changeset 12:2088a8d469c9 draft

Fix datatype defs - metagenomics.py

--- a/mothur/lib/galaxy/datatypes/metagenomics.py	Fri Nov 30 10:51:36 2012 -0600
+++ b/mothur/lib/galaxy/datatypes/metagenomics.py	Fri Nov 30 11:46:37 2012 -0600
@@ -6,11 +6,7 @@
 
 import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re
 import galaxy.model
-from galaxy.datatypes import data
 from galaxy.datatypes.sniff import *
-from galaxy.datatypes import metadata
-from galaxy.datatypes import tabular
-from galaxy.datatypes import sequence
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.data import Text
 from galaxy.datatypes.tabular import Tabular
@@ -21,10 +17,8 @@
 pkg_resources.require("simplejson")
 import simplejson
 
-
 log = logging.getLogger(__name__)
 
-
 ## Mothur Classes 
 
 class Otu( Text ):
@@ -873,59 +867,9 @@
                         column_types.append('int')
                     dataset.metadata.column_types = column_types
                     dataset.metadata.comment_lines = 1
-            while (line = fh.readline())
-                data_lines += 1
-            dataset.metadata.data_lines = data_lines
-        finally:
-            close(fh)
-
-class SampleMetadata(Tabular):
-    MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] )
-    MetadataElement( name="", default=[], desc="Group Variables", readonly=True, visible=True, no_value=[] )
-    file_ext = 'metadata'
-
-    def __init__(self, **kwd):
-        """
-        A table with first column being sample names and following columns are variables 
-        # Example 1:
-        group	dpw	description
-        F003D000	0	"F003D000 description"
-        F003D002	2	"F003D002 description"
-        F003D004	4 	"F003D004 description"
-        F003D006	6       "F003D006 description"
-        F003D008	8       "F003D008 description"
-        F003D142	142     "F003D142 description"
-        # Example 2:
-	group   dpw	temp
-	F003D000        0	30.2
-	F003D008        8	32.7
-	F003D142        142 	31.4
-        """
-        Tabular.__init__( self, **kwd )
-
-    def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ):
-        try:
-            data_lines = 0;
-            fh = open( dataset.file_name )
-            line = fh.readline()
-            if line:
-                line = line.strip()
-                fields = line.split() 
-                if len(fields) > 0:
-                    # check if the first row is column headings, not number values
-                    for colname in colnames[1:]:
-                            f = float(linePieces[1])
-
-                    
-                    dataset.metadata.columns = len( colnames )
-                    if len(colnames) > 2:
-                        dataset.metadata.groups = colnames[2:]
-                    column_types = ['str']
-                    for i in range(1,len(colnames)):
-                        column_types.append('int')
-                    dataset.metadata.column_types = column_types
-                    dataset.metadata.comment_lines = 1
-            while (line = fh.readline())
+            while line:
+                line = fh.readline()
+                if not line: break
                 data_lines += 1
             dataset.metadata.data_lines = data_lines
         finally:
@@ -1476,7 +1420,7 @@
     MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] )
     file_ext = 'qiimeotutable'
     def init_meta( self, dataset, copy_from=None ):
-        tabular.Tabular.init_meta( self, dataset, copy_from=copy_from )
+        Tabular.init_meta( self, dataset, copy_from=copy_from )
     def set_meta( self, dataset, overwrite = True, skip = None, **kwd ):
         self.set_column_names(dataset) 
     def set_column_names(self, dataset):
@@ -1498,7 +1442,7 @@
     """
     file_ext = 'qiimedistmat'
     def init_meta( self, dataset, copy_from=None ):
-        tabular.Tabular.init_meta( self, dataset, copy_from=copy_from )
+        Tabular.init_meta( self, dataset, copy_from=copy_from )
     def set_meta( self, dataset, overwrite = True, skip = None, **kwd ):
         self.set_column_names(dataset) 
     def set_column_names(self, dataset):