Merge

2026-09-24 16:30:27 +08:00 · 2013-03-08 14:15:11 -05:00
parent 5141541219 5d5895326e
commit e80abf9214
3 changed files with 120 additions and 174 deletions
@@ -2,15 +2,20 @@
 Upload class
 """

-from galaxy.web.base.controller import *
+import logging
+import galaxy.util
+
+from galaxy import web
+from galaxy.tools import DefaultToolState
+from galaxy.tools.actions import upload_common
+from galaxy.tools.parameters import params_to_incoming, visit_input_values
+from galaxy.tools.parameters.basic import DataToolParameter, UnvalidatedValue
 from galaxy.util.bunch import Bunch
 from galaxy.util.hash_util import is_hashable
-from galaxy.tools import DefaultToolState
-from galaxy.tools.parameters.basic import UnvalidatedValue
-from galaxy.tools.parameters import params_to_incoming
-from galaxy.tools.actions import upload_common
+from galaxy.web import error, url_for
+from galaxy.web.base.controller import BaseUIController
+from galaxy.web.form_builder import SelectField

-import logging
 log = logging.getLogger( __name__ )

 class AddFrameData:
@@ -47,7 +52,7 @@ class ToolRunner( BaseUIController ):
        tools = []
        tool = None
        # Backwards compatibility for datasource tools that have default tool_id configured, but which are now using only GALAXY_URL.
-        tool_ids = util.listify( tool_id )
+        tool_ids = galaxy.util.listify( tool_id )
        for tool_id in tool_ids:
            if get_loaded_tools_by_lineage:
                tools = toolbox.get_loaded_tools_by_lineage( tool_id )
@@ -83,7 +88,7 @@ class ToolRunner( BaseUIController ):
                                                          message=message,
                                                          status=status,
                                                          redirect=redirect ) )
-        params = util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers
+        params = galaxy.util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers
        #do param translation here, used by datasource tools
        if tool.input_translator:
            tool.input_translator.translate( params )
@@ -103,7 +108,7 @@ class ToolRunner( BaseUIController ):
                                    toolbox=self.get_toolbox(),
                                    tool_version_select_field=tool_version_select_field,
                                    tool=tool,
-                                    util=util,
+                                    util=galaxy.util,
                                    add_frame=add_frame,
                                    **vars )
        
@@ -215,7 +220,7 @@ class ToolRunner( BaseUIController ):
        #create an incoming object from the original job's dataset-modified param objects
        incoming = {}
        params_to_incoming( incoming, tool.inputs, params_objects, trans.app )
-        incoming[ "tool_state" ] = util.object_to_string( state.encode( tool, trans.app ) )
+        incoming[ "tool_state" ] = galaxy.util.object_to_string( state.encode( tool, trans.app ) )
        template, vars = tool.handle_input( trans, incoming, old_errors=upgrade_messages ) #update new state with old parameters
        # Is the "add frame" stuff neccesary here?
        add_frame = AddFrameData()
@@ -228,7 +233,7 @@ class ToolRunner( BaseUIController ):
                                    toolbox=self.get_toolbox(),
                                    tool_version_select_field=tool_version_select_field,
                                    tool=tool,
-                                    util=util,
+                                    util=galaxy.util,
                                    add_frame=add_frame,
                                    tool_id_version_message=tool_id_version_message,
                                    **vars )
@@ -288,9 +293,9 @@ class ToolRunner( BaseUIController ):
        tool = self.get_toolbox().get_tool( tool_id )
        if not tool:
            return False # bad tool_id
-        nonfile_params = util.Params( kwd, sanitize=False )
+        nonfile_params = galaxy.util.Params( kwd, sanitize=False )
        if kwd.get( 'tool_state', None ) not in ( None, 'None' ):
-            encoded_state = util.string_to_object( kwd["tool_state"] )
+            encoded_state = galaxy.util.string_to_object( kwd["tool_state"] )
            tool_state = DefaultToolState()
            tool_state.decode( encoded_state, tool, trans.app )
        else:
@@ -1,49 +1,59 @@
 """
-Sorts tabular data on one or more columns.
-
-usage: %prog [options]
-   -i, --input=i: Tabular file to be sorted
-   -o, --out_file1=o: Sorted output file
-   -c, --column=c: First column to sort on
-   -s, --style=s: Sort style (numerical or alphabetical)
-   -r, --order=r: Order (ASC or DESC)
-
-usage: %prog input out_file1 column style order [column style ...]
+    Sorts tabular data on one or more columns. All comments of the file are collected
+    and placed at the beginning of the sorted output file.
+    
+    usage: sorter.py [options]
+    -i, --input: Tabular file to be sorted
+    -o, --output: Sorted output file
+    -k, --key: Key (see manual for bash/sort)
+    
+    usage: sorter.py input output [key ...]
 """
+# 03/05/2013 guerler

+# imports
 import os, re, string, sys
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from bx.cookbook import doc_optparse
+from optparse import OptionParser

+# error
 def stop_err( msg ):
    sys.stderr.write( "%s\n" % msg )
    sys.exit()

+# main
 def main():
-    #Parse Command Line
-    options, args = doc_optparse.parse( __doc__ )
-    try:
-        inputfile = options.input
-        outputfile = '-o %s' % options.out_file1
-        columns = [options.column]
-        styles = [('','n')[options.style == 'num']]
-        orders = [('','r')[options.order == 'DESC']]
-        col_style_orders = sys.argv[6:]
-        if len(col_style_orders) > 1:
-            columns.extend([col_style_orders[i] for i in range(0,len(col_style_orders),3)])
-            styles.extend([('','n')[col_style_orders[i] == 'num'] for i in range(1,len(col_style_orders),3)])
-            orders.extend([('','r')[col_style_orders[i] == 'DESC'] for i in range(2,len(col_style_orders),3)])
-        cols = [ '-k%s,%s%s%s'%(columns[i], columns[i], styles[i], orders[i]) for i in range(len(columns)) ]
-    except Exception, ex:
-        stop_err('Error parsing input parameters\n' + str(ex))
+    # define options
+    parser = OptionParser()
+    parser.add_option("-i", "--input")
+    parser.add_option("-o", "--output")
+    parser.add_option("-k", "--key", action="append")

-    # Launch sort.
-    cmd = "sort -f -t '	' %s %s %s" % (' '.join(cols), outputfile, inputfile)
+    # parse
+    options, args = parser.parse_args()
+    
    try:
-        os.system(cmd)
+        # retrieve options
+        input   = options.input
+        output  = options.output
+        key     = [" -k" + k for k in options.key]
+        
+        # grep comments
+        grep_comments = "(grep '^#' %s) > %s" % (input, output)
+        #print grep_comments
+        
+        # grep and sort columns
+        sort_columns  = "(grep '^[^#]' %s | sort -f -t '\t' %s) >> %s" % (input, ' '.join(key), output)
+        #print sort_columns
+        
+        # execute
+        os.system(grep_comments)
+        os.system(sort_columns)
+    
    except Exception, ex:
-        stop_err('Error running sort command\n' + str(ex))
+        stop_err('Error running sorter.py\n' + str(ex))
+
+    # exit
+    sys.exit(0)

 if __name__ == "__main__":
    main()
@@ -1,130 +1,61 @@
-<tool id="sort1" name="Sort" version="1.0.1">
-  <description>data in ascending or descending order</description>
-  <command interpreter="python">
-    sorter.py 
-      --input=$input 
-      --out_file1=$out_file1 
-      --column=$column
-      --style=$style
-      --order=$order 
-      #for $col in $column_set:
-        ${col.other_column}
-        ${col.other_style}
-        ${col.other_order}
-      #end for
-  </command>
-  <inputs>
-    <param format="tabular" name="input" type="data" label="Sort Dataset" />
-    <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/>
-    <param name="style" type="select" label="with flavor">
-      <option value="num">Numerical sort</option>
-      <option value="alpha">Alphabetical sort</option>
-    </param>
-    <param name="order" type="select" label="everything in">
-      <option value="DESC">Descending order</option>
-      <option value="ASC">Ascending order</option>
-    </param>
-    <repeat name="column_set" title="Column selection">
-      <param name="other_column" label="on column" type="data_column" data_ref="input" accept_default="true" />
-      <param name="other_style" type="select" label="with flavor">
-        <option value="num">Numerical sort</option>
-        <option value="alpha">Alphabetical sort</option>
-      </param>
-      <param name="other_order" type="select" label="everything in">
-        <option value="DESC">Descending order</option>
-        <option value="ASC">Ascending order</option>
-      </param>
-    </repeat>
-  </inputs>
-  <outputs>
-    <data format="input" name="out_file1" metadata_source="input"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="sort_in1.bed"/>
-      <param name="column" value="1"/>
-      <param name="style" value="num"/>
-      <param name="order" value="ASC"/>
-      <param name="other_column" value="3"/>
-      <param name="other_style" value="num"/>
-      <param name="other_order" value="ASC"/>
-      <output name="out_file1" file="sort_out1.bed"/>
-    </test>
-    <test>
-      <param name="input" value="sort_in1.bed"/>
-      <param name="column" value="3"/>
-      <param name="style" value="alpha"/>
-      <param name="order" value="ASC"/>
-      <param name="other_column" value="1"/>
-      <param name="other_style" value="alpha"/>
-      <param name="other_order" value="ASC"/>
-      <output name="out_file1" file="sort_out2.bed"/>
-    </test>
-  </tests>
-  <help>
+<tool id="sort1" name="Sort" version="1.0.2">
+    <description>data in ascending or descending order</description>
+    <command interpreter="python">
+        sorter.py
+        --input=$input
+        --output=$output
+        --key=$column,$column$style$order
+        #for $col in $column_set:
+        --key=${col.other_column},${col.other_column}${col.other_style}${col.other_order}
+        #end for
+    </command>
+    <inputs>
+        <param format="tabular" name="input" type="data" label="Sort Dataset" />
+        <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/>
+        <param name="style" type="select" label="with flavor">
+            <option value="n">Numerical sort</option>
+            <option value="">Alphabetical sort</option>
+        </param>
+        <param name="order" type="select" label="everything in">
+            <option value="r">Descending order</option>
+            <option value="">Ascending order</option>
+        </param>
+        <repeat name="column_set" title="Column selection">
+            <param name="other_column" label="on column" type="data_column" data_ref="input" accept_default="true" />
+            <param name="other_style" type="select" label="with flavor">
+                <option value="n">Numerical sort</option>
+                <option value="">Alphabetical sort</option>
+            </param>
+            <param name="other_order" type="select" label="everything in">
+                <option value="r">Descending order</option>
+                <option value="">Ascending order</option>
+            </param>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="input" name="output" metadata_source="input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="sort_in1.bed"/>
+            <param name="column" value="1"/>
+            <param name="style" value=""/>
+            <param name="order" value=""/>
+            <param name="other_column" value="3"/>
+            <param name="other_style" value="n"/>
+            <param name="other_order" value="r"/>
+            <output name="output" file="sort_out1.bed"/>
+        </test>
+        <test>
+            <param name="input" value="sort_in1.bed"/>
+            <param name="column" value="1"/>
+            <param name="style" value=""/>
+            <param name="order" value=""/>
+            <param name="other_column" value="3"/>
+            <param name="other_style" value="n"/>
+            <param name="other_order" value=""/>
+            <output name="output" file="sort_out2.bed"/>
+        </test>
+    </tests>

-.. class:: infomark
-
-**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-
-----
-
-**Syntax**
-
-This tool sorts the dataset on any number of columns in either ascending or descending order.
-
-* Numerical sort orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify.  
-* Alphabetical sort is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 &lt; 2).
-
-----
-
-**Examples**
-
-The list of numbers 4,17,3,5 collates to 3,4,5,17 by numerical sorting, while it collates to 17,3,4,5 by alphabetical sorting.
-
-Sorting the following::
-
-  Q     d    7   II    jhu  45
-  A     kk   4   I     h    111
-  Pd    p    1   ktY   WS   113
-  A     g    10  H     ZZ   856
-  A     edf  4   tw    b    234
-  BBB   rt   10  H     ZZ   100
-  A     rew  10  d     b    1111
-  C     sd   19  YH    aa   10
-  Hah   c    23  ver   bb   467
-  MN    gtr  1   a     X    32
-  N     j    9   a     T    205
-  BBB   rrf  10  b     Z    134
-  odfr  ws   6   Weg   dew  201
-  C     f    3   WW    SW   34
-  A     jhg  4   I     b    345
-  Pd    gf   7   Gthe  de   567
-  rS    hty  90  YY    LOp  89
-  A     g    10  H     h    43
-  A     g    4   I     h    500
-
-on columns 1 (alpha), 3 (num), and 6 (num) in ascending order will yield::
-
-  A     kk   4   I     h    111
-  A     edf  4   tw    b    234
-  A     jhg  4   I     b    345
-  A     g    4   I     h    500
-  A     g    10  H     h    43
-  A     g    10  H     ZZ   856
-  A     rew  10  d     b    1111
-  BBB   rt   10  H     ZZ   100
-  BBB   rrf  10  b     Z    134
-  C     f    3   WW    SW   34
-  C     sd   19  YH    aa   10
-  Hah   c    23  ver   bb   467
-  MN    gtr  1   a     X    32
-  N     j    9   a     T    205
-  odfr  ws   6   Weg   dew  201
-  Pd    p    1   ktY   WS   113
-  Pd    gf   7   Gthe  de   567
-  Q     d    7   II    jhu  45
-  rS    hty  90  YY    LOp  89
-
-  </help>
 </tool>