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[hg] galaxy 2392: New quickie
by Greg Von Kuster 01 May '09

01 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/84ecf82a2ce7 changeset: 2392:84ecf82a2ce7 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri May 01 11:09:04 2009 -0400 description: New quickie 3 file(s) affected in this change: static/images/qk/quickie5_lrg.png static/images/qk/quickie5_small.png static/welcome.html diffs (99 lines): diff -r 9ad7b4abbfc7 -r 84ecf82a2ce7 static/images/qk/quickie5_lrg.png Binary file static/images/qk/quickie5_lrg.png has changed diff -r 9ad7b4abbfc7 -r 84ecf82a2ce7 static/images/qk/quickie5_small.png Binary file static/images/qk/quickie5_small.png has changed diff -r 9ad7b4abbfc7 -r 84ecf82a2ce7 static/welcome.html --- a/static/welcome.html Fri May 01 10:11:00 2009 -0400 +++ b/static/welcome.html Fri May 01 11:09:04 2009 -0400 @@ -71,15 +71,15 @@ <div class="current-quickie"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> - <tr> - <td align="center"> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsnew/flow.html',width:640,height:500,scroll:'no'})"> - <img src="images/qk/quickie4_lrg.png" border="0"> - <br> - </a> + <tr> + <td align="center"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:500,scroll:'no'})"> + <img src="images/qk/quickie5_lrg.png" border="0"> + <br> + </a> - </td> - </tr> + </td> + </tr> </table> </div> @@ -87,34 +87,40 @@ <hr> <div class="previous"> - <table border="0" cellpadding="0" cellspacing="0" width="100%"> - <tr> - <td width="32%" style="border-right: solid white 10px;"> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:500,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie1_small.png" border="0"> - </div> - </a> - </td> - <td width="32%" style="border-left: solid white 5px; border-right: solid white 5px"> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:500,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie2_small.png" border="0"> - </div> - </a> - </div> - </td> - <td width="32%" style="border-left: solid white 10px;" > - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:500,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie3_small.png" border="0"> - </div> - </a> - </td> - - </tr> + <table border="0" cellpadding="0" cellspacing="0" width="100%"> + <tr> + <td width="50%" style="border-right: solid white 10px; border-bottom: solid white 10px"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:500,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie1_small.png" border="0"> + </div> + </a> + </td> + <td width="50%" style="border-left: solid white 10px; border-bottom: solid white 10px"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:500,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie2_small.png" border="0"> + </div> + </a> + </td> + </tr> + <tr> + <td width="50%" style="border-right: solid white 10px; border-top: solid white 10px" > + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:500,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie3_small.png" border="0"> + </div> + </a> + </td> + <td width="50%" style="border-left: solid white 10px; border-top: solid white 10px" > + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:500,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie4_small.png" border="0"> + </div> + </a> + </td> + </tr> </table> -</div> </div> <br/>

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[hg] galaxy 2391: Fix for pasting data in the upload utility - n...
by Greg Von Kuster 01 May '09

01 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9ad7b4abbfc7 changeset: 2391:9ad7b4abbfc7 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri May 01 10:11:00 2009 -0400 description: Fix for pasting data in the upload utility - no longer results in a UnicodeWarning, added new tests to cover case. 3 file(s) affected in this change: lib/galaxy/datatypes/sniff.py test/base/twilltestcase.py test/functional/test_get_data.py diffs (136 lines): diff -r ee9a29c9efc1 -r 9ad7b4abbfc7 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Thu Apr 30 16:12:59 2009 -0400 +++ b/lib/galaxy/datatypes/sniff.py Fri May 01 10:11:00 2009 -0400 @@ -30,9 +30,11 @@ if zipfile.is_zipfile( temp_name ): is_compressed = True else: - magic_check = chunk[:2] - if magic_check == util.gzip_magic: - is_compressed = True + try: + if unicode( chunk[:2] ) == unicode( util.gzip_magic ): + is_compressed = True + except: + pass if not is_compressed: # See if we have a multi-byte character file chars = chunk[:100] diff -r ee9a29c9efc1 -r 9ad7b4abbfc7 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Apr 30 16:12:59 2009 -0400 +++ b/test/base/twilltestcase.py Fri May 01 10:11:00 2009 -0400 @@ -82,6 +82,18 @@ errmsg = 'The file doesn\'t exsit. Please check' % file errmsg += str( err ) raise AssertionError( errmsg ) + def upload_url_paste( self, url_paste, ftype='auto', dbkey='unspecified (?)' ): + """Pasted data in the upload utility""" + self.visit_page( "tool_runner/index?tool_id=upload1" ) + try: + tc.fv( "1", "file_type", ftype ) + tc.fv( "1", "dbkey", dbkey ) + tc.fv( "1", "url_paste", url_paste ) + tc.submit( "runtool_btn" ) + self.home() + except Exception, e: + errmsg = "Problem executing upload utility using url_paste: %s" % str( e ) + raise AssertionError( e ) # Functions associated with histories def check_history_for_errors( self ): @@ -663,16 +675,23 @@ self.home() # Tests associated with roles - def create_role( self, name='Role One', description="This is Role One", in_user_ids=[], in_group_ids=[], private_role='' ): + def create_role( self, name='Role One', description="This is Role One", in_user_ids=[], in_group_ids=[], create_group_for_role='no', private_role='' ): """Create a new role""" url = "%s/admin/create_role?create_role_button=Save&name=%s&description=%s" % ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) ) if in_user_ids: url += "&in_users=%s" % ','.join( in_user_ids ) if in_group_ids: url += "&in_groups=%s" % ','.join( in_group_ids ) + if create_group_for_role == 'yes': + url += '&create_group_for_role=yes' self.home() self.visit_url( url ) - check_str = "Role '%s' has been created with %d associated users and %d associated groups" % ( name, len( in_user_ids ), len( in_group_ids ) ) + if create_group_for_role == 'yes': + check_str = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ + ( name, name, len( in_user_ids ), len( in_group_ids ) ) + else: + check_str = "Role '%s' has been created with %d associated users and %d associated groups" % \ + ( name, len( in_user_ids ), len( in_group_ids ) ) self.check_page_for_string( check_str ) if private_role: # Make sure no private roles are displayed @@ -800,16 +819,35 @@ def rename_library( self, library_id, old_name, name='Library One Renamed', description='This is Library One Re-described' ): """Rename a library""" self.home() - self.visit_url( "%s/admin/library?manage=True&id=%s" % ( self.url, library_id ) ) + self.visit_url( "%s/admin/library?information=True&id=%s" % ( self.url, library_id ) ) self.check_page_for_string( 'Change library name and description' ) # Since twill barfs on the form submisson, we ar forced to simulate it - url = "%s/admin/library?manage=True&id=%s&rename_library_button=Save&description=%s&name=%s" % \ + url = "%s/admin/library?information=True&id=%s&rename_library_button=Save&description=%s&name=%s" % \ ( self.url, library_id, description.replace( ' ', '+' ), name.replace( ' ', '+' ) ) self.home() self.visit_url( url ) check_str = "Library '%s' has been renamed to '%s'" % ( old_name, name ) self.check_page_for_string( check_str ) self.home() + def add_library_info_template( self, library_id, library_name ): + """Add a new info template to a library""" + self.home() + url = "%s/admin/info_template?library_id=%s&new_template=True&num_fields=2&create_info_template_button=Go" % ( self.url, library_id ) + self.home() + self.visit_url( url ) + check_str = "Create a new information template for library '%s'" % library_name + self.check_page_for_string ( check_str ) + # TODO: finish this... + def add_folder_info_template( self, library_id, library_name, folder_id, folder_name ): + """Add a new info template to a folder""" + self.home() + url = "%s/admin/info_template?library_id=%s&folder_id=%s&new_template=True&num_fields=2&create_info_template_button=Go" % \ + ( self.url, library_id, folder_id ) + self.home() + self.visit_url( url ) + check_str = "Create a new information template for folder '%s'" % folder_name + self.check_page_for_string ( check_str ) + # TODO: finish this... def add_folder( self, library_id, folder_id, name='Folder One', description='NThis is Folder One' ): """Create a new folder""" self.home() diff -r ee9a29c9efc1 -r 9ad7b4abbfc7 test/functional/test_get_data.py --- a/test/functional/test_get_data.py Thu Apr 30 16:12:59 2009 -0400 +++ b/test/functional/test_get_data.py Fri May 01 10:11:00 2009 -0400 @@ -3,7 +3,6 @@ """ Tests are executed in order, sorted by name""" class UploadData( TwillTestCase ): - def test_00_multi_upload( self ): """test_get_data.test_multi_upload: Testing multiple uploads""" self.login() @@ -19,12 +18,20 @@ self.verify_dataset_correctness('1.scf') self.upload_file('1.scf.zip', ftype='binseq.zip') self.verify_dataset_correctness('1.scf.zip') + self.upload_url_paste( 'hello world' ) + self.check_history_for_string( 'Pasted Entry' ) + self.check_history_for_string( 'hello world' ) self.delete_history_item( 1 ) self.delete_history_item( 2 ) self.delete_history_item( 3 ) self.delete_history_item( 4 ) self.delete_history_item( 5 ) self.delete_history_item( 6 ) + self.delete_history_item( 7 ) + self.upload_url_paste( u'hello world' ) + self.check_history_for_string( 'Pasted Entry' ) + self.check_history_for_string( 'hello world' ) + self.delete_history_item( 8 ) def test_9999_clean_up( self ): self.delete_history() self.logout()

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[hg] galaxy 2390: Reintroduce the ability to copy a history item...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ee9a29c9efc1 changeset: 2390:ee9a29c9efc1 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Apr 30 16:12:59 2009 -0400 description: Reintroduce the ability to copy a history item between histories (and within the same). 3 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py templates/dataset/copy_view.mako templates/dataset/edit_attributes.mako diffs (53 lines): diff -r 54be726b7711 -r ee9a29c9efc1 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Thu Apr 30 15:37:37 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Thu Apr 30 16:12:59 2009 -0400 @@ -157,6 +157,7 @@ user = trans.get_user() history = trans.get_history() create_new_history = False + refresh_frames = [] if source_dataset_ids: if not isinstance( source_dataset_ids, list ): source_dataset_ids = source_dataset_ids.split( "," ) @@ -203,6 +204,8 @@ else: for hist in target_histories: hist.add_dataset( data.copy( copy_children = True ) ) + if history in target_histories: + refresh_frames = ['history'] trans.app.model.flush() done_msg = "%i datasets copied to %i histories." % ( len( source_dataset_ids ) - invalid_datasets, len( target_histories ) ) history.refresh() @@ -220,4 +223,5 @@ target_histories = target_histories, new_history_name = new_history_name, done_msg = done_msg, - error_msg = error_msg ) + error_msg = error_msg, + refresh_frames = refresh_frames ) diff -r 54be726b7711 -r ee9a29c9efc1 templates/dataset/copy_view.mako --- a/templates/dataset/copy_view.mako Thu Apr 30 15:37:37 2009 -0400 +++ b/templates/dataset/copy_view.mako Thu Apr 30 16:12:59 2009 -0400 @@ -1,5 +1,8 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="javascripts" /> <%def name="title()">Copy History Items</%def> + +${javascripts()} %if error_msg: <p> diff -r 54be726b7711 -r ee9a29c9efc1 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Thu Apr 30 15:37:37 2009 -0400 +++ b/templates/dataset/edit_attributes.mako Thu Apr 30 16:12:59 2009 -0400 @@ -155,3 +155,10 @@ </div> </div> %endif +<p/> +<div class="toolForm"> +<div class="toolFormTitle">Copy History Item</div> +<div class="toolFormBody"> + Click <a href="${h.url_for( controller='dataset', action='copy_datasets', source_dataset_ids=data.id, target_history_ids=data.history_id )}" target="galaxy_main">here</a> to make a copy of this history item. +</div> +</div>

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[hg] galaxy 2389: Fix for HID incrementing by two when importing...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/54be726b7711 changeset: 2389:54be726b7711 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Apr 30 15:37:37 2009 -0400 description: Fix for HID incrementing by two when importing from a library. 2 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/web/controllers/library.py diffs (44 lines): diff -r ff2fca65799e -r 54be726b7711 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Apr 30 11:07:34 2009 -0400 +++ b/lib/galaxy/model/__init__.py Thu Apr 30 15:37:37 2009 -0400 @@ -777,8 +777,7 @@ self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association self.library_dataset = library_dataset self.user = user - def to_history_dataset_association( self, target_history, parent_id=None ): - hid = target_history._next_hid() + def to_history_dataset_association( self, target_history, parent_id = None, add_to_history = False ): hda = HistoryDatasetAssociation( name=self.name, info=self.info, blurb=self.blurb, @@ -790,12 +789,13 @@ deleted=self.deleted, parent_id=parent_id, copied_from_library_dataset_dataset_association=self, - history=target_history, - hid=hid ) + history=target_history ) hda.flush() hda.metadata = self.metadata #need to set after flushed, as MetadataFiles require dataset.id + if add_to_history and target_history: + target_history.add_dataset( hda ) for child in self.children: - child_copy = child.to_history_dataset_association( target_history=target_history, parent_id=hda.id ) + child_copy = child.to_history_dataset_association( target_history = target_history, parent_id = hda.id, add_to_history = False ) if not self.datatype.copy_safe_peek: hda.set_peek() #in some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs hda.flush() diff -r ff2fca65799e -r 54be726b7711 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Thu Apr 30 11:07:34 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Thu Apr 30 15:37:37 2009 -0400 @@ -175,9 +175,7 @@ history = trans.get_history() for ldda_id in ldda_ids: ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id ) - hda = ldda.to_history_dataset_association( target_history=history ) - history.add_dataset( hda ) - hda.flush() + hda = ldda.to_history_dataset_association( target_history=history, add_to_history = True ) history.flush() msg = "%i dataset(s) have been imported into your history" % len( ldda_ids ) return trans.response.send_redirect( web.url_for( controller='library',

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[hg] galaxy 2388: A tiny bug fix for linear regression tool.
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ff2fca65799e changeset: 2388:ff2fca65799e user: guru date: Thu Apr 30 11:07:34 2009 -0400 description: A tiny bug fix for linear regression tool. 1 file(s) affected in this change: tools/regVariation/linear_regression.py diffs (12 lines): diff -r 609ee7376d0d -r ff2fca65799e tools/regVariation/linear_regression.py --- a/tools/regVariation/linear_regression.py Thu Apr 30 10:54:43 2009 -0400 +++ b/tools/regVariation/linear_regression.py Thu Apr 30 11:07:34 2009 -0400 @@ -17,7 +17,7 @@ print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1) fout = open(outfile,'w') - +elems = [] for i, line in enumerate( file ( infile )): line = line.rstrip('\r\n') if len( line )>0 and not line.startswith( '#' ):

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[hg] galaxy 2386: Change variable names in validation from min/m...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/799a333342c4 changeset: 2386:799a333342c4 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Apr 30 10:24:41 2009 -0400 description: Change variable names in validation from min/max to range/length_min/max. 1 file(s) affected in this change: lib/galaxy/tools/parameters/validation.py diffs (40 lines): diff -r add0911007d9 -r 799a333342c4 lib/galaxy/tools/parameters/validation.py --- a/lib/galaxy/tools/parameters/validation.py Wed Apr 29 17:37:22 2009 -0400 +++ b/lib/galaxy/tools/parameters/validation.py Thu Apr 30 10:24:41 2009 -0400 @@ -102,10 +102,10 @@ @classmethod def from_element( cls, param, elem ): return cls( elem.get( 'message', None ), elem.get( 'min' ), elem.get( 'max' ) ) - def __init__( self, message, min, max ): - self.message = message or ( "Value must be between %f and %f" % ( min, max ) ) - self.min = float( min ) - self.max = float( max ) + def __init__( self, message, range_min, range_max ): + self.message = message or ( "Value must be between %f and %f" % ( range_min, range_max ) ) + self.min = float( range_min ) + self.max = float( range_max ) def validate( self, value, history=None ): if not( self.min <= float( value ) <= self.max ): raise ValueError( self.message ) @@ -134,14 +134,14 @@ @classmethod def from_element( cls, param, elem ): return cls( elem.get( 'message', None ), elem.get( 'min', None ), elem.get( 'max', None ) ) - def __init__( self, message, min, max ): + def __init__( self, message, length_min, length_max ): self.message = message - if min is not None: - min = int( min ) - if max is not None: - max = int( max ) - self.min = min - self.max = max + if length_min is not None: + length_min = int( length_min ) + if length_max is not None: + length_max = int( length_max ) + self.min = length_min + self.max = length_max def validate( self, value, history=None ): if self.min is not None and len( value ) < self.min: raise ValueError( self.message or ( "Must have length of at least %d" % self.min ) )

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[hg] galaxy 2387: Added test datasets for qualityscore unit tests.
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/609ee7376d0d changeset: 2387:609ee7376d0d user: guru date: Thu Apr 30 10:54:43 2009 -0400 description: Added test datasets for qualityscore unit tests. 2 file(s) affected in this change: lib/galaxy/datatypes/test/sequence.qual454 lib/galaxy/datatypes/test/sequence.qualsolid diffs (38 lines): diff -r 799a333342c4 -r 609ee7376d0d lib/galaxy/datatypes/test/sequence.qual454 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/test/sequence.qual454 Thu Apr 30 10:54:43 2009 -0400 @@ -0,0 +1,16 @@ +>EYKX4VC04IWAEA length=68 xy=3531_0528 region=4 run=R_2007_11_07_16_15_57_ +22 13 9 6 4 3 2 2 1 1 1 1 24 44 33 23 16 11 7 2 28 33 23 18 28 27 27 28 20 21 42 35 21 6 24 25 31 21 28 27 41 34 15 28 28 27 28 28 33 24 27 28 28 24 27 36 27 28 28 28 +28 28 36 30 8 34 25 18 +>EYKX4VC04JKOGH length=48 xy=3808_3903 region=4 run=R_2007_11_07_16_15_57_ +28 28 27 28 38 31 10 28 28 27 27 34 25 28 24 26 27 28 27 37 29 34 25 31 21 28 21 36 28 31 20 24 27 37 28 28 34 27 3 34 25 24 28 28 26 28 35 28 +>EYKX4VC04JIUVK length=84 xy=3788_0830 region=4 run=R_2007_11_07_16_15_57_ +29 20 14 11 8 6 3 1 25 27 25 28 28 27 28 27 28 28 36 28 27 28 36 29 7 28 28 28 27 27 27 35 26 35 26 27 36 28 28 28 38 32 11 28 36 28 27 26 35 25 28 38 31 11 27 28 37 28 27 27 +28 36 29 8 33 24 41 34 19 3 26 28 28 28 35 26 36 29 8 38 32 11 28 28 +>EYKX4VC04JWDRY length=78 xy=3942_1068 region=4 run=R_2007_11_07_16_15_57_ +36 24 14 5 27 20 28 27 28 32 22 28 27 43 36 23 11 27 28 28 28 32 23 36 27 28 28 26 38 32 11 34 25 27 43 36 23 11 38 31 11 37 28 28 28 27 28 30 20 28 32 22 28 36 27 37 30 9 27 28 +28 27 28 42 35 20 5 28 28 28 35 26 27 27 26 39 32 12 +>EYKX4VC04JWMUW length=55 xy=3945_0550 region=4 run=R_2007_11_07_16_15_57_ +36 24 14 4 28 17 34 25 35 25 31 20 28 28 36 27 28 28 24 27 28 28 37 28 27 27 35 25 31 21 27 39 32 12 28 36 28 28 26 27 28 27 26 28 42 35 20 6 28 27 28 28 28 28 28 +>EYKX4VC04JH4RG length=85 xy=3779_3850 region=4 run=R_2007_11_07_16_15_57_ +37 28 35 26 38 31 10 27 37 28 28 38 31 10 27 35 25 25 28 28 28 28 28 28 28 28 27 28 33 23 28 32 22 35 25 31 20 34 25 31 21 26 28 27 26 26 15 36 29 7 27 27 24 36 27 28 37 28 36 28 +27 28 28 28 37 28 28 40 34 14 37 28 28 26 28 36 28 26 28 37 28 28 28 28 27 \ No newline at end of file diff -r 799a333342c4 -r 609ee7376d0d lib/galaxy/datatypes/test/sequence.qualsolid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/test/sequence.qualsolid Thu Apr 30 10:54:43 2009 -0400 @@ -0,0 +1,12 @@ +>946_21_302_F3 +2 10 2 2 4 2 21 2 2 4 4 17 5 2 5 2 11 4 2 2 2 10 7 3 15 2 2 2 3 19 3 2 6 3 2 +>946_21_659_F3 +3 31 3 2 2 2 34 3 2 2 2 31 2 2 3 4 31 8 3 2 2 30 4 8 3 3 2 2 6 9 4 4 6 2 2 +>946_21_1071_F3 +5 5 2 2 2 8 5 3 2 3 7 7 2 3 4 6 5 2 2 2 5 5 2 2 2 3 8 2 3 3 3 8 2 3 2 +>946_21_1115_F3 +21 5 2 8 13 31 6 2 17 24 10 27 4 21 29 8 20 2 11 21 13 24 5 5 6 24 31 2 13 6 22 17 6 27 10 +>946_21_1218_F3 +11 21 2 13 13 16 27 16 19 27 22 28 14 26 24 23 29 10 15 13 6 4 7 16 26 22 11 6 16 22 21 6 4 7 21 +>946_21_1232_F3 +17 16 2 28 21 31 15 16 10 11 8 20 6 5 18 6 13 23 7 13 4 12 19 8 6 9 10 19 7 10 6 10 20 14 8 \ No newline at end of file

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[hg] galaxy 2383: Accidently commited a testing change, removed
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/656f1df80b46 changeset: 2383:656f1df80b46 user: James Taylor <james(a)jamestaylor.org> date: Wed Apr 29 14:47:18 2009 -0400 description: Accidently commited a testing change, removed 1 file(s) affected in this change: tools/maf/interval2maf.xml diffs (11 lines): diff -r 89541ac4983f -r 656f1df80b46 tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml Wed Apr 29 13:56:59 2009 -0400 +++ b/tools/maf/interval2maf.xml Wed Apr 29 14:47:18 2009 -0400 @@ -6,7 +6,6 @@ #end if </command> <inputs> - <param type="text" name="TEST" label="Test" /> <param format="interval" name="input1" type="data" label="Choose intervals"> <validator type="unspecified_build" /> </param>

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[hg] galaxy 2382: Fix for reporting job errors - somehow necessa...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/89541ac4983f changeset: 2382:89541ac4983f user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Apr 29 13:56:59 2009 -0400 description: Fix for reporting job errors - somehow necessary imported stuff got eliminated. 1 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py diffs (24 lines): diff -r dae0313bf5bb -r 89541ac4983f lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Wed Apr 29 13:46:02 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Wed Apr 29 13:56:59 2009 -0400 @@ -1,7 +1,7 @@ -import logging, os, mimetypes, smtplib +import logging, os, sets, string, shutil, re, socket, mimetypes, smtplib from galaxy.web.base.controller import * -from galaxy import web, model +from galaxy import util, datatypes, jobs, web, model from cgi import escape, FieldStorage from email.MIMEText import MIMEText @@ -89,8 +89,8 @@ s.sendmail( frm, [ to ], msg.as_string() ) s.close() return trans.show_ok_message( "Your error report has been sent" ) - except: - return trans.show_error_message( "An error occurred sending the report by email" ) + except Exception, e: + return trans.show_error_message( "An error occurred sending the report by email: %s" % str( e ) ) @web.expose def default(self, trans, dataset_id=None, **kwd):

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[hg] galaxy 2385: PyTables and GeneTrack eggs. Still need to bu...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/add0911007d9 changeset: 2385:add0911007d9 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Apr 29 17:37:22 2009 -0400 description: PyTables and GeneTrack eggs. Still need to bundle up pychartdir. 2 file(s) affected in this change: dist-eggs.ini eggs.ini diffs (55 lines): diff -r cd1bcec32519 -r add0911007d9 dist-eggs.ini --- a/dist-eggs.ini Wed Apr 29 16:32:23 2009 -0400 +++ b/dist-eggs.ini Wed Apr 29 17:37:22 2009 -0400 @@ -24,9 +24,15 @@ py2.5-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.5 [groups] -py2.4-linux = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 -py2.5-linux = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 -linux = py2.4-linux py2.5-linux +py2.4-linux-i686 = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 +py2.4-linux-x86_64 = py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 +py2.5-linux-i686 = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 +py2.5-linux-x86_64 = py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 +py2.4-linux = py2.4-linux-i686 py2.4-linux-x86_64 +py2.5-linux = py2.5-linux-i686 py2.5-linux-x86_64 +linux-i686 = py2.4-linux-i686 py2.5-linux-i686 +linux-x86_64 = py2.4-linux-x86_64 py2.5-linux-x86_64 +linux = linux-i686 linux-x86_64 py2.4-macosx = py2.4-macosx-10.3-fat-ucs2 py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 py2.5-macosx-10.5-i386-ucs2 macosx = py2.4-macosx py2.5-macosx diff -r cd1bcec32519 -r add0911007d9 eggs.ini --- a/eggs.ini Wed Apr 29 16:32:23 2009 -0400 +++ b/eggs.ini Wed Apr 29 17:37:22 2009 -0400 @@ -24,6 +24,7 @@ threadframe = 0.2 guppy = 0.1.8 numpy = 1.2.1 +tables = 2.1.1 [eggs:noplatform] Beaker = 0.5 @@ -51,6 +52,7 @@ wsgiref = 0.1.2 Babel = 0.9.4 wchartype = 0.1 +GeneTrack = 1.0.3 ; extra version information [tags] @@ -61,6 +63,7 @@ flup = .dev_r2311 bx_python = _dev_r4bf1f32e6b76 nose = .dev_r101 +tables = _hdf5_1.8.2_lzo_2.03_bzip2_1.0.5_static ; source location, necessary for scrambling [source] @@ -100,3 +103,5 @@ wsgiref = http://pypi.python.org/packages/source/w/wsgiref/wsgiref-0.1.2.zip Babel = http://ftp.edgewall.com/pub/babel/Babel-0.9.4.zip wchartype = http://ginstrom.com/code/wchartype-0.1.zip +tables = http://www.pytables.org/download/stable/tables-2.1.1.tar.gz ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.8.2.tar.gz http://www.oberhumer.com/opensource/lzo/download/lzo-2.03.tar.gz http://www.bzip.org/1.0.5/bzip2-1.0.5.tar.gz +GeneTrack = http://genetrack.googlecode.com/files/GeneTrack-1.0.3.zip http://dalchemy.com/opensource/formkit/FormKit_0.9b2.tar.gz

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