse_args()
     assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
     assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
diff -r 9d58cc32a12d -r ce5ec1d989fd rgToolFactory2.xml
--- a/rgToolFactory2.xml	Mon Jan 12 05:27:52 2015 -0500
+++ b/rgToolFactory2.xml	Wed Jan 14 19:17:11 2015 -0500
@@ -1,15 +1,17 @@
-<tool id="rgTF2" name="Tool Factory Two" version="1.15">
+<tool id="rgTF2" name="Tool Factory Two" version="1.16">
   <description>Scripts into tools</description>
    <requirements>
       <requirement type="package" version="9.10">ghostscript</requirement>
       <requirement type="package" version="1.3.20">graphicsmagick</requirement>
   </requirements>
+  <code file="getlocalrpackages.py"/>
   <command interpreter="python">
 #if ( $__user_email__ not in $__admin_users__ ):
      rgToolFactory2.py --bad_user $__user_email__
 #else:
-    rgToolFactory2.py --script_path "$runme" --interpreter "$interpreter" 
+    rgToolFactory2.py --script_path "$runme" --interpreter "$interp.interpreter" 
      --tool_name "$tool_name"  --user_email "$__user_email__" --citations "$citeme"
+     --envshpath "$interp.envpath"
 
     #if $make_TAB.value=="yes":
           --output_tab "$output1"
@@ -96,7 +98,7 @@
                     </param>
                     <when value="doi">
                         <param name="doi" label="DOI" type="text" value="" 
-                        help="Supply a DOI (e.g. 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." />
+                        help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." />
                     </when>
                     <when value="bibtex">
                         <param name="bibtex" label="BibTex" type="text" area="true" size="8x120"
@@ -135,6 +137,7 @@
         <column name="value" index="0"/>
      </options>
     </param>
+    <conditional name="interp">
     <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
         <option value="Rscript" selected="true">Rscript</option>
         <option value="python">python</option>
@@ -142,6 +145,19 @@
         <option value="bash">bash</option>
         <option value="sh">sh</option>
     </param>
+    <when value="Rscript">
+        <param name="envpath"  type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_r_')"
+        help = "Select the R interpreter to use when running this code - should show all installed tool shed package_r_..." /> 
+    </when>
+    <when value="python">
+        <param name="envpath"  type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_python_')"
+        help = "Select the python dependency to use when running this code - should show all installed tool shed package_python_..." /> 
+    </when>
+    <when value="perl">
+        <param name="envpath"  type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_perl_')"
+        help = "Select the Perl interpreter to use when running this code - should show all installed tool shed package_perl_..." /> 
+    </when>
+    </conditional>
     <param name="edit_params" type="select" label="Add all additional parameters to the generated tool form so they are user editable?" 
          help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
         <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option>
@@ -244,6 +260,7 @@
     <param name="output_format" value="tabular" />
     <param name="input_formats" value="tabular" />
     <param name="interpreter" value='python' />
+    <param name="envpath" value='system' />
     <param name="runme" value="tf2_test_runme.py"/>
     <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/>
     <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/>
@@ -418,7 +435,7 @@
 
 </help>
 <citations>
-    <citation type="doi">doi: 10.1093/bioinformatics/bts573</citation>
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
 </citations>
 </tool>
 
diff -r 9d58cc32a12d -r ce5ec1d989fd test-data/tf2_test.html
--- a/test-data/tf2_test.html	Mon Jan 12 05:27:52 2015 -0500
+++ b/test-data/tf2_test.html	Wed Jan 14 19:17:11 2015 -0500
@@ -8,18 +8,18 @@
         <body> 
         <div class="toolFormBody"> 
         
-<div class="infomessage">Galaxy Tool "tf2_test" run at 02/01/2015 11:50:01</div><br/>
+<div class="infomessage">Galaxy Tool "tf2_test" run at 15/01/2015 11:06:33</div><br/>
 <div class="toolFormTitle">tf2 log output</div>
 tf2_test_error.log is empty<br/>
 <div class="toolFormTitle">Other log output</div>
-/tmp/tmpsyPOyw/job_working_directory/000/2/dataset_3_files/tf2_test_runner.log is empty<br/>
+/tmp/tmp5bLHi4/job_working_directory/000/2/dataset_3_files/tf2_test_runner.log is empty<br/>
 <div class="toolFormTitle">All output files available for downloading</div>
 
 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
 
 <tr><td><a href="tf2_test.python">tf2_test.python</a></td><td>0 B</td></tr>
 <tr class="odd_row"><td><a href="tf2_test_error.log">tf2_test_error.log</a></td><td>0 B</td></tr>
-<tr><td><a href="tf2_test_runner.log">tf2_test_runner.log</a></td><td>177 B</td></tr>
+<tr><td><a href="tf2_test_runner.log">tf2_test_runner.log</a></td><td>216 B</td></tr>
 </table></div><br/>
 </div></body></html>
 
diff -r 9d58cc32a12d -r ce5ec1d989fd test-data/tf2_test.toolshed.gz
Binary file test-data/tf2_test.toolshed.gz has changed