fix prog/tool naming issues

Author: bernt-matthias

argparse2tool/__init__.py

@@ -48,3 +48,11 @@ def load_conflicting_package(name, not_name, module_number):
             imp.load_module(random_name, f, pathname, desc)
             return sys.modules[random_name]
     return None
+
+
+def remove_extension(name):
+    if name is not None:
+        name = name.replace('.py', '')
+        name = name.replace('-', '_')
+        name = name.replace(' ', '_')
+    return name

argparse2tool/dropins/argparse/__init__.py

@@ -1,6 +1,9 @@
 import re
 import sys
-from argparse2tool import load_argparse
+from argparse2tool import (
+    load_argparse,
+    remove_extension
+)
 from argparse2tool.cmdline2gxml import Arg2GxmlParser
 from argparse2tool.cmdline2cwl import Arg2CWLParser
 
@@ -53,9 +56,9 @@ def __init__(self,
         self.argument_names = []
         tools.append(self)
         if len(parents) > 0:
-            p = set([_.prog.split()[-1] for _ in parents])
+            p = set([remove_extension(_.prog) for _ in parents])
             macros = macros.union(p)
-            used_macros[prog.split()[-1]] = p
+            used_macros[remove_extension(prog)] = p
         super(ArgumentParser, self).__init__(prog=prog,
                                              usage=usage,
                                              description=description,
@@ -177,7 +180,7 @@ def parse_args_galaxy(self, *args, **kwargs):
                     if directory:
                         if directory[-1] != '/':
                             directory += '/'
-                        filename = argp.prog.split()[-1] + ".xml"
+                        filename = remove_extension(argp.prog) + ".xml"
                         filename = directory + filename
                         with open(filename, 'w') as f:
                             f.write(data)
@@ -196,21 +199,15 @@ def _parse_args_galaxy_argp(self, argp, macro):
         except AttributeError:  # handle the potential absence of print_version
             version = '1.0'
 
-        prog = argp.prog
-        if prog is not None:
-            prog = prog.replace("-", "_")
-            prog = prog.replace(".py ", " ")
-            if prog.endswith(".py"):
-                prog = prog[:-3]
-        
+        prog = remove_extension(argp.prog)
 
-        tid = argp.prog.split()[-1]
+        # tid = argp.prog.split()[-1]
 
         # get the list of file names of the used macros
-        mx = used_macros.get(tid, [])
-        mx = ["%s.xml" % _ for _ in mx]
+        mx = used_macros.get(prog, [])
+        mx = sorted(["%s.xml" % _.split(" ")[-1] for _ in mx])
 
-        if tid not in macros:
+        if prog not in macros:
             tpe = gxt.Tool
             if macro:
                 mx.append(macro)
@@ -244,12 +241,12 @@ def _parse_args_galaxy_argp(self, argp, macro):
                     else:
                         outputs.append(gxt_parameter)
 
-        if tid in used_macros:
-            for m in used_macros[tid]:
+        if prog in used_macros:
+            for m in sorted(used_macros[prog]):
                 inputs.append(gxtp.ExpandIO(m + "_inmacro"))
                 outputs.append(gxtp.ExpandIO(m + "_outmacro"))
 
-        if tid not in macros:
+        if prog not in macros:
             # TODO: replace with argparse-esque library to do this.
             stdout = gxtp.OutputData('default', 'txt')
             stdout.command_line_override = '> $default'

examples/example-sub.py

@@ -17,7 +17,7 @@
 parser_foo.add_argument('integers', metavar='N', type=int, nargs='+',
                         help='an integer for the accumulator')
 parser_foo.add_argument('--sum', '-s', dest='accumulate', action='store_const',
-                        const=sum, default=max, 
+                        const=sum, default=max,
                         help='sum the integers (default: find the max)')
 parser_foo.add_argument('--foo', nargs='?', help='foo help')
 parser_foo.add_argument('--bar', nargs='*', default=[1, 2, 3], help='BAR!')

examples/example-sub/bar.xml examples/example-sub/example_sub_bar.xmlexamples/example-sub/bar.xml renamed to examples/example-sub/example_sub_bar.xml

@@ -1,7 +1,7 @@
-<tool name="example_sub bar" id="example_sub_bar" version="2.0">
+<tool name="example_sub_bar" id="example_sub_bar" version="2.0">
   <description/>
   <macros>
-    <import>qux.xml</import>
+    <import>example_sub_qux.xml</import>
   </macros>
   <stdio>
     <exit_code range="1:" level="fatal"/>
@@ -18,8 +18,8 @@
 #if $mode and $mode is not None:
 --mode $mode
 #end if
-@QUX_INMACRO@
-@QUX_OUTMACRO@
+@EXAMPLE_SUB_QUX_INMACRO@
+@EXAMPLE_SUB_QUX_OUTMACRO@
 > $default]]></command>
   <inputs>
     <param label="Store a false" checked="false" type="boolean" name="false" argument="--false" truevalue="--false" falsevalue=""/>
@@ -34,10 +34,10 @@
       <option value="rock">rock</option>
       <option selected="true" value="scissors">scissors</option>
     </param>
-    <expand macro="qux_inmacro"/>
+    <expand macro="example_sub_qux_inmacro"/>
   </inputs>
   <outputs>
-    <expand macro="qux_outmacro"/>
+    <expand macro="example_sub_qux_outmacro"/>
     <data name="default" format="txt" hidden="false"/>
   </outputs>
   <help><![CDATA[TODO: Write help]]></help>

examples/example-sub/baz.xml examples/example-sub/example_sub_baz.xmlexamples/example-sub/baz.xml renamed to examples/example-sub/example_sub_baz.xml

@@ -1,12 +1,12 @@
 <macros>
   <token name="EXAMPLE_SUB_BAZ_INMACRO"><![CDATA[--baz $baz
-@QUX_INMACRO@]]></token>
-  <token name="EXAMPLE_SUB_BAZ_OUTMACRO"><![CDATA[@QUX_OUTMACRO@]]></token>
+@EXAMPLE_SUB_QUX_INMACRO@]]></token>
+  <token name="EXAMPLE_SUB_BAZ_OUTMACRO"><![CDATA[@EXAMPLE_SUB_QUX_OUTMACRO@]]></token>
   <xml name="example_sub_baz_inmacro">
     <param optional="true" label="baz help" type="text" name="baz" argument="--baz"/>
-    <expand macro="qux_inmacro"/>
+    <expand macro="example_sub_qux_inmacro"/>
   </xml>
   <xml name="example_sub_baz_outmacro">
-    <expand macro="qux_outmacro"/>
+    <expand macro="example_sub_qux_outmacro"/>
   </xml>
 </macros>

examples/example-sub/foo.xml examples/example-sub/example_sub_foo.xmlexamples/example-sub/foo.xml renamed to examples/example-sub/example_sub_foo.xml

@@ -1,8 +1,8 @@
-<tool name="example_sub foo" id="example_sub_foo" version="1.0">
+<tool name="example_sub_foo" id="example_sub_foo" version="1.0">
   <description/>
   <macros>
-    <import>qux.xml</import>
-    <import>baz.xml</import>
+    <import>example_sub_baz.xml</import>
+    <import>example_sub_qux.xml</import>
   </macros>
   <stdio>
     <exit_code range="1:" level="fatal"/>
@@ -23,10 +23,10 @@ $sum
 --bar "$repeat_var_4"
 
 $true
-@QUX_INMACRO@
-@BAZ_INMACRO@
-@QUX_OUTMACRO@
-@BAZ_OUTMACRO@
+@EXAMPLE_SUB_BAZ_INMACRO@
+@EXAMPLE_SUB_QUX_INMACRO@
+@EXAMPLE_SUB_BAZ_OUTMACRO@
+@EXAMPLE_SUB_QUX_OUTMACRO@
 > $default]]></command>
   <inputs>
     <param label="action keyword" type="text" name="keyword"/>
@@ -39,12 +39,12 @@ $true
       <param optional="true" label="BAR!" value="1" type="text" name="bar" argument="--bar"/>
     </repeat>
     <param label="Store a true" checked="false" type="boolean" name="true" argument="--true" truevalue="--true" falsevalue=""/>
-    <expand macro="qux_inmacro"/>
-    <expand macro="baz_inmacro"/>
+    <expand macro="example_sub_baz_inmacro"/>
+    <expand macro="example_sub_qux_inmacro"/>
   </inputs>
   <outputs>
-    <expand macro="qux_outmacro"/>
-    <expand macro="baz_outmacro"/>
+    <expand macro="example_sub_baz_outmacro"/>
+    <expand macro="example_sub_qux_outmacro"/>
     <data name="default" format="txt" hidden="false"/>
   </outputs>
   <help><![CDATA[TODO: Write help]]></help>

examples/example-sub/qux.xml examples/example-sub/example_sub_qux.xmlexamples/example-sub/qux.xml renamed to examples/example-sub/example_sub_qux.xml

@@ -1,4 +1,4 @@
-<tool name="example.py" id="example.py" version="2.0">
+<tool name="example" id="example" version="2.0">
   <description>Process some integers.</description>
   <stdio>
     <exit_code range="1:" level="fatal"/>