Changeset 653:815684d0b377

Timestamp:

10/05/07 14:02:33 (1 year ago)

Author:

Greg Von Kuster <greg@bx.psu.edu>

branch:

default

convert_revision:

svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@1992

Message:

Added functional tests for sniffing and metadata settings on file upload. Fixed a test in the 'Filter Maf Blocks by size' tool. Added new test data. Commited the bug fix I really wanted in Axt.sniff().

Files:

• lib/galaxy/datatypes/sequence.py (modified) (1 diff)
• run_functional_tests.sh (modified) (1 diff)
• test-data/1.fasta (added)
• test-data/1.lav (added)
• test-data/1.wig (added)
• test-data/3.maf (modified) (1 diff)
• test-data/5.gff (modified) (1 diff)
• test-data/5.gff3 (added)
• test-data/maf_limit_size1_out.maf (added)
• test/base/twilltestcase.py (modified) (1 diff)
• test/functional/test_get_data.py (modified) (1 diff)
• test/functional/test_history_functions.py (moved) (moved from test/functional/test_components.py) (2 diffs)
• test/functional/test_metadata_editing.py (added)
• test/functional/test_sniffing_and_metadata_settings.py (added)
• tools/filters/maf/maf_limit_size.xml (modified) (1 diff)

lib/galaxy/datatypes/sequence.py

@@ -165 +165 @@
-        if len(headers) < 4:
-            return False
-
-
-
-
+
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-                    return True
-                if line and not line.startswith("#"):
-                    if len(line) != 9:
-                        return False
-                    try:
-                        map ( int, [line[0], line[2], line[3], line[5], line[6], line[8]] )
-                    except:
-                        return False
-                    if line[7] not in data.valid_strand:
-                        return False
-        return True
-
-class Lav( Alignment ):

run_functional_tests.sh

@@ -14 +14 @@
-        echo "'run_functional_tests.sh -list'                 for listing all the tool ids"
-elif [ $1 = '-id' ]; then
-GeneratedToolTestCase
+TestForTool
-elif [ $1 = '-list' ]; then
-    python tool_list.py

test-data/3.maf

@@ -1 +1 @@
-##maf version=1
-a score=60426.0
- 
- 
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-a score=8157.0
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-a score=43613.0
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-a score=63217.0
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-a score=8913.0
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-a score=91878.0
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-a score=82819.0
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-a score=15522.0
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-a score=28088.0
- 
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-

test-data/5.gff

@@ -1 @@
- 
- 
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-
-chr1    bed2gff CCDS1000.1_cds_0_0_chr1_148325916_f     148325916       148325975       .       +       .       score "0";

test/base/twilltestcase.py

@@ -205 +205 @@
-        if hid is None: # take last hid
-            elem = data_list[-1]
-elem.get('hid'
+int( elem.get('hid') 
-        self.assertTrue( hid )
-        self.visit_page( "edit?hid=%d" % hid )

test/functional/test_get_data.py

@@ -15 +15 @@
-        self.new_history()
-        self.upload_file('1.bed')
-, hid=1
+
-        self.upload_file('2.bed', dbkey='hg17')
-, hid=2
+
-        self.upload_file('3.bed', dbkey='hg17', ftype='bed')
-, hid=3
+
-
-class GetEncodeData( TwillTestCase ):

test/functional/test_history_functions.py

@@ -4 +4 @@
-
-    def test_new_history( self ):
-test_componments.test_new_history: 
+
-        self.new_history()
-        if len(self.get_datasets_in_history()) > 0:
-            raise AssertionError("test_framework.test_new_history failed")
-    def test_delete_history_item( self ):
-test_components.test_delete_history_item: 
+
-        self.new_history()
-        self.upload_file('1.bed', dbkey='hg15')
@@ -17 +17 @@
-        self.check_history_for_string("Your history is empty")
-        self.assertEqual ( len(self.get_datasets_in_history()), 0)
-
-class TestMetadata( TwillTestCase ):
-
-    def test_metadata_edit(self):
-        """test_components.test_metadata_edit: Testing metadata editing"""
-        self.new_history()
-        self.upload_file('1.bed')
-        self.check_history_for_string('\? bed')
-        self.check_metadata_for_string('1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=1)
-        """test editing attributes"""
-        self.edit_metadata(hid=1, form=1,  name='Testdata', info="Uploaded my file", dbkey='hg16')
-        self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes"', hid=1)
-        """test converting formats"""
-        self.edit_metadata(hid=1, form=2, target_type='gff')
-        self.check_history_for_string('hg16 Testdata Convert BED to GFF')
-        self.check_metadata_for_string('"gff" selected="yes"', hid=1)
-        """test changing data type"""
-        self.edit_metadata(hid=1, form=3, datatype='gff3')
-        self.check_history_for_string('hg16 Testdata Convert BED to GFF format: gff3')
-        

tools/filters/maf/maf_limit_size.xml

@@ -17 +17 @@
-      <param name="min_size" value="0"/>
-      <param name="max_size" value="0"/>
-3
+maf_limit_size1_out
-    </test>
-  </tests>