Tool versioning: now store version information in hda/ldda tables. Information is kept when copied between hda/ldda, and now displayed in the "Show Info" pages for hdas and lddas.

2026-09-24 16:30:27 +08:00 · 2011-08-24 00:45:31 -04:00
parent d073792e38
commit eb6bf73cab
6 changed files with 61 additions and 4 deletions
@@ -534,7 +534,7 @@ class JobWrapper( object ):
        if self.version_string_cmd:
            version_filename = self.get_version_string_path()
            if os.path.exists(version_filename):
-                self.version_string = "Tool version: %s" % open(version_filename).read()
+                self.version_string = open(version_filename).read()
                os.unlink(version_filename)
            
        if self.app.config.outputs_to_working_directory:
@@ -587,7 +587,8 @@ class JobWrapper( object ):
            
                dataset.blurb = 'done'
                dataset.peek  = 'no peek'
-                dataset.info  = context['stdout'] + context['stderr'] + self.version_string
+                dataset.info  = context['stdout'] + context['stderr']
+                dataset.tool_version = self.version_string
                dataset.set_size()
                if context['stderr']:
                    dataset.blurb = "error"
@@ -753,7 +753,7 @@ class DatasetInstance( object ):
    """A base class for all 'dataset instances', HDAs, LDAs, etc"""
    states = Dataset.states
    permitted_actions = Dataset.permitted_actions
-    def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None,
+    def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None,
                  dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None,
                  parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None ):
        self.name = name or "Unnamed dataset"
@@ -761,6 +761,7 @@ class DatasetInstance( object ):
        self.info = info
        self.blurb = blurb
        self.peek = peek
+        self.tool_version = tool_version
        self.extension = extension
        self.designation = designation
        self.metadata = metadata or dict()
@@ -1020,6 +1021,7 @@ class HistoryDatasetAssociation( DatasetInstance ):
                                         info=self.info, 
                                         blurb=self.blurb, 
                                         peek=self.peek, 
+                                         tool_version=self.tool_version, 
                                         extension=self.extension, 
                                         dbkey=self.dbkey, 
                                         dataset = self.dataset, 
@@ -1057,6 +1059,7 @@ class HistoryDatasetAssociation( DatasetInstance ):
                                                 info=self.info,
                                                 blurb=self.blurb, 
                                                 peek=self.peek, 
+                                                 tool_version=self.tool_version, 
                                                 extension=self.extension, 
                                                 dbkey=self.dbkey, 
                                                 dataset=self.dataset, 
@@ -1410,6 +1413,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
                                         info=self.info,
                                         blurb=self.blurb, 
                                         peek=self.peek, 
+                                         tool_version=self.tool_version, 
                                         extension=self.extension, 
                                         dbkey=self.dbkey, 
                                         dataset=self.dataset, 
@@ -1434,6 +1438,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
                                                 info=self.info, 
                                                 blurb=self.blurb, 
                                                 peek=self.peek, 
+                                                 tool_version=self.tool_version, 
                                                 extension=self.extension, 
                                                 dbkey=self.dbkey, 
                                                 dataset=self.dataset, 
@@ -113,6 +113,7 @@ HistoryDatasetAssociation.table = Table( "history_dataset_association", metadata
    Column( "info", TrimmedString( 255 ) ),
    Column( "blurb", TrimmedString( 255 ) ),
    Column( "peek" , TEXT ),
+    Column( "tool_version" , TEXT ),
    Column( "extension", TrimmedString( 64 ) ),
    Column( "metadata", MetadataType(), key="_metadata" ),
    Column( "parent_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ),
@@ -305,6 +306,7 @@ LibraryDatasetDatasetAssociation.table = Table( "library_dataset_dataset_associa
    Column( "info", TrimmedString( 255 ) ),
    Column( "blurb", TrimmedString( 255 ) ),
    Column( "peek" , TEXT ),
+    Column( "tool_version" , TEXT ),
    Column( "extension", TrimmedString( 64 ) ),
    Column( "metadata", MetadataType(), key="_metadata" ),
    Column( "parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ),
@@ -0,0 +1,41 @@
+"""
+Migration script to add a 'tool_version' column to the hda/ldda tables.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+from galaxy.model.custom_types import *
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    try:
+        hda_table = Table( "history_dataset_association", metadata, autoload=True )
+        c = Column( "tool_version", TEXT )
+        c.create( hda_table )
+        assert c is hda_table.c.tool_version
+        
+        ldda_table = Table( "library_dataset_dataset_association", metadata, autoload=True )
+        c = Column( "tool_version", TEXT )
+        c.create( ldda_table )
+        assert c is ldda_table.c.tool_version
+        
+    except Exception, e:
+        print "Adding the tool_version column to the hda/ldda tables failed: ", str( e )
+
+def downgrade():
+    metadata.reflect()
+    try:
+        hda_table = Table( "history_dataset_association", metadata, autoload=True )
+        hda_table.c.tool_version.drop()
+        
+        ldda_table = Table( "library_dataset_dataset_association", metadata, autoload=True )
+        ldda_table.c.tool_version.drop()
+    except Exception, e:
+        print "Dropping the tool_version column from hda/ldda table failed: ", str( e )
@@ -100,6 +100,13 @@
            ${ldda.get_size( nice_size=True )}
            <div style="clear: both"></div>
        </div>
+        %if ldda.tool_version:
+            <div class="form-row">
+                <label>Tool version:</label>
+                ${ldda.tool_version}
+                <div style="clear: both"></div>
+            </div>
+        %endif
        <div class="form-row">
            <label>Data type:</label>
            ${ldda.ext}
@@ -154,7 +161,7 @@
        %endfor
        %if ldda.peek != "no peek":
            <div class="form-row">
-               <div id="info${ldda.id}" class="historyItemBody">
+                <div id="info${ldda.id}" class="historyItemBody">
                    <label>Peek:</label>
                    <div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div>
                </div>
@@ -49,6 +49,7 @@
        <tr><td>Filesize:</td><td>${nice_size(hda.dataset.file_size)}</td></tr>
        <tr><td>Dbkey:</td><td>${hda.dbkey}</td></tr>
        <tr><td>Format:</td><td>${hda.ext}</td></tr>
+        <tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr>
 </table>
 <br />
 <table class="tabletip">