April 2010 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3632: Enable user to change dbkey from a known key b...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0dc1fc63c945 changeset: 3632:0dc1fc63c945 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Apr 13 10:22:27 2010 -0400 description: Enable user to change dbkey from a known key back to unspecified. This is a hack, but there's no straightforward way to accomplish this without modifying the jquery autocomplete script. diffstat: static/scripts/galaxy.base.js | 11 +++++++++-- 1 files changed, 9 insertions(+), 2 deletions(-) diffs (30 lines): diff -r 968161f35d50 -r 0dc1fc63c945 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Tue Apr 13 10:16:46 2010 -0400 +++ b/static/scripts/galaxy.base.js Tue Apr 13 10:22:27 2010 -0400 @@ -149,10 +149,10 @@ var select_mapping = {}; select_elt.children('option').each( function() { // Get text, value for option. - var text = $(this).text(); + var text = $(this).text(); var value = $(this).attr('value'); - // Ignore values that are '?' + // HACK: dbkey-specific: ignore values that are '?' if (value == '?') { return; } @@ -169,6 +169,13 @@ } }); + // HACK: dbkey-specific: add an unspecified option. We need to add this at the end b/c adding it first mucks + // up the autocomplete sorting for some reason. (I.e. All options that start with the first character of the + // first option are listed before the other, alphabetized options.) + select_options.push( "unspecified (?)" ); + select_mapping[ "unspecified (?)" ] = "?"; + select_mapping[ "?" ] = "?"; + // Set initial text if it's empty. if ( text_input_elt.attr('value') == '' ) { text_input_elt.attr('value', 'Click to Search or Select');

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[hg] galaxy 3631: fixed forms and user_info functional tests
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/968161f35d50 changeset: 3631:968161f35d50 user: rc date: Tue Apr 13 10:16:46 2010 -0400 description: fixed forms and user_info functional tests removed a debugging print stmt diffstat: lib/galaxy/model/__init__.py | 2 +- lib/galaxy/web/controllers/forms.py | 1 - test/functional/test_forms_and_requests.py | 8 ++++---- test/functional/test_user_info.py | 2 +- 4 files changed, 6 insertions(+), 7 deletions(-) diffs (74 lines): diff -r fdf5c92e7fae -r 968161f35d50 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Apr 12 19:11:36 2010 -0400 +++ b/lib/galaxy/model/__init__.py Tue Apr 13 10:16:46 2010 -0400 @@ -1326,7 +1326,7 @@ # the user had already filled out this field and the same form is re-rendered # due to some reason like required fields have been left out. if field[ 'type' ] == 'CheckboxField': - value = CheckboxField.is_checked( util.restore_text( params.get( field_name, False ) ) ) + value = CheckboxField.is_checked( params.get( field_name, False ) ) else: value = util.restore_text( params.get( field_name, '' ) ) elif contents: diff -r fdf5c92e7fae -r 968161f35d50 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Mon Apr 12 19:11:36 2010 -0400 +++ b/lib/galaxy/web/controllers/forms.py Tue Apr 13 10:16:46 2010 -0400 @@ -541,7 +541,6 @@ self.selectbox_options = [] # if the form is for defining samples, then use the sample field types # which does not include TextArea & AddressField - print >> sys.stderr, 'form_type', form_type if form_type == trans.app.model.FormDefinition.types.SAMPLE: for ft in BaseField.sample_field_types(): self.fieldtype.add_option(ft, ft) diff -r fdf5c92e7fae -r 968161f35d50 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Mon Apr 12 19:11:36 2010 -0400 +++ b/test/functional/test_forms_and_requests.py Tue Apr 13 10:16:46 2010 -0400 @@ -106,7 +106,7 @@ """Testing address & library creation""" # first create a regular user self.logout() - self.login( email='test1(a)bx.psu.edu' ) + self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) self.logout() self.login( email='test(a)bx.psu.edu' ) # first create a library for the request so that it can be submitted later @@ -191,7 +191,7 @@ self.check_page_for_string( name ) # create address self.logout() - self.login( email='test1(a)bx.psu.edu' ) + self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) self.add_user_address( regular_user1.id, address1 ) global regular_user regular_user = sa_session.query( galaxy.model.User ) \ @@ -206,7 +206,7 @@ """Testing creating, editing and submitting a request as a regular user""" # login as a regular user self.logout() - self.login( email='test1(a)bx.psu.edu' ) + self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) # set field values fields = ['option1', str(user_address.id), 'field three value'] # create the request @@ -259,7 +259,7 @@ self.home() sa_session.refresh( request_one ) self.logout() - self.login( email='test1(a)bx.psu.edu' ) + self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) # check if the request's state is now set to 'complete' self.check_request_grid(state='Complete', request_name=request_one.name) assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ diff -r fdf5c92e7fae -r 968161f35d50 test/functional/test_user_info.py --- a/test/functional/test_user_info.py Mon Apr 12 19:11:36 2010 -0400 +++ b/test/functional/test_user_info.py Tue Apr 13 10:16:46 2010 -0400 @@ -162,7 +162,7 @@ # Test changing email and user name - first try an invalid user name self.edit_login_info( new_email='test12_new(a)bx.psu.edu', new_username='test12_new', - check_str1='User name must contain only letters, numbers and' ) + check_str1="User name must contain only lower-case letters, numbers and '-'" ) # Now try a valid user name self.edit_login_info( new_email='test12_new(a)bx.psu.edu', new_username='test12-new',

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[hg] galaxy 3630: Fixed a bug in the new joiner tool
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/fdf5c92e7fae changeset: 3630:fdf5c92e7fae user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Mon Apr 12 19:11:36 2010 -0400 description: Fixed a bug in the new joiner tool diffstat: tools/new_operations/column_join.py | 97 +++++++++++++++++++++++------------ tools/new_operations/column_join.xml | 8 +- 2 files changed, 68 insertions(+), 37 deletions(-) diffs (213 lines): diff -r 6b93e705c8a4 -r fdf5c92e7fae tools/new_operations/column_join.py --- a/tools/new_operations/column_join.py Mon Apr 12 17:24:17 2010 -0400 +++ b/tools/new_operations/column_join.py Mon Apr 12 19:11:36 2010 -0400 @@ -19,6 +19,32 @@ sys.stderr.write( msg ) sys.exit() +def hinge_compare( hinge1, hinge2 ): + """ + Compares items like 'chr10' and 'chrM' or 'scaffold2' and scaffold10' so that + first part handled as text but last part as number + """ + pat = re.compile( '(?P<text>\D*)(?P<number>\d+)?' ) + split_hinge1 = hinge1.split( '\t' ) + split_hinge2 = hinge2.split( '\t' ) + for i in range( len( split_hinge1 ) ): + if split_hinge1[ i ] == split_hinge2[ i ]: + continue + try: + if int( split_hinge1[ i ] ) > int( split_hinge2[ i ] ): + return 1 + else: + return -1 + except ValueError: + try: + if float( split_hinge1[ i ] ) > float( split_hinge2[ i ] ): + return 1 + else: + return -1 + except ValueError: + return ref_compare( split_hinge1[ i ], split_hinge2[ i ]) + return 0 + def ref_compare( ref1, ref2 ): """ Compares items like 'chr10' and 'chrM' or 'scaffold2' and scaffold10' so that @@ -52,35 +78,31 @@ elif text1 < text2: return -1 -def ref_pos_sort( infile, outfile ): +def hinge_sort( infile, outfile, hinge ): """Given input file name, sorts logically (text vs. numeric) into provided output file name.""" - ref_locs = {} + hinge_locs = {} bad_lines = [] fin = open( infile, 'rb' ) line = fin.readline() while line.strip(): - if True: + try: + hinge_parts = line.split( '\t' )[ :hinge ] try: - ref_seq, ref_loc = line.split( '\t' )[:2] - try: - ref_locs[ ref_seq ][ long( ref_loc ) ] = fin.tell() - len( line.strip() ) - 1 - except KeyError: - ref_locs[ ref_seq ] = { long( ref_loc ): fin.tell() - len( line.strip() ) - 1 } - except ValueError: - bad_lines.append( line ) - except ValueError: - bad_line.append( line ) + hinge_locs[ '\t'.join( hinge_parts ) ].append( fin.tell() - len( line.strip() ) - 1 ) + except KeyError: + hinge_locs[ '\t'.join( hinge_parts ) ] = [ fin.tell() - len( line.strip() ) - 1 ] + except ValueError: + bad_line.append( line ) line = fin.readline() fin.close() - refs = ref_locs.keys() - refs.sort( ref_compare ) fin = open( infile, 'rb' ) fout = open( outfile, 'wb' ) - for ref in refs: - locs = ref_locs[ ref ].keys() - locs.sort() + hinge_locs_sorted = hinge_locs.keys() + hinge_locs_sorted.sort( hinge_compare ) + for hinge_loc in hinge_locs_sorted: + locs = hinge_locs[ hinge_loc ] for loc in locs: - fin.seek( ref_locs[ ref ][ loc ] ) + fin.seek( loc ) fout.write( fin.readline() ) fout.close() fin.close() @@ -90,14 +112,17 @@ if len( chr_pos ) == 0 and ''.join( chr_pos ): return '' min_loc = len( chr_pos ) - min_ref_pos = [] + min_hinge = [] loc = 0 for c_pos in chr_pos: if c_pos.strip(): + split_c = c_pos.split( '\t' ) + + ref, pos = c_pos.split( '\t' )[:2] pos = int( pos ) - if not min_ref_pos: - min_ref_pos = [ ref, pos ] + if not min_hinge: + min_hinge = split_c min_loc = loc else: ref_comp = ref_compare( ref, min_ref_pos[0] ) @@ -126,25 +151,33 @@ tmp_file = tempfile.NamedTemporaryFile() tmp_file_name = tmp_file.name tmp_file.close() - ref_pos_sort( in_file, tmp_file_name ) + hinge_sort( in_file, tmp_file_name, hinge ) tmp_file = open( tmp_file_name, 'rb' ) tmp_input_files.append( tmp_file ) # cycle through files, getting smallest line of all files one at a time # also have to keep track of vertical position of extra columns fout = file( output, 'w' ) - old_current_chr_pos = '' + old_current = '' first_line = True current_lines = [ f.readline() for f in tmp_input_files ] last_lines = ''.join( current_lines ).strip() last_loc = -1 + i = 0 while last_lines: # get the "minimum" hinge, which should come first, and the file location in list - current_chr_pos, loc = min_chr_pos( [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ] ) + hinges = [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ] + hinge_dict = {} + for i in range( len( hinges ) ): + if not hinge_dict.has_key( hinges[ i ] ): + hinge_dict[ hinges[ i ] ] = i + hinges.sort( hinge_compare ) + hinges = [ h for h in hinges if h ] + current, loc = hinges[0], hinge_dict[ hinges[0] ] # first output empty columns for vertical alignment (account for "missing" files) - if current_chr_pos != old_current_chr_pos: + if current != old_current: last_loc = -1 if loc - last_loc > 1: - current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( cols[ hinge: ] ) ) ] + current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( [ col for col in cols if col > hinge ] ) ) ] else: current_data = [] # now output actual data @@ -154,22 +187,20 @@ if col > hinge: current_data.append( split_line[ col - 1 ] ) current_lines[ loc ] = tmp_input_files[ loc ].readline() - if current_chr_pos == old_current_chr_pos: - fout.write( '\t%s' % '\t'.join( current_data ) ) + if current == old_current: + if current_data: + fout.write( '\t%s' % '\t'.join( current_data ) ) else: if not first_line: fout.write( '\n' ) - fout.write( '%s\t%s' % ( current_chr_pos, '\t'.join( current_data ) ) ) + fout.write( '%s\t%s' % ( current, '\t'.join( current_data ) ) ) first_line = False - old_current_chr_pos = current_chr_pos - if last_lines == ''.join( current_lines ).strip(): - break + old_current = current last_lines = ''.join( current_lines ).strip() last_loc = loc fout.write( '\n' ) for f in tmp_input_files: os.unlink( f.name ) fout.close() -# sys.stderr.write('******************\n'+file(fout.name, 'r').read()+'\n******************\n') if __name__ == "__main__" : __main__() diff -r 6b93e705c8a4 -r fdf5c92e7fae tools/new_operations/column_join.xml --- a/tools/new_operations/column_join.xml Mon Apr 12 17:24:17 2010 -0400 +++ b/tools/new_operations/column_join.xml Mon Apr 12 19:11:36 2010 -0400 @@ -21,7 +21,7 @@ </repeat> </inputs> <outputs> - <data name="output" format="pileup" /> + <data name="output" format="tabular" /> </outputs> <tests> <test> @@ -30,7 +30,7 @@ <param name="hinge" value="1,2" /> <param name="input2" value="column_join_in2.pileup" ftype="pileup" /> <param name="input" value="column_join_in3.pileup" ftype="pileup" /> - <output name="output" file="column_join_out1.pileup" ftype="pileup" /> + <output name="output" file="column_join_out1.pileup" ftype="tabular" /> </test> <test> <param name="input1" value="column_join_in4.pileup" ftype="pileup" /> @@ -38,7 +38,7 @@ <param name="hinge" value="1,2" /> <param name="input2" value="column_join_in5.pileup" ftype="pileup" /> <param name="input" value="column_join_in6.pileup" ftype="pileup" /> - <output name="output" file="column_join_out2.pileup" ftype="pileup" /> + <output name="output" file="column_join_out2.pileup" ftype="tabular" /> </test> <test> <param name="input1" value="column_join_in7.pileup" ftype="pileup" /> @@ -46,7 +46,7 @@ <param name="hinge" value="1,2" /> <param name="input2" value="column_join_in8.pileup" ftype="pileup" /> <param name="input" value="column_join_in9.pileup" ftype="pileup" /> - <output name="output" file="column_join_out3.pileup" ftype="pileup" /> + <output name="output" file="column_join_out3.pileup" ftype="tabular" /> </test> </tests> <help>

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[hg] galaxy 3629: If a subdir of the library import dir is a sym...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6b93e705c8a4 changeset: 3629:6b93e705c8a4 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Apr 12 17:24:17 2010 -0400 description: If a subdir of the library import dir is a symlink and we are linking instead of copying data on import, dereference that symlink diffstat: lib/galaxy/web/controllers/library_common.py | 15 +++++++++++++-- 1 files changed, 13 insertions(+), 2 deletions(-) diffs (25 lines): diff -r c19605dca27d -r 6b93e705c8a4 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Apr 12 15:56:13 2010 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Mon Apr 12 17:24:17 2010 -0400 @@ -915,8 +915,19 @@ for entry in os.listdir( full_dir ): # Only import regular files path = os.path.join( full_dir, entry ) - if os.path.islink( path ) and os.path.isfile( path ) and params.get( 'link_data_only', False ): - # If we're linking instead of copying, link the file the link points to, not the link itself. + if os.path.islink( full_dir ) and params.get( 'link_data_only', False ): + # If we're linking instead of copying and the + # sub-"directory" in the import dir is actually a symlink, + # dereference the symlink, but not any of its contents. + link_path = os.readlink( full_dir ) + if os.path.isabs( link_path ): + path = os.path.join( link_path, entry ) + else: + path = os.path.abspath( os.path.join( link_path, entry ) ) + elif os.path.islink( path ) and os.path.isfile( path ) and params.get( 'link_data_only', False ): + # If we're linking instead of copying and the "file" in the + # sub-directory of the import dir is actually a symlink, + # dereference the symlink (one dereference only, Vasili). link_path = os.readlink( path ) if os.path.isabs( link_path ): path = link_path

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[hg] galaxy 3628: Updated NGS tools' stderr handling to use file...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c19605dca27d changeset: 3628:c19605dca27d user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Mon Apr 12 15:56:13 2010 -0400 description: Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output diffstat: tools/metag_tools/megablast_wrapper.py | 13 +++++++++- tools/samtools/sam_merge.py | 15 ++++++++++-- tools/samtools/sam_pileup.py | 18 ++++++++++++--- tools/samtools/sam_to_bam.py | 27 ++++++++++++++++++----- tools/sr_mapping/bowtie_wrapper.py | 26 +++++++++++++++++----- tools/sr_mapping/bowtie_wrapper.xml | 4 +- tools/sr_mapping/bwa_wrapper.py | 38 +++++++++++++++++++++++++-------- 7 files changed, 109 insertions(+), 32 deletions(-) diffs (406 lines): diff -r f32497f2e001 -r c19605dca27d tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/metag_tools/megablast_wrapper.py Mon Apr 12 15:56:13 2010 -0400 @@ -74,24 +74,33 @@ print megablast_command + tmp = tempfile.NamedTemporaryFile().name try: - proc = subprocess.Popen( args=megablast_command, shell=True, stderr=subprocess.PIPE ) + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=megablast_command, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr + if os.path.exists( tmp ): + os.unlink( tmp ) except Exception, e: if os.path.exists( mega_temp_output ): os.unlink( mega_temp_output ) + if os.path.exists( tmp ): + os.unlink( tmp ) stop_err( 'Error indexing reference sequence. ' + str( e ) ) output = open( output_filename, 'w' ) diff -r f32497f2e001 -r c19605dca27d tools/samtools/sam_merge.py --- a/tools/samtools/sam_merge.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/samtools/sam_merge.py Mon Apr 12 15:56:13 2010 -0400 @@ -9,7 +9,7 @@ [input3[,input4[,input5[,...]]]] """ -import os, subprocess, sys +import os, subprocess, sys, tempfile def stop_err( msg ): sys.stderr.write( '%s\n' % msg ) @@ -22,22 +22,31 @@ stop_err( 'There are not enough files to merge' ) filenames = sys.argv[3:] cmd = 'samtools merge %s %s %s' % ( outfile, infile, ' '.join( filenames ) ) + tmp = tempfile.NamedTemporaryFile().name try: - proc = subprocess.Popen( args=cmd, shell=True, stderr=subprocess.PIPE ) + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr + if os.path.exists( tmp ): + os.unlink( tmp ) except Exception, e: + if os.path.exists( tmp ): + os.unlink( tmp ) stop_err( 'Error running SAMtools merge tool\n' + str( e ) ) if os.path.getsize( outfile ) > 0: sys.stdout.write( '%s files merged.' % ( len( sys.argv ) - 2 ) ) diff -r f32497f2e001 -r c19605dca27d tools/samtools/sam_pileup.py --- a/tools/samtools/sam_pileup.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/samtools/sam_pileup.py Mon Apr 12 15:56:13 2010 -0400 @@ -88,36 +88,46 @@ elif options.ref == 'history': os.symlink( options.ownFile, tmpf1_name ) cmdIndex = 'samtools faidx %s' % ( tmpf1_name ) - proc = subprocess.Popen( args=cmdIndex, shell=True, cwd=tmpDir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmdIndex, shell=True, cwd=tmpDir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() #did index succeed? if returncode != 0: raise Exception, 'Error creating index file\n' + stderr cmd = cmd % ( opts, tmpf1_name, tmpf0bam_name, options.output1 ) #perform pileup command - proc = subprocess.Popen( args=cmd, shell=True, cwd=tmpDir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=tmpDir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() #did it succeed? # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: diff -r f32497f2e001 -r c19605dca27d tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/samtools/sam_to_bam.py Mon Apr 12 15:56:13 2010 -0400 @@ -75,18 +75,23 @@ os.symlink( options.ref_file, fai_index_file_base ) fai_index_file_path = '%s.fai' % fai_index_file_base command = 'samtools faidx %s' % fai_index_file_base - proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr if len( open( fai_index_file_path ).read().strip() ) == 0: @@ -104,18 +109,23 @@ # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning, # and the docs do not currently state that this occurs ( very bad ). command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) - proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr if len( open( tmp_aligns_file_name ).read() ) == 0: @@ -133,18 +143,23 @@ tmp_sorted_aligns_file_name = tmp_sorted_aligns_file.name tmp_sorted_aligns_file.close() command = 'samtools sort %s %s' % ( tmp_aligns_file_name, tmp_sorted_aligns_file_name ) - proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: diff -r f32497f2e001 -r c19605dca27d tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Mon Apr 12 15:56:13 2010 -0400 @@ -186,25 +186,34 @@ ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc, inoref, options.ioffrate, iftab, intoa, iendian, iseed, icutoff, colorspace ) - except ValueError: - indexing_cmds = '%s' % colorspace + except ValueError, e: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( 'Something is wrong with the indexing parameters and the indexing and alignment could not be run\n' + str( e ) ) ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) ref_file_name = ref_file.name ref_file.close() os.symlink( options.ref, ref_file_name ) cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name ) try: - proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=subprocess.PIPE, stdout=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: @@ -358,18 +367,23 @@ else: cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output ) # align - proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr # check that there are results in the output file diff -r f32497f2e001 -r c19605dca27d tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Mon Apr 12 15:56:13 2010 -0400 @@ -181,8 +181,8 @@ --maxAlignAttempt="None" --forwardAlign="None" --reverseAlign="None" - #end if - #end if + #end if + #end if </command> <inputs> <conditional name="refGenomeSource"> diff -r f32497f2e001 -r c19605dca27d tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/sr_mapping/bwa_wrapper.py Mon Apr 12 15:56:13 2010 -0400 @@ -91,18 +91,23 @@ indexing_cmds = '-a %s' % indexingAlg cmd1 = 'bwa index %s %s' % ( indexing_cmds, ref_file_name ) try: - proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: @@ -166,52 +171,67 @@ try: # align try: - proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: raise Exception, 'Error aligning sequence. ' + str( e ) # and again if paired data try: - if cmd2b: - proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + if cmd2b: + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: raise Exception, 'Error aligning second sequence. ' + str( e ) # generate align try: - proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e:

1 0

[hg] galaxy 3627: Allow FASTQ parser to handle extra space padde...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f32497f2e001 changeset: 3627:f32497f2e001 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Apr 12 10:30:25 2010 -0400 description: Allow FASTQ parser to handle extra space padded decimal scores, e.g. '0 ' diffstat: lib/galaxy_utils/sequence/fastq.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 5536d57237a3 -r f32497f2e001 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py Fri Apr 09 18:09:54 2010 -0400 +++ b/lib/galaxy_utils/sequence/fastq.py Mon Apr 12 10:30:25 2010 -0400 @@ -60,7 +60,7 @@ else: quality = self.quality.rstrip() #decimal scores should have a trailing space if quality: - return map( int, quality.split( ' ' ) ) + return [ int( val ) for val in quality.split( ' ' ) if val.strip() ] else: return [] def convert_read_to_format( self, format, force_quality_encoding = None ):

1 0

[hg] galaxy 3626: - Update jQuery.jStore, JSON2
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5536d57237a3 changeset: 3626:5536d57237a3 user: Kanwei Li <kanwei(a)gmail.com> date: Fri Apr 09 18:09:54 2010 -0400 description: - Update jQuery.jStore, JSON2 - Fix issue with all local prefs being deleted on "collapse all" - Refactored history display code into galaxy.base diffstat: static/jStore.Flash.html | 19 - static/jStore.swf | 0 static/scripts/class.js | 80 + static/scripts/galaxy.base.js | 87 + static/scripts/jquery.jstore-all.js | 748 ----------- static/scripts/jquery.jstore.js | 1810 ++++++++++++++++++++++++++++ static/scripts/json2.js | 26 +- static/scripts/packed/class.js | 7 + static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/jquery.jstore-all.js | 1 - static/scripts/packed/jquery.jstore.js | 17 + static/scripts/packed/json2.js | 2 +- templates/display_base.mako | 29 +- templates/history/display.mako | 264 +--- templates/history/view.mako | 259 +--- templates/page/display.mako | 272 +--- templates/root/history.mako | 222 +-- templates/workflow/editor.mako | 42 +- 18 files changed, 2216 insertions(+), 1671 deletions(-) diffs (truncated from 4199 to 3000 lines): diff -r a9402fc7ce1b -r 5536d57237a3 static/jStore.Flash.html --- a/static/jStore.Flash.html Fri Apr 09 13:02:15 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"> - <head> - <title>Flash External Object</title> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <script type="text/javascript"> - /** - * This function captures the flash_ready event. We need to relay this - * back to the parent so it knows flash is ready. - */ - function flash_ready(){ - parent.flash_ready(); - } - </script> - </head> - <body> - <object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#versi…" width="1" height="1" id="jStoreFlash"><param name="allowScriptAccess" value="always" /><param name="movie" value="jStore.swf" /><param name="quality" value="high" /><param name="bgcolor" value="#ffcc00" /><embed src="jStore.swf" quality="high" bgcolor="#ffcc00" width="1" height="1" name="jStoreFlash" align="middle" allowScriptAccess="always" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" /></object> - </body> -</html> \ No newline at end of file diff -r a9402fc7ce1b -r 5536d57237a3 static/jStore.swf Binary file static/jStore.swf has changed diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/class.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/class.js Fri Apr 09 18:09:54 2010 -0400 @@ -0,0 +1,80 @@ +/*! + * Class definition + * + * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) + * Inspired by base2 and Prototype + */ + +"use strict"; + +(function () { + + var initializing = false, + + fnTest = /xyz/.test(function(){xyz;}) ? /\b_super\b/ : /.*/; + + // The base Class implementation (does nothing) + this.Class = function(){}; + + // Create a new Class that inherits from this class + Class.extend = function (prop) + { + var _super = this.prototype; + + // Instantiate a base class (but only create the instance, don't run the init constructor) + initializing = true; + + var prototype = new this(); + + initializing = false; + + // Copy the properties over onto the new prototype + for (var name in prop) + { + + // Check if we're overwriting an existing function + prototype[name] = (typeof prop[name] === "function" && typeof _super[name] === "function" && fnTest.test(prop[name]) ? + + (function(name, fn) + { + return function() + { + var tmp = this._super; + + // Add a new ._super() method that is the same method + // but on the super-class + this._super = _super[name]; + + // The method only need to be bound temporarily, so we + // remove it when we're done executing + var ret = fn.apply(this, arguments); + this._super = tmp; + + return ret; + }; + }(name, prop[name])) : prop[name]); + } + + // The dummy class constructor + function Class() + { + // All construction is actually done in the init method + if (!initializing && this.init) + { + this.init.apply(this, arguments); + } + } + + // Populate our constructed prototype object + Class.prototype = prototype; + + // Enforce the constructor to be what we expect + Class.constructor = Class; + + // And make this class extendable + Class.extend = arguments.callee; + + return Class; + }; + +}()); diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Apr 09 13:02:15 2010 -0400 +++ b/static/scripts/galaxy.base.js Fri Apr 09 18:09:54 2010 -0400 @@ -275,6 +275,93 @@ }); } +function init_history_items(historywrapper, noinit) { + + var action = function() { + // Load saved state and show as necessary + try { + var stored = $.jStore.store("history_expand_state"); + if (stored) { + for (var id in stored) { + $("#" + id + " div.historyItemBody" ).show(); + } + } + } catch(err) { + // Something was wrong with values in storage, so clear storage + $.jStore.remove("history_expand_state"); + } + + // If Mozilla, hide scrollbars in hidden items since they cause animation bugs + if ( $.browser.mozilla ) { + $( "div.historyItemBody" ).each( function() { + if ( ! $(this).is( ":visible" ) ) $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + }) + } + + historywrapper.each( function() { + var id = this.id; + var body = $(this).children( "div.historyItemBody" ); + var peek = body.find( "pre.peek" ) + $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { + if ( body.is(":visible") ) { + // Hiding stuff here + if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } + body.slideUp( "fast" ); + + if (!noinit) { // Ignore embedded item actions + // Save setting + var prefs = $.jStore.store("history_expand_state"); + if (prefs) { + delete prefs[id]; + $.jStore.store("history_expand_state", prefs); + } + } + } else { + // Showing stuff here + body.slideDown( "fast", function() { + if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } + }); + + if (!noinit) { + // Save setting + var prefs = $.jStore.store("history_expand_state"); + if (prefs === undefined) { prefs = {}; } + prefs[id] = true; + $.jStore.store("history_expand_state", prefs); + } + } + return false; + }); + }); + + // Generate 'collapse all' link + $("#top-links > a.toggle").click( function() { + var prefs = $.jStore.store("history_expand_state"); + if (prefs === undefined) { prefs = {}; } + $( "div.historyItemBody:visible" ).each( function() { + if ( $.browser.mozilla ) { + $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + } + $(this).slideUp( "fast" ); + if (prefs) { + delete prefs[$(this).parent().attr("id")]; + } + }); + $.jStore.store("history_expand_state", prefs); + }).show(); + } + + if (noinit) { + action(); + } else { + // Load jStore for local storage + $.jStore.init("galaxy"); // Auto-select best storage + $.jStore.engineReady(function() { + action(); + }); + } +} + $(document).ready( function() { // Links with confirmation $( "a[confirm]" ).click( function() { diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/jquery.jstore-all.js --- a/static/scripts/jquery.jstore-all.js Fri Apr 09 13:02:15 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,748 +0,0 @@ -/* - * jStore - Persistent Client-Side Storage - * - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - * - * Dual licensed under: - * MIT: http://www.opensource.org/licenses/mit-license.php - * GPLv3: http://www.opensource.org/licenses/gpl-3.0.html - *//** - * Javascript Class Framework - * - * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) - * Inspired by base2 and Prototype - */ -(function(){ - var initializing = false, fnTest = /xyz/.test(function(){xyz;}) ? /\b_super\b/ : /.*/; - - // The base Class implementation (does nothing) - this.Class = function(){}; - - // Create a new Class that inherits from this class - Class.extend = function(prop) { - var _super = this.prototype; - - // Instantiate a base class (but only create the instance, - // don't run the init constructor) - initializing = true; - var prototype = new this(); - initializing = false; - - // Copy the properties over onto the new prototype - for (var name in prop) { - // Check if we're overwriting an existing function - prototype[name] = typeof prop[name] == "function" && - typeof _super[name] == "function" && fnTest.test(prop[name]) ? - (function(name, fn){ - return function() { - var tmp = this._super; - - // Add a new ._super() method that is the same method - // but on the super-class - this._super = _super[name]; - - // The method only need to be bound temporarily, so we - // remove it when we're done executing - var ret = fn.apply(this, arguments); - this._super = tmp; - - return ret; - }; - })(name, prop[name]) : - prop[name]; - } - - // The dummy class constructor - function Class() { - // All construction is actually done in the init method - if ( !initializing && this.init ) - this.init.apply(this, arguments); - } - - // Populate our constructed prototype object - Class.prototype = prototype; - - // Enforce the constructor to be what we expect - Class.constructor = Class; - - // And make this class extendable - Class.extend = arguments.callee; - - return Class; - }; -})(); -/* - * jStore Delegate Framework - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - this.jStoreDelegate = Class.extend({ - init: function(parent){ - // The Object this delgate operates for - this.parent = parent; - // Container for callbacks to dispatch. - // eventType => [ callback, callback, ... ] - this.callbacks = {}; - }, - bind: function(event, callback){ - if ( !$.isFunction(callback) ) return this; - if ( !this.callbacks[ event ] ) this.callbacks[ event ] = []; - - this.callbacks[ event ].push(callback); - - return this; - }, - trigger: function(){ - var parent = this.parent, - args = [].slice.call(arguments), - event = args.shift(), - handlers = this.callbacks[ event ]; - - if ( !handlers ) return false; - - $.each(handlers, function(){ this.apply(parent, args) }); - return this; - } - }); - -})(jQuery);/** - * jStore-jQuery Interface - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Setup the jStore namespace in jQuery for options storage - $.jStore = {}; - - // Seed the options in - $.extend($.jStore, { - EngineOrder: [], - // Engines should put their availability tests within jStore.Availability - Availability: {}, - // Defined engines should enter themselves into the jStore.Engines - Engines: {}, - // Instanciated engines should exist within jStore.Instances - Instances: {}, - // The current engine to use for storage - CurrentEngine: null, - // Provide global settings for overwriting - defaults: { - project: null, - engine: null, - autoload: true, - flash: 'jStore.Flash.html' - }, - // Boolean for ready state handling - isReady: false, - // Boolean for flash ready state handling - isFlashReady: false, - // An event delegate - delegate: new jStoreDelegate($.jStore) - .bind('jStore-ready', function(engine){ - $.jStore.isReady = true; - if ($.jStore.defaults.autoload) engine.connect(); - }) - .bind('flash-ready', function(){ - $.jStore.isFlashReady = true; - }) - }); - - // Enable ready callback for jStore - $.jStore.ready = function(callback){ - if ($.jStore.isReady) callback.apply($.jStore, [$.jStore.CurrentEngine]); - else $.jStore.delegate.bind('jStore-ready', callback); - } - - // Enable failure callback registration for jStore - $.jStore.fail = function(callback){ - $.jStore.delegate.bind('jStore-failure', callback); - } - - // Enable ready callback for Flash - $.jStore.flashReady = function(callback){ - if ($.jStore.isFlashReady) callback.apply($.jStore, [$.jStore.CurrentEngine]); - else $.jStore.delegate.bind('flash-ready', callback); - } - - // Enable and test an engine - $.jStore.use = function(engine, project, identifier){ - project = project || $.jStore.defaults.project || location.hostname.replace(/\./g, '-') || 'unknown'; - - var e = $.jStore.Engines[engine.toLowerCase()] || null, - name = (identifier ? identifier + '.' : '') + project + '.' + engine; - - if ( !e ) throw 'JSTORE_ENGINE_UNDEFINED'; - - // Instanciate the engine - e = new e(project, name); - - // Prevent against naming conflicts - if ($.jStore.Instances[name]) throw 'JSTORE_JRI_CONFLICT'; - - // Test the engine - if (e.isAvailable()){ - $.jStore.Instances[name] = e; // The Easy Way - if (!$.jStore.CurrentEngine){ - $.jStore.CurrentEngine = e; - } - $.jStore.delegate.trigger('jStore-ready', e); - } else { - if (!e.autoload) // Not available - throw 'JSTORE_ENGINE_UNAVILABLE'; - else { // The hard way - e.included(function(){ - if (this.isAvailable()) { // Worked out - $.jStore.Instances[name] = this; - // If there is no current engine, use this one - if (!$.jStore.CurrentEngine){ - $.jStore.CurrentEngine = this; - } - $.jStore.delegate.trigger('jStore-ready', this); - } - else $.jStore.delegate.trigger('jStore-failure', this); - }).include(); - } - } - } - - // Set the current storage engine - $.jStore.setCurrentEngine = function(name){ - if (!$.jStore.Instances.length ) // If no instances exist, attempt to load one - return $.jStore.FindEngine(); - - if (!name && $.jStore.Instances.length >= 1) { // If no name is specified, use the first engine - $.jStore.delegate.trigger('jStore-ready', $.jStore.Instances[0]); - return $.jStore.CurrentEngine = $.jStore.Instances[0]; - } - - if (name && $.jStore.Instances[name]) { // If a name is specified and exists, use it - $.jStore.delegate.trigger('jStore-ready', $.jStore.Instances[name]); - return $.jStore.CurrentEngine = $.jStore.Instances[name]; - } - - throw 'JSTORE_JRI_NO_MATCH'; - } - - // Test all possible engines for straightforward useability - $.jStore.FindEngine = function(){ - $.each($.jStore.EngineOrder, function(k){ - if ($.jStore.Availability[this]()){ // Find the first, easiest option and use it. - $.jStore.use(this, $.jStore.defaults.project, 'default'); - return false; - } - }) - } - - // Provide a simple interface for storing/getting values - $.jStore.store = function(key, value){ - if (!$.jStore.CurrentEngine) return false; - - if ( !value ) // Executing a get command - return $.jStore.CurrentEngine.get(key); - // Executing a set command - return $.jStore.CurrentEngine.set(key, value); - } - // Provide a simple interface for storing/getting values - $.jStore.remove = function(key){ - if (!$.jStore.CurrentEngine) return false; - - return $.jStore.CurrentEngine.rem(key); - } - - // Provide a chainable interface for storing values/getting a value at the end of a chain - $.fn.store = function(key, value){ - if (!$.jStore.CurrentEngine) return this; - - var result = $.jStore.store(key, value); - - return !value ? result : this; - } - - // Provide a chainable interface for removing values - $.fn.removeStore = function(key){ - $.jStore.remove(key); - - return this; - } - - // Provide a way for users to call for auto-loading - $.jStore.load = function(){ - if ($.jStore.defaults.engine) - return $.jStore.use($.jStore.defaults.engine, $.jStore.defaults.project, 'default'); - - // Attempt to find a valid engine, and catch any exceptions if we can't - try { - $.jStore.FindEngine(); - } catch (e) {} - } - -})(jQuery); -/** - * jStore Engine Core - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - this.StorageEngine = Class.extend({ - init: function(project, name){ - // Configure the project name - this.project = project; - // The JRI name given by the manager - this.jri = name; - // Cache the data so we can work synchronously - this.data = {}; - // The maximum limit of the storage engine - this.limit = -1; - // Third party script includes - this.includes = []; - // Create an event delegate for users to subscribe to event triggers - this.delegate = new jStoreDelegate(this) - .bind('engine-ready', function(){ - this.isReady = true; - }) - .bind('engine-included', function(){ - this.hasIncluded = true; - }); - // If enabled, the manager will check availability, then run include(), then check again - this.autoload = false; // This should be changed by the engines, if they have required includes - // When set, we're ready to transact data - this.isReady = false; - // When the includer is finished, it will set this to true - this.hasIncluded = false; - }, - // Performs all necessary script includes - include: function(){ - var self = this, - total = this.includes.length, - count = 0; - - $.each(this.includes, function(){ - $.ajax({type: 'get', url: this, dataType: 'script', cache: true, - success: function(){ - count++; - if (count == total) self.delegate.trigger('engine-included'); - } - }) - }); - }, - // This should be overloaded with an actual functionality presence check - isAvailable: function(){ - return false; - }, - /** Event Subscription Shortcuts **/ - ready: function(callback){ - if (this.isReady) callback.apply(this); - else this.delegate.bind('engine-ready', callback); - return this; - }, - included: function(callback){ - if (this.hasIncluded) callback.apply(this); - else this.delegate.bind('engine-included', callback); - return this; - }, - /** Cache Data Access **/ - get: function(key){ - return this.data[key] || null; - }, - set: function(key, value){ - this.data[key] = value; - return value; - }, - rem: function(key){ - var beforeDelete = this.data[key]; - this.data[key] = null; - return beforeDelete; - } - }); - -})(jQuery); -/* - * jStore DOM Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Set up a static test function for this instance - var sessionAvailability = $.jStore.Availability.session = function(){ - return !!window.sessionStorage; - }, - localAvailability = $.jStore.Availability.local = function(){ - return !!(window.localStorage || window.globalStorage); - }; - - this.jStoreDom = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'DOM'; - - // Set the Database limit - this.limit = 5 * 1024 * 1024; - }, - connect: function(){ - // Fire our delegate to indicate we're ready for data transactions - this.delegate.trigger('engine-ready'); - }, - get: function(key){ - var out = this.db.getItem(key); - // Gecko's getItem returns {value: 'the value'}, WebKit returns 'the value' - return out && out.value ? out.value : out - }, - set: function(key, value){ - this.db.setItem(key,value); - return value; - }, - rem: function(key){ - var out = this.get(key); - this.db.removeItem(key); - return out - } - }) - - this.jStoreLocal = jStoreDom.extend({ - connect: function(){ - // Gecko uses a non-standard globalStorage[ www.example.com ] DOM access object for persistant storage. - this.db = !window.globalStorage ? window.localStorage : window.globalStorage[location.hostname]; - this._super(); - }, - isAvailable: localAvailability - }) - - this.jStoreSession = jStoreDom.extend({ - connect: function(){ - this.db = sessionStorage; - this._super(); - }, - isAvailable: sessionAvailability - }) - - $.jStore.Engines.local = jStoreLocal; - $.jStore.Engines.session = jStoreSession; - - // Store the ordering preference - $.jStore.EngineOrder[ 1 ] = 'local'; - -})(jQuery); -/* - * jStore Flash Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - * jStore.swf Copyright (c) 2008 Daniel Bulli (http://www.nuff-respec.com) - */ -(function($){ - - // Set up a static test function for this instance - var avilability = $.jStore.Availability.flash = function(){ - return !!($.jStore.hasFlash('8.0.0')); - } - - this.jStoreFlash = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'Flash'; - - // Bind our flashReady function to the jStore Delegate - var self = this; - $.jStore.flashReady(function(){ self.flashReady() }); - }, - connect: function(){ - var name = 'jstore-flash-embed-' + this.project; - - // To make Flash Storage work on IE, we have to load up an iFrame - // which contains an HTML page that embeds the object using an - // object tag wrapping an embed tag. Of course, this is unnecessary for - // all browsers except for IE, which, to my knowledge, is the only browser - // in existance where you need to complicate your code to fix bugs. Goddamnit. :( - $(document.body) - .append('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" ' + - 'id="jStoreFlashFrame" src="' +$.jStore.defaults.flash + '"></iframe>'); - }, - flashReady: function(e){ - var iFrame = $('#jStoreFlashFrame')[0]; - - // IE - if (iFrame.Document && $.isFunction(iFrame.Document['jStoreFlash'].f_get_cookie)) this.db = iFrame.Document['jStoreFlash']; - // Safari && Firefox - else if (iFrame.contentWindow && iFrame.contentWindow.document){ - var doc = iFrame.contentWindow.document; - // Safari - if ($.isFunction($('object', $(doc))[0].f_get_cookie)) this.db = $('object', $(doc))[0]; - // Firefox - else if ($.isFunction($('embed', $(doc))[0].f_get_cookie)) this.db = $('embed', $(doc))[0]; - } - - // We're ready to process data - if (this.db) this.delegate.trigger('engine-ready'); - }, - isAvailable: avilability, - get: function(key){ - var out = this.db.f_get_cookie(key); - return out == 'null' ? null : out; - }, - set: function(key, value){ - this.db.f_set_cookie(key, value); - return value; - }, - rem: function(key){ - var beforeDelete = this.get(key); - this.db.f_delete_cookie(key); - return beforeDelete; - } - }) - - $.jStore.Engines.flash = jStoreFlash; - - // Store the ordering preference - $.jStore.EngineOrder[ 2 ] = 'flash'; - - /** - * Flash Detection functions copied from the jQuery Flash Plugin - * Copyright (c) 2006 Luke Lutman (http://jquery.lukelutman.com/plugins/flash) - * Dual licensed under the MIT and GPL licenses. - * http://www.opensource.org/licenses/mit-license.php - * http://www.opensource.org/licenses/gpl-license.php - */ - $.jStore.hasFlash = function(version){ - var pv = $.jStore.flashVersion().match(/\d+/g), - rv = version.match(/\d+/g); - - for(var i = 0; i < 3; i++) { - pv[i] = parseInt(pv[i] || 0); - rv[i] = parseInt(rv[i] || 0); - // player is less than required - if(pv[i] < rv[i]) return false; - // player is greater than required - if(pv[i] > rv[i]) return true; - } - // major version, minor version and revision match exactly - return true; - } - - $.jStore.flashVersion = function(){ - // ie - try { - try { - // avoid fp6 minor version lookup issues - // see: http://blog.deconcept.com/2006/01/11/getvariable-setvariable-crash-internet… - var axo = new ActiveXObject('ShockwaveFlash.ShockwaveFlash.6'); - try { axo.AllowScriptAccess = 'always'; } - catch(e) { return '6,0,0'; } - } catch(e) {} - return new ActiveXObject('ShockwaveFlash.ShockwaveFlash').GetVariable('$version').replace(/\D+/g, ',').match(/^,?(.+),?$/)[1]; - // other browsers - } catch(e) { - try { - if(navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin){ - return (navigator.plugins["Shockwave Flash 2.0"] || navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g, ",").match(/^,?(.+),?$/)[1]; - } - } catch(e) {} - } - return '0,0,0'; - } - -})(jQuery); - -// Callback fired when ExternalInterface is established -function flash_ready(){ - $.jStore.delegate.trigger('flash-ready'); -} -/* - * jStore Google Gears Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Set up a static test function for this instance - var avilability = $.jStore.Availability.gears = function(){ - return !!(window.google && window.google.gears) - } - - this.jStoreGears = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'Google Gears'; - - // Add required third-party scripts - this.includes.push('http://code.google.com/apis/gears/gears_init.js'); - - // Allow Autoloading on fail - this.autoload = true; - }, - connect: function(){ - // Create our database connection - var db = this.db = google.gears.factory.create('beta.database'); - db.open( 'jstore-' + this.project ); - db.execute( 'CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)' ); - - // Cache the data from the table - this.updateCache(); - }, - updateCache: function(){ - // Read the database into our cache object - var result = this.db.execute( 'SELECT k,v FROM jstore' ); - while (result.isValidRow()){ - this.data[result.field(0)] = result.field(1); - result.next(); - } result.close(); - - // Fire our delegate to indicate we're ready for data transactions - this.delegate.trigger('engine-ready'); - }, - isAvailable: avilability, - set: function(key, value){ - // Update the database - var db = this.db; - db.execute( 'BEGIN' ); - db.execute( 'INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key,value] ); - db.execute( 'COMMIT' ); - return this._super(key, value); - }, - rem: function(key){ - // Update the database - var db = this.db; - db.execute( 'BEGIN' ); - db.execute( 'DELETE FROM jstore WHERE k = ?', [key] ); - db.execute( 'COMMIT' ); - return this._super(key); - } - }) - - $.jStore.Engines.gears = jStoreGears; - - // Store the ordering preference - $.jStore.EngineOrder[ 3 ] = 'gears'; - -})(jQuery); -/* - * jStore HTML5 Specification Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Set up a static test function for this instance - var avilability = $.jStore.Availability.html5 = function(){ - return !!window.openDatabase - } - - this.jStoreHtml5 = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'HTML5'; - - // Set the Database limit - this.limit = 1024 * 200; - }, - connect: function(){ - // Create our database connection - var db = this.db = openDatabase('jstore-' + this.project, '1.0', this.project, this.limit); - if (!db) throw 'JSTORE_ENGINE_HTML5_NODB'; - db.transaction(function(db){ - db.executeSql( 'CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)' ); - }); - - // Cache the data from the table - this.updateCache(); - }, - updateCache: function(){ - var self = this; - // Read the database into our cache object - this.db.transaction(function(db){ - db.executeSql( 'SELECT k,v FROM jstore', [], function(db, result){ - var rows = result.rows, i = 0, row; - for (; i < rows.length; ++i){ - row = rows.item(i); - self.data[row.k] = row.v; - } - - // Fire our delegate to indicate we're ready for data transactions - self.delegate.trigger('engine-ready'); - }); - }); - }, - isAvailable: avilability, - set: function(key, value){ - // Update the database - this.db.transaction(function(db){ - db.executeSql( 'INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key,value]); - }); - return this._super(key, value); - }, - rem: function(key){ - // Update the database - this.db.transaction(function(db){ - db.executeSql( 'DELETE FROM jstore WHERE k = ?', [key] ) - }) - return this._super(key); - } - }) - - $.jStore.Engines.html5 = jStoreHtml5; - - // Store the ordering preference - $.jStore.EngineOrder[ 0 ] = 'html5'; - -})(jQuery); -/* - * jStore IE Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Set up a static test function for this instance - var avilability = $.jStore.Availability.ie = function(){ - return !!window.ActiveXObject; - } - - this.jStoreIE = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'IE'; - - // Allow Autoloading on fail - this.limit = 64 * 1024; - }, - connect: function(){ - // Create a hidden div to store attributes in - this.db = $('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-' + this.project + '"></div>') - .appendTo(document.body).get(0); - // Fire our delegate to indicate we're ready for data transactions - this.delegate.trigger('engine-ready'); - }, - isAvailable: avilability, - get: function(key){ - this.db.load(this.project); - return this.db.getAttribute(key); - }, - set: function(key, value){ - this.db.setAttribute(key, value); - this.db.save(this.project); - return value; - }, - rem: function(key){ - var beforeDelete = this.get(key); - this.db.removeAttribute(key); - this.db.save(this.project); - return beforeDelete; - } - }) - - $.jStore.Engines.ie = jStoreIE; - - // Store the ordering preference - $.jStore.EngineOrder[ 4 ] = 'ie'; - -})(jQuery); diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/jquery.jstore.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/jquery.jstore.js Fri Apr 09 18:09:54 2010 -0400 @@ -0,0 +1,1810 @@ +/*! + * jStore 2.0 - Persistent Client Side Storage + * + * Copyright (c) 2010 Eric Garside (http://eric.garside.name/) + * Dual licensed under: + * MIT: http://www.opensource.org/licenses/mit-license.php + * GPLv3: http://www.opensource.org/licenses/gpl-3.0.html + * + * --------------------------- + * + * jStore Flash Storage Component + * + * Copyright (c) 2006 Jeff Lerman (jeff(a)blip.tv) + * Licensed under the Creative Commons Attribution 3.0 United States License: + * http://creativecommons.org/licenses/by/3.0/us + */ + +"use strict"; + +/*global Class, window, jQuery, ActiveXObject, google */ + +/*jslint white: true, browser: true, onevar: true, undef: true, eqeqeq: true, bitwise: true, regexp: false, strict: true, newcap: true, immed: true, maxerr: 50, indent: 4 */ + +(function ($, window) { + + //------------------------------ + // + // Constants + // + //------------------------------ + + //------------------------------ + // Exceptions + //------------------------------ + + /** + * An exception thrown by the StorageEngine class whenever its data accessor methods + * are called before the engine is ready to transact data. + */ + var EX_UNSTABLE = 'JSTORE_ENGINE_UNSTABLE', + + /** + * An exception thrown by jStore whenever an undefined storage engine is referenced for + * some task by an invalid JRI (jStore Resource Identifier). + */ + EX_UNKNOWN = 'JSTORE_UNKNOWN_ENGINE_REQUESTED', + + /** + * An exception thrown by jStore whenever a given flavor of storage is double defined. + */ + EX_COLLISION = 'JSTORE_ENGINE_NAMESPACE_COLLISION', + + /** + * An exception thrown by jStore whenever a jri is double applied to a resource. + */ + EX_DUPLICATE = 'JSTORE_RESOURCE_NAMESPACE_COLLISION', + + /** + * An exception thrown by jStore whenever a given flavor of storage has no defined engine. + */ + EX_UNAVAILABLE = 'JSTORE_ENGINE_UNAVAILABLE', + + /** + * An exception thrown by jStore whenever an invalid flavor type is used. + */ + EX_INVALID = 'JSTORE_INVALID_FLAVOR', + + //------------------------------ + // Regular Expressions + //------------------------------ + + /** + * Regular expression to test property values for being JSON. + */ + RX_JSON = (function () + { + try + { + return new RegExp('^("(\\\\.|[^"\\\\\\n\\r])*?"|[,:{}\\[\\]0-9.\\-+Eaeflnr-u \\n\\r\\t])+?$'); + } + catch (e) + { + return (/^(true|false|null|\[.*\]|\{.*\}|".*"|\d+|\d+\.\d+)$/); + } + }()), + + //------------------------------ + // Storage Flavors + //------------------------------ + + /** + * The storage flavor identifier for HTML5 local storage. + */ + FLAVOR_LOCAL = 'jstore-html5-local', + + /** + * The storage flavor identifier for HTML5 database storage. + */ + FLAVOR_SQL = 'jstore-html5-sql', + + /** + * The storage flavor identifier for Adobe Flash SharedObject storage. + */ + FLAVOR_FLASH = 'jstore-flash', + + /** + * The storage flavor identifier for Google Gears storage. + */ + FLAVOR_GEARS = 'jstore-google-gears', + + /** + * The storage flavor identifier for Internet Explorer storage, available to IE7 and IE6. + */ + FLAVOR_MSIE = 'jstore-msie', + + //------------------------------ + // + // Property Declaration + // + //------------------------------ + + /** + * The base StorageEngine class which each "storage flavor" will extend to meet the + * requirements for its specific implementation. + */ + StorageEngine, + + /** + * The jStore object. Internal to this closure, jStore is referenced by "_". It is + * exposed to jQuery below, and made publicly accessible through jQuery.jStore + */ + _ = {}, + + /** + * The engines available to jStore for use. These are the class definitions for flavored + * storage engines. + * + * Signature: + * { + * <storageFlavor>: <flavoredStorageEngineDefinition>, + * + * ... + * } + */ + definitions = {}, + + /** + * Active engines instantiated by jStore, indexed by their JRI. + * + * Signature: + * { + * <engineJRI>: <engineInstance>, + * + * ... + * } + */ + engines = {}, + + /** + * If we are going to be using the flash storage engine, we want to postpone the jStore ready event until the jStore + * isFlashReady flag is also true. This property is set whenever flash is determined to be the storage engine. + */ + waitForFlash = false, + + /** + * Storage for listeners, indexed by content and event type. + * + * Signature: + * { + * <context>: + * { + * <eventType>: [<listener>, ...], + * + * ... + * }, + * + * ... + * } + */ + events = {}, + + /** + * The configuration for this implementation. + * + * Signature: + * { + * project: <defaultProjectName>, + * + * flash: <pathToFlashBootloader>, + * + * json: <pathToJSONFile>, + * + * errorCallback: <listenerToNotifyOnError> + * } + */ + configurations = + { + project: undefined, + + flash: 'jStore.Flash.html', + + json: 'browser.json.js' + }, + + /** + * The active storage engine, being used to satisfy the get/set/remove functions on the jStore and jQuery + * objects. + */ + active; + + //------------------------------ + // + // Internal Methods + // + //------------------------------ + + /** + * Determine if the given flavor is valid. + * + * @param flavor The flavor to test. + * + * @return True if the flavor is valid, false otherwise. + */ + function validFlavor(flavor) + { + switch (flavor) + { + + case FLAVOR_LOCAL: + case FLAVOR_SQL: + case FLAVOR_FLASH: + case FLAVOR_GEARS: + case FLAVOR_MSIE: + return true; + + default: + return false; + + } + } + + /** + * Performs enhanced type comparison on an object. This is more reliable method + * of type checking a variable than a simple typeof comparison. The reason is that, + * typeof will reduce to the lowest common type. + * + * "typeof []" returns Object, and not Array. + * "typeof {}" returns Object as well. + * + * typecheck( [], 'Array' ) : returns true; + * typecheck( [], 'Object' ) : returns false; + * + * @param type The variable type to check. + * + * @param compare A string representing the literal type to check. + * + * @return True if the variable "type" matches the compare literal. + */ + function typecheck(type, compare) + { + return !type ? false : type.constructor.toString().match(new RegExp(compare + '\$\$', 'i')) !== null; + } + + /** + * If the provided listener is a valid function, it will be triggered with the provided context + * and parameters. + * + * @param listener The listener being triggered. + * + * @param context The context to provide to the listener. + * + * @param parameters The parameters to pass to the listener as arguments. + * + * @return The response of the notified listener. + */ + function notify(listener, context, parameters) + { + if (typecheck(listener, 'Function')) + { + return listener.apply(context || _, typecheck(parameters, 'Array') ? parameters : [parameters]); + } + } + + /** + * Load the given script. + * + * @param path The path to the file to include. + * + * @param listener The listener to notify when the file finishes loading. + */ + function loadScript(path, listener) + { + $.ajax( + { + url: path, + complete: listener || $.noop(), + type: 'GET', + dataType: 'script', + cache: false + }); + } + + /** + * Checks the type of the value, and returns a value safe to persist in any client-side mechanism. + * + * @param value The value which should be prepared for storage. + * + * @return A value safe for storage. + */ + function prepareForStorage(value) + { + if (value === undefined) + { + return ''; + } + + if (typecheck(value, 'Object') || + typecheck(value, 'Array') || + typecheck(value, 'Function')) + { + return JSON.stringify(value); + } + + return value; + } + + /** + * Checks the type of the value, and returns a value safe for access in any client-side mechanism. + * + * @param value The value which should be prepared for use. + * + * @return A value safe for use. + */ + function prepareForRevival(value) + { + return RX_JSON.test(value) ? JSON.parse(value) : value; + } + + /** + * Normalize a key before using it, to ensure it's valid. + * + * @param key The key to normalize. + * + * @return A normalized key, safe for storage. + */ + function normalizeKey(key) + { + return key.replace(/^\s+|\s+$/g, ""); + } + + /** + * Define a flavored storage engine. + * + * @throws EX_COLLISION, EX_INVALID + * + * @param flavor The flavor of engine being defined. + * + * @param definition An object containing the new properties and methods for the engine extension. + * + * @param availability A function to invoke which must return a boolean value indicating the + * availability of the storage flavor on this browser. + */ + function define(flavor, definition, availability) + { + if (!validFlavor(flavor)) + { + throw EX_INVALID; + } + + if (availability[flavor] !== undefined) + { + throw EX_COLLISION; + } + + /** + * The logic here has been reworked so unavailable flavors are discarded, so we don't needlessly + * bloat the runtime size of jStore. + */ + if (notify(availability) === true) + { + _.available[flavor] = true; + + definition.flavor = flavor; + + definitions[flavor] = StorageEngine.extend(definition); + } + else + { + _.available[flavor] = false; + + // Filter the invalid flavor out of the priority list. + _.enginePriority = $.map(_.enginePriority, function (engine) + { + if (engine === flavor) + { + return null; + } + else + { + return engine; + } + }); + } + } + + /** + * Make the jStore library ready. + */ + function makeReady() + { + if (_.isReady) + { + return; + } + + if ((waitForFlash && _.isFlashReady) || !waitForFlash) + { + _.isReady = true; + _.trigger('jstore-ready', [engines[active]]); + } + } + + /** + * Create a best-fit engine. + */ + function createBestFitEngine() + { + _.create(_.enginePriority[0], undefined, 'best-fit'); + } + + /** + * Get the flash version currently supported in this browser. + * + * @return The flash version. + */ + function flashVersion() + { + // MSIE + try + { + // avoid fp6 minor version lookup issues + // see: http://blog.deconcept.com/2006/01/11/getvariable-setvariable-crash-internet… + var axo = new ActiveXObject('ShockwaveFlash.ShockwaveFlash.6'); + + try + { + axo.AllowScriptAccess = 'always'; + } + catch (axo_e) + { + return '6,0,0'; + } + + return new ActiveXObject('ShockwaveFlash.ShockwaveFlash').GetVariable('$version').replace(/\D+/g, ',').match(/^,?(.+),?$/)[1]; + } + + // Real browsers + catch (e) + { + try + { + if (navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin) + { + return (navigator.plugins["Shockwave Flash 2.0"] || navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g, ",").match(/^,?(.+),?$/)[1]; + } + } + catch (flash_e) + {} + } + + return '0,0,0'; + } + + /** + * Flash Detection functions copied from the jQuery Flash Plugin + * + * Copyright (c) 2006 Luke Lutman (http://jquery.lukelutman.com/plugins/flash) + * + * Dual licensed under the MIT and GPL licenses. + * http://www.opensource.org/licenses/mit-license.php + * http://www.opensource.org/licenses/gpl-license.php + * + * @param version The version to compare to. + * + * @return True if the version is greater than or equal to the required version, false otherwise. + */ + function hasFlashVersion(version) + { + var playerVersion = flashVersion().match(/\d+/g), + requiredVersion = version.match(/\d+/g), + index = 0, + player, + required; + + for (; index < 3; index++) + { + player = parseInt(playerVersion[index], 10); + required = parseInt(requiredVersion[index], 10); + + // Player version is less than what is required. + if (player < required) + { + return false; + } + + // Player version is greater than what is required. + else if (player > required) + { + return true; + } + } + + // Player and required version match exactly. + return true; + } + + //------------------------------ + // + // Plugin Definition + // + //------------------------------ + + //------------------------------ + // Error Declaration + //------------------------------ + + //------------------------------ + // Plugin Creation + //------------------------------ + + /** + * The jStore object. Manages a collection of StorageEngines for particular "storage flavors", or the types + * of storage solutions available to each browser. + * + * 2.0 Version Notes: + * + * - The user is now responsible for third-party script includes, with the exception of flash. + * + * - jStore has been given sole responsibility for testing engine availability. + * + * - For the sake of naming conventions, all property names now start with a lowercase, and are camel-cased. + * + * The following properties have been changed since the 1.2.x release: + * + * - EngineOrder: For the sake of naming conventions, renamed to enginePriority. + * + * The following properties and methods have been removed since the 1.2.x release: + * + * - Availability: jStore's engines would add their availability tests to this object, so jStore could test + * them. With the changes to how availability testing works, this property has been removed. + * A new property, "available" on jStore contains a set of available engines. + * + * - Engines: Formerly contained the definitions of storage engines. This property has been removed, and + * storage of these definitions has been moved internal to the closure. + * + * - Instances: Formerly contained instantiated storage engines. This property has been removed, and storage + * of instantiated engines has been moved internal to the closure. + * + * - CurrentEngine: Formerly contained the active storage engine being used for transacting data through the jStore + * and/or jQuery objects. This property has been removed, and storage of the current engine has + * been moved internal to the closure. A new method, "activeEngine" has been added to jQuery to + * get and set the active engine to use. + * + * - defaults: Formerly used to set the implementation options for jStore. This property has been removed and + * replaced with a new configuration metho on the jStore object. + * + * - delegate: The delegate class has been removed in favor of a much simpler bind/trigger accessor system, which + * is accessible contextually through storage engines, or generically through jStore. + * + * + fail: This registration class bound events on the delegate for jstore-fail events. Instead, use: + * jStore.bind('jstore-failure', listener); + * + * + flashReady: This registration class bound events on the delegate for flash-ready events. The jstore-ready method + * now accounts for waiting for flash readyness, if and only if the flash engine is being used. Simply + * call to jStore.ready(). + * + * + load: Replaced with the init() method, which performs the same basic functions as the old load() method. Also, + * the init function is now domready safe, meaning it wraps itself in a domready listener, so the end user + * doesn't have to. + * + * + FindEngine: Removed entirely. The functionality provided by this method now implicitly occurs with the new define() + * system implemented for engine flavors. + * + * + setCurrentEngine: Replaced by activeEngine(). Set the current active engine by passing in the JRI. + * + * + safeStore: Replaced by a method internal to this closure, "prepareForStorage". + * + * + safeResurrect: Replaced by a method internal to this closure, "prepareForRevival". + * + * + use: Replaced by "create". + */ + $.extend(_, { + + //------------------------------ + // Properties + //------------------------------ + + /** + * The priority order in which engines should be tested for use. The lower their index in the array, the higher + * their priority for use. + * + * Be weary when reconfiguring the priority order of engines! jStore will use the first available engine it finds + * based on its priority when autoloading. + * + * This array is filtered out as engines are defined, with invalid engines being removed. + * + * Signature: + * [FLAVOR_<storageFlavor>, ...] + */ + enginePriority: [FLAVOR_LOCAL, FLAVOR_SQL, FLAVOR_FLASH, FLAVOR_MSIE], + + /** + * A collection of the availability states of engines, indexed by their flavor. + * + * Signature: + * { + * <storageFlavor>: true|false, + * + * ... + * } + */ + available: {}, + + /** + * Flag to determine if the jStore library is ready. jStore becomes ready once the dom is ready and all necessary + * startup procedures required by jStore to function properly are completed. + */ + isReady: false, + + /** + * With the flash storage engine, we have to jump through a couple of hoops before the flash engine is ready to work. + * This flag tracks whether or not the flash storage is available. + */ + isFlashReady: false, + + /** + * The available engine flavors. + */ + flavors: + { + local: FLAVOR_LOCAL, + + sql: FLAVOR_SQL, + + flash: FLAVOR_FLASH, + + gears: FLAVOR_GEARS, + + msie: FLAVOR_MSIE + }, + + //------------------------------ + // Constructor + //------------------------------ + + /** + * Constructor. + * + * @throws EX_INVALID + * + * @param project The name of the jStore project. Used to generate a JRI for the engine we create. + * + * @param configuration Optionally, an object containing configuration options for this implementation. + * + * @param flavor Optionally, the flavor of storage to use. If not provided, jStore will pick the + * best flavor, based on the current browser. + * + * @return jStore + */ + init: function (project, configuration, flavor) + { + // Extend our plugin configurations + $.extend(configurations, {project: project}, configuration); + + $(function () + { + // If JSON parsing isn't defined in this browser, include it. + if (window.JSON === undefined) + { + loadScript(configurations.json); + } + + // If we have an explicit flavor to use, use it. + if (flavor !== undefined) + { + _.create(flavor, project, 'default'); + } + + // Otherwise, attempt to create a best-fit engine. + else + { + createBestFitEngine(); + } + }); + + return _; + }, + + //------------------------------ + // Methods + //------------------------------ + + /** + * Create an instance of a flavored engine. + * + * @throws EX_INVALID, EX_UNAVAILABLE, EX_DUPLICATE + * + * @param flavor The flavor to create the engine with. + * + * @param project The project identifier for this instance. + * + * @param identifier Some arbitrary identifier for this project instance of the engine. + * + * @return The created instance. + */ + create: function (flavor, project, identifier) + { + project = project || configurations.project || location.hostname.replace(/\./g, '-') || 'unknown'; + + if (!validFlavor(flavor)) + { + throw EX_INVALID; + } + + if (definitions[flavor] === undefined) + { + throw EX_UNAVAILABLE; + } + + var jri = (identifier !== undefined ? identifier + '.' : '') + project + '.' + flavor, + engine; + + if (engines[jri] !== undefined) + { + throw EX_DUPLICATE; + } + + // Create our engine instance. + engine = engines[jri] = new definitions[flavor](project, jri); + + // Set up a listener for our jstore-engine-ready event. + engine.ready(function () + { + _.trigger('jstore-engine-ready', [engine]); + }); + + if (flavor === FLAVOR_FLASH && !_.isFlashReady) + { + if (active === undefined) + { + waitForFlash = true; + } + + // Define a window-accessible function for flash to call via ExternalInterface + window.jstore_ready = function () + { + _.isFlashReady = true; + _.trigger('flash-ready'); + + if (active === undefined) + { + makeReady(); + } + + // Remove the callback from the window scope, as it is no longer necessary + window.flash_ready = undefined; + }; + + window.jstore_error = function (message) + { + _.trigger('jstore-error', ['JSTORE_FLASH_EXCEPTION', null, message]); + }; + + $('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" id="jStoreFlashFrame" src="' + + configurations.flash + '"></iframe>').appendTo('body'); + } + else if (active === undefined) + { + active = jri; + makeReady(); + } + + return engine; + }, + + /** + * Fetch an engine by it's JRI. + * + * @param jri The JRI of the engine to retrieve. + * + * @return The requested engine. + */ + engine: function (jri) + { + return engines[jri]; + }, + + /** + * Returns the active storage engine being used. If a value is passed, sets that engine as the active engine. + * + * @throws EX_UNKNOWN + * + * @param jri Optionally, the JRI of the engine to make active, if it should be changed. + * + * @return The active storage engine. + */ + activeEngine: function (jri) + { + if (jri !== undefined) + { + if (engines[jri] === undefined) + { + throw EX_UNKNOWN; + } + else + { + active = jri; + } + } + + return engines[active]; + }, + + /** + * Bind an event listener. + * + * @param event The event to bind a listener on. + * + * @param listener The listener to notify when the event occurs. + * + * @param context The context of the binding. A string representing the engine flavor + * binding the event, or undefined to indicate it's a jStore event. + * + * @return jStore + */ + bind: function (event, listener, context) + { + context = context || 'jstore'; + + if (events[context] === undefined) + { + events[context] = {}; + } + + if (events[context][event] === undefined) + { + events[context][event] = [listener]; + } + else + { + events[context][event].push(listener); + } + + return _; + }, + + /** + * Trigger an event, notifying any bound listeners. + * + * @param event The event to trigger. + * + * @param parameters Any additional parameters to pass to the listeners being notified. + * + * @param context The context of the binding. A string representing the engine flavor + * binding the event, or undefined to indicate it's a jStore event. + * + * @return jStore + */ + trigger: function (event, parameters, context) + { + context = context || 'jstore'; + + if (events[context] !== undefined) + { + if (events[context][event] !== undefined) + { + $.each(events[context][event], function () + { + notify(this, _, parameters); + }); + } + } + + return _; + }, + + /** + * Bind a listener to be notified when jStore causes a non-fatal exception. + * + * @param listener The listener to notify when a failure occurs. + */ + error: function (listener) + { + _.bind('jstore-error', listener); + }, + + /** + * Bind a listener to be notified when jStore is ready. + * + * @param listener The listener to notify when jStore is ready. + * + * @return jStore + */ + ready: function (listener) + { + if (_.isReady) + { + notify(listener); + } + else + { + _.bind('jstore-ready', listener); + } + + return _; + }, + + /** + * Bind a listener to be notified when jStore and the default engine are ready. + * + * @param listener The listener to notify when jStore and it's default engine are ready. + * + * @return jStore + */ + engineReady: function (listener) + { + if (_.isReady) + { + notify(listener); + } + else + { + _.bind('jstore-engine-ready', listener); + } + + return _; + }, + + /** + * A combined getter/setter for the active engine. + * + * @param key The key of the property to get, or set. + * + * @param value If a valid value is provided, sets the engine. + * + * @return The requested property value. + */ + store: function (key, value) + { + return value === undefined ? _.get(key) : _.set(key, value); + }, + + /** + * Remove a property from the active engine. + * + * @param key The key of the property to remove. + * + * @return The value of the property before removal. + */ + remove: function (key) + { + return _.activeEngine().remove(key); + }, + + /** + * Get a property from the active engine. + * + * @param key The key of the property to get. + * + * @return The value of the property. + */ + get: function (key) + { + return _.activeEngine().get(key); + }, + + /** + * Set a property on the active engine. + * + * @param key The key of the property to set. + * + * @param value The value to set the property to. + * + * @return The new value of the property. + */ + set: function (key, value) + { + return _.activeEngine().set(key, value); + } + + }); + + //------------------------------ + // Core Extension + //------------------------------ + + //------------------------------ + // + // Class Definition + // + //------------------------------ + + /** + * The StorageEngine class is the unified API through which jStore accesses and manipulates + * the various storage flavors available. + * + * 2.0 Version Notes: + * + * - All third-party loading is now the responsibility of the developer. + * + * - The delegate class has been removed entirely. Engines have been given "bind" and "trigger" methods + * to interact directly with the delegate like-replacement that has been added to jStore. + * + * - Engine availability has been moved out of the engines themselves, and elevated to a jStore + * responsibility. + * + * The following methods have changed since the 1.2.x release: + * + * - get: When "get"ting a non-stored property, the get function will now return "undefined" + * instead of "null". "null" can now be used as a valid property value. + * + * - rem: Renamed to "remove". I always felt dirty about "rem" being vaguely explicit. + * + * The following properties have been removed since the 1.2.x release: + * + * - autoload: Part of the third-party loading logic. + * + * - hasIncluded: Part of the third-party loading logic. + * + * - includes: Part of the third-party loading logic. + * + * - isAvailable: Part of the availability logic elevated to jStore. + * + * @throws EX_UNSTABLE + */ + StorageEngine = Class.extend({ + + //------------------------------ + // Properties + //------------------------------ + + /** + * The project which owns this storage engine. + */ + project: undefined, + + /** + * The JRI (jStore Resource Identifier) acts as a uuid for this specific instance + * of the storage engine. + */ + jri: undefined, + + /** + * The flavor of this engine. + */ + flavor: undefined, + + /** + * The actual database object which data is transacted through. + */ + database: undefined, + + /** + * A StorageEngine should always respond to fetch requests synchronously. However, some + * of the storage flavors require callback-based asynchronous access. To get around this, + * we simlpy require all engines to function off a primary data cache, to allow for + * synchronous access across all implementations. + * + * Signature: + * { + * <propertyKey>: <propertyValue>, + * + * ... + * } + */ + data: undefined, + + /** + * A number of storage engines enforce a size limit as to what they will persist for a given site. + * This limit is not monitored or computed by jStore currently, and this property will merely give + * a static indication of the total size alloted to the engine, as defined by the storage flavor. + */ + limit: undefined, + + /** + * Each storage flavor has a different process to go through before it's "ready" to transact data. This + * property stores the state of the engine's readyness, and uses it to notify listeners whenever jStore + * is ready to function. + */ + isReady: undefined, + + //------------------------------ + // Constructor + //------------------------------ + + /** + * Constructor. + * + * @param project The project which instantiated this engine. + * + * @param jri The uuid assigned to this instance by jStore. + */ + init: function (project, jri) + { + this.project = project; + this.jri = jri; + this.data = {}; + this.isReady = false; + this.updateCache(); + }, + + //------------------------------ + // Methods + //------------------------------ + + /** + * Update the cache. + */ + updateCache: function () + { + this.isReady = true; + this.trigger('engine-ready', [this]); + }, + + /** + * Bind a listener to an event dispatched by this engine. + * + * @param event The event to bind on. + * + * @param listener The listener to notify when the event occurs. + */ + bind: function (event, listener) + { + _.bind(event, listener, this.jri); + }, + + /** + * Trigger an event, notifying all bound listeners. + * + * @param event The event to trigger. + * + * @param parameters An optional Array of parameters to pass to the listeners. + */ + trigger: function (event, parameters) + { + _.trigger(event, parameters, this.jri); + }, + + /** + * Bind a listener to the StorageEngine's ready event. + * + * @param listener The listener to notify whenever this engine is ready to transact data. + */ + ready: function (listener) + { + if (this.isReady) + { + notify(listener, this); + } + else + { + this.bind('engine-ready', listener); + } + }, + + /** + * Get a property from the StorageEngine. + * + * @param key The property key of the data to retrieve. + * + * @return The property value, or "undefined" if the property isn't stored. + */ + get: function (key) + { + this.__interruptAccess(); + + return this.data[key]; + }, + + /** + * Sets a property in the StorageEngine. + * + * @param key The key of the property. + * + * @param value The value of the property. + * + * @return The new value of the property. + */ + set: function (key, value) + { + this.__interruptAccess(); + + key = normalizeKey(key); + + try + { + this.__set(key, value); + } + catch (e) + { + _.trigger('jstore-error', ['JSTORE_STORAGE_FAILURE', this.jri, e]); + } + + this.data[key] = value; + + return value; + }, + + /** + * Removes a property from the StorageEngine. + * + * @param key The property key of the data to remove. + * + * @return The value of the property, before it was removed. + */ + remove: function (key) + { + this.__interruptAccess(); + + key = normalizeKey(key); + + try + { + this.__remove(key); + } + catch (e) + { + _.trigger('jstore-error', ['JSTORE_REMOVE_FAILURE', this.jri, e]); + } + + var buffer = this.data[key]; + + this.data[key] = undefined; + + return buffer; + }, + + //------------------------------ + // Internal Methods + //------------------------------ + + /** + * Ensures the engine is in a stable state for transacting data. + * + * @throws EX_UNSTABLE + */ + __interruptAccess: function () + { + if (!this.isReady) + { + throw EX_UNSTABLE; + } + }, + + /** + * Sets a property in the StorageEngine. This method should be overloaded to provide actual + * storage flavor integration. + * + * @param key The key of the property. + * + * @param value The value of the property. + * + * @return The new value of the property. + */ + __set: function (key, value) + { + return; + }, + + /** + * Removes a property from the StorageEngine. This method should be overloaded to provide actual + * storage flavor integration. + * + * @param key The property key of the data to remove. + * + * @return The value of the property, before it was removed. + */ + __remove: function (key) + { + return; + } + + }); + + //------------------------------ + // + // jQuery Hooks + // + //------------------------------ + + $.extend($.fn, { + + //------------------------------ + // Methods + //------------------------------ + + /** + * A combined getter/setter for the active engine. + * + * @param key The key of the property to get, or set. + * + * @param value If a valid value is provided, sets the engine. + * + * @return jQuery + */ + store: function (key, value) + { + if (value === undefined) + { + _.get(key); + } + else + { + _.set(key, value); + } + + return this; + }, + + /** + * Remove a property from the active engine. + * + * @param key The key of the property to remove. + * + * @return jQuery + */ + removeStore: function (key) + { + _.activeEngine().remove(key); + + return this; + }, + + /** + * Get a property from the active engine. + * + * @param key The key of the property to get. + * + * @return The value of the property. + */ + getStore: function (key) + { + return _.activeEngine().get(key); + }, + + /** + * Set a property on the active engine. + * + * @param key The key of the property to set. + * + * @param value The value to set the property to. + * + * @return jQuery + */ + setStore: function (key, value) + { + _.activeEngine().set(key, value); + + return this; + } + + }); + + //------------------------------ + // + // Event Bindings + // + //------------------------------ + + //------------------------------ + // + // Startup Code + // + //------------------------------ + + //------------------------------ + // Expose jStore through jQuery + //------------------------------ + + window.jStore = $.jStore = _; + + //------------------------------ + // + // Engine Definitions + // + //------------------------------ + + //------------------------------ + // Local + //------------------------------ + + define(FLAVOR_LOCAL, + { + //------------------------------ + // Properties + //------------------------------ + + limit: parseInt(5e5, 16), + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + this.database = window.globalStorage === undefined ? window.localStorage : window.globalStorage[location.hostname]; + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function () + { + var key, value; + + for (key in this.database) + { + var has_key = false; + if (this.database.hasOwnProperty) { + if (this.database.hasOwnProperty(key)) { + has_key = true; + } + } else { // IE 8 + if (this.database.getItem(key) !== null) { + has_key = true; + } + } + + if (has_key) { + value = this.database.getItem(key); + + // Gecko's getItem returns {value: 'the value'}, WebKit returns 'the value' + this.data[key] = prepareForRevival(value && value.value ? value.value : value); + } + } + + this._super(); + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + this.database.setItem(key, prepareForStorage(value)); + }, + + __remove: function (key) + { + this.database.removeItem(key); + } + }, + + function () + { + return window.localStorage !== undefined || window.globalStorage !== undefined; + }); + + //------------------------------ + // SQL + //------------------------------ + + define(FLAVOR_SQL, + { + //------------------------------ + // Properties + //------------------------------ + + limit: parseInt(32e3, 16), + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + this.database = window.openDatabase('jstore-' + project, '1.0', project, this.limit); + + if (!this.database) + { + throw 'JSTORE_SQL_NO_DB'; + } + + this.database.transaction(function (database) + { + database.executeSql('CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)'); + }); + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function () + { + var self = this, + _super = this._super; + + this.database.transaction(function (database) + { + database.executeSql('SELECT k,v FROM jstore', [], function (database, result) + { + var rows = result.rows, + index = 0, + row; + + for (; index < rows.length; ++index) + { + row = rows.item(index); + self.data[row.k] = prepareForRevival(row.v); + } + + _super.apply(self); + }); + }); + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + this.database.transaction(function (database) + { + database.executeSql('INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key, prepareForStorage(value)]); + }); + }, + + __remove: function (key) + { + this.database.transaction(function (database) + { + database.executeSql('DELETE FROM jstore WHERE k = ?', [key]); + }); + } + }, + + function () + { + return window.openDatabase !== undefined; + }); + + //------------------------------ + // Flash + //------------------------------ + + define(FLAVOR_FLASH, + { + //------------------------------ + // Properties + //------------------------------ + + limit: -1, + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + var self = this; + + _.bind('flash-ready', function () + { + self.__flashReadyListener(); + }); + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function (enable) + { + /** + * The default call to updateCache passes no variable, so we can short circuit the + * ready state until we explictly call this after flash ready. + */ + if (enable === true) + { + var key, + dataset = this.database.jstore_get_all(); + + for (key in dataset) + { + if (dataset.hasOwnProperty(key)) + { + this.data[key] = prepareForRevival(this.database.jstore_get(key)); + } + } + + this._super(); + } + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + if (!this.database.jstore_set(key, prepareForStorage(value))) + { + _.trigger('jstore-error', ['JSTORE_STORAGE_FAILURE', this.jri, 'Flash Exception']); + } + }, + + __remove: function (key) + { + this.database.jstore_remove(key); + }, + + /** + * Triggered whenever flash is ready. + */ + __flashReadyListener: function () + { + var iFrame = $('#jStoreFlashFrame')[0], + frameDocument; + + // MSIE + if (iFrame.Document !== undefined && typecheck(iFrame.Document.jStoreFlash.jstore_get, 'Function')) + { + this.database = iFrame.Document.jStoreFlash; + } + + // Real Browsers + else if (iFrame.contentWindow && iFrame.contentWindow.document) + { + frameDocument = $(iFrame.contentWindow.document); + + // Webkit + if (typecheck($('object', frameDocument)[0].jstore_get, 'Function')) + { + this.database = $('object', frameDocument)[0]; + } + + // Gecko + else if (typecheck($('embed', frameDocument)[0].jstore_get, 'Function')) + { + this.database = $('embed', frameDocument)[0]; + } + } + + if (this.database === undefined) + { + throw 'JSTORE_FLASH_REFERENCE_ISSUE'; + } + else + { + this.updateCache(true); + } + } + }, + + function () + { + return hasFlashVersion('9.0.0'); + }); + + //------------------------------ + // Gears + //------------------------------ + + define(FLAVOR_GEARS, + { + //------------------------------ + // Properties + //------------------------------ + + limit: -1, + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + this.database = google.gears.factory.create('beta.database'); + this.database.open('jstore-' + project); + this.database.execute('CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)'); + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function () + { + var result = this.database.execute('SELECT k,v FROM jstore'); + + while (result.isValidRow()) + { + this.data[result.field(0)] = prepareForRevival(result.field(1)); + result.next(); + } + + result.close(); + + this._super(); + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + this.database.execute('BEGIN'); + this.database.execute('INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key, prepareForStorage(value)]); + this.database.execute('COMMIT'); + }, + + __remove: function (key) + { + this.database.execute('BEGIN'); + this.database.execute('DELETE FROM jstore WHERE k = ?', [key]); + this.database.execute('COMMIT'); + } + }, + + function () + { + return window.google !== undefined && window.google.gears !== undefined; + }); + + //------------------------------ + // MSIE + //------------------------------ + + define(FLAVOR_MSIE, + { + //------------------------------ + // Properties + //------------------------------ + + limit: parseInt(1e4, 16), + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + this.database = $('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-' + project + '"></div>') + .appendTo(document.body).get(0); + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function () + { + this.database.load(this.project); + + var node = document.getElementById('jstore-' + this.project), + xmlDoc = node.XMLDocument, + root, + index = 0; + + if (xmlDoc && xmlDoc.documentElement && xmlDoc.documentElement.attributes) + { + root = xmlDoc.documentElement; + + for (; index < root.attributes.length; ++index) + { + this.data[root.attributes.item(index).nodeName] = prepareForRevival(root.attributes.item(index).nodeValue); + } + } + + this._super(); + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + this.database.setAttribute(key, prepareForStorage(value)); + this.database.save(this.project); + }, + + __remove: function (key) + { + this.database.removeAttribute(key); + this.database.save(this.project); + } + }, + + function () + { + return window.ActiveXObject !== undefined; + }); + +}(jQuery, window)); diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/json2.js --- a/static/scripts/json2.js Fri Apr 09 13:02:15 2010 -0400 +++ b/static/scripts/json2.js Fri Apr 09 18:09:54 2010 -0400 @@ -1,6 +1,6 @@ /* http://www.JSON.org/json2.js - 2009-06-29 + 2010-03-20 Public Domain. @@ -8,6 +8,14 @@ See http://www.JSON.org/js.html + + This code should be minified before deployment. + See http://javascript.crockford.com/jsmin.html + + USE YOUR OWN COPY. IT IS EXTREMELY UNWISE TO LOAD CODE FROM SERVERS YOU DO + NOT CONTROL. + + This file creates a global JSON object containing two methods: stringify and parse. @@ -33,7 +41,7 @@ value represented by the name/value pair that should be serialized, or undefined if nothing should be serialized. The toJSON method will be passed the key associated with the value, and this will be - bound to the object holding the key. + bound to the value For example, this would serialize Dates as ISO strings. @@ -136,15 +144,9 @@ This is a reference implementation. You are free to copy, modify, or redistribute. - - This code should be minified before deployment. - See http://javascript.crockford.com/jsmin.html - - USE YOUR OWN COPY. IT IS EXTREMELY UNWISE TO LOAD CODE FROM SERVERS YOU DO - NOT CONTROL. */ -/*jslint evil: true */ +/*jslint evil: true, strict: false */ /*members "", "\b", "\t", "\n", "\f", "\r", "\"", JSON, "\\", apply, call, charCodeAt, getUTCDate, getUTCFullYear, getUTCHours, @@ -153,10 +155,13 @@ test, toJSON, toString, valueOf */ + // Create a JSON object only if one does not already exist. We create the // methods in a closure to avoid creating global variables. -var JSON = JSON || {}; +if (!this.JSON) { + this.JSON = {}; +} (function () { @@ -428,6 +433,7 @@ // Unicode characters with escape sequences. JavaScript handles many characters // incorrectly, either silently deleting them, or treating them as line endings. + text = String(text); cx.lastIndex = 0; if (cx.test(text)) { text = text.replace(cx, function (a) { diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/packed/class.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/class.js Fri Apr 09 18:09:54 2010 -0400 @@ -0,0 +1,7 @@ +/* + * Class definition + * + * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) + * Inspired by base2 and Prototype + */ +"use strict";(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=(typeof g[d]==="function"&&typeof f[d]==="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}}(d,g[d])):g[d])}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}}()); \ No newline at end of file diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Apr 09 13:02:15 2010 -0400 +++ b/static/scripts/packed/galaxy.base.js Fri Apr 09 18:09:54 2010 -0400 @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmen! 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4)})}if(/^[\],:{}\s]*$/.test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))){j=eval("("+text+")");return typeof reviver==="function"?walk({"":j},""):j}throw new SyntaxError("JSON.parse")}}}()); \ No newline at end of file diff -r a9402fc7ce1b -r 5536d57237a3 templates/display_base.mako --- a/templates/display_base.mako Fri Apr 09 13:02:15 2010 -0400 +++ b/templates/display_base.mako Fri Apr 09 18:09:54 2010 -0400 @@ -32,29 +32,25 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery", "jquery.tipsy", "galaxy.base", "json2", "jquery.autocomplete", "jquery.jstore-all", "autocomplete_tagging" )} + ${h.js( "jquery", "jquery.tipsy", "galaxy.base", "json2", "class", "jquery.jstore", "jquery.autocomplete", "autocomplete_tagging" )} <script type="text/javascript"> - // + // Handle click on community tag. - // - function community_tag_click(tag_name, tag_value) - { + function community_tag_click(tag_name, tag_value) { <% controller_name = get_controller_name( item ) %> var href = '${h.url_for ( controller='/' + controller_name , action='list_published')}'; href = href + "?f-tags=" + tag_name; - if (tag_value != undefined && tag_value != "") + if (tag_value != undefined && tag_value != "") { href = href + ":" + tag_value; + } self.location = href; } - $(document).ready( function() - { + $(function() { // Set links to Galaxy screencasts to open in overlay. - $(this).find("a[href^='http://screencast.g2.bx.psu.edu/']").each( function() - { - $(this).click( function() - { + $(this).find("a[href^='http://screencast.g2.bx.psu.edu/']").each( function() { + $(this).click( function() { var href = $(this).attr('href'); show_in_overlay( { @@ -67,7 +63,8 @@ return false; }); }); - + // Init history boxes + init_history_items( $("div.historyItemWrapper") ); }); </script> </%def> @@ -76,14 +73,12 @@ ${parent.stylesheets()} ${h.css( "autocomplete_tagging", "embed_item" )} <style type="text/css"> - .page-body - { + .page-body { padding: 10px; ## float: left; ## width: 65%; } - .page-meta - { + .page-meta { float: right; width: 27%; padding: 0.5em; diff -r a9402fc7ce1b -r 5536d57237a3 templates/history/display.mako --- a/templates/history/display.mako Fri Apr 09 13:02:15 2010 -0400 +++ b/templates/history/display.mako Fri Apr 09 18:09:54 2010 -0400 @@ -1,207 +1,14 @@ <%inherit file="/display_base.mako"/> <%namespace file="/root/history_common.mako" import="render_dataset" /> +## Set vars so that there's no need to change the code below. +<% + history = published_item + datasets = published_item_data +%> + <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery.jstore-all" )} - - ## Set vars so that there's no need to change the code below. - <% - history = published_item - datasets = published_item_data - %> - - <script type="text/javascript"> - $(function() { - // Load jStore for local storage - $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '/static/jStore.Flash.html' }) - $.jStore.load(); // Auto-select best storage

1 0

[hg] galaxy 3625: Rollback text + autocomplete for big selects. ...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a9402fc7ce1b changeset: 3625:a9402fc7ce1b user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Apr 09 13:02:15 2010 -0400 description: Rollback text + autocomplete for big selects. Only use text + autocomplete for dbkey. diffstat: static/scripts/galaxy.base.js | 5 ++--- static/scripts/packed/galaxy.base.js | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diffs (24 lines): diff -r 58ba6fbe22b3 -r a9402fc7ce1b static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Apr 09 11:35:02 2010 -0400 +++ b/static/scripts/galaxy.base.js Fri Apr 09 13:02:15 2010 -0400 @@ -120,10 +120,9 @@ } // Replace any select box with 20+ options with a text input box + autocomplete. -// TODO: make this work _well_ on pages with multiple forms; currently, value is reverted when any form is submitted - -// value should be reverted when only the form that element is in is submitted. +// TODO: make work with dynamic tool inputs and then can replace all big selects. function replace_big_select_inputs() { - $('select').each( function() { + $('select[name=dbkey]').each( function() { var select_elt = $(this); // Skip if there are < 20 options. if (select_elt.find('option').length < 20) diff -r 58ba6fbe22b3 -r a9402fc7ce1b static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Apr 09 11:35:02 2010 -0400 +++ b/static/scripts/packed/galaxy.base.js Fri Apr 09 13:02:15 2010 -0400 @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmen! u(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function replace_big_select_inputs(){$("select").each(function(){var a=$(this);if(a.find("optio! n").length<20){return}var b=a.attr("value");var c=$("<input type='text ' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",a.attr("name"));c.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var f=[];var e={};a.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}f.push(h);e[h]=g;e[g]=g;if(g==b){c.attr("value",h)}});if(c.attr("value")==""){c.attr("value","Click to Search or Select")}var d={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};c.autocomplete(f,d);a.replaceWith(c);c.parents("form").submit(function(){var h=c.attr("value");var g=e[h];if(g!==null&&g!==undefined){c.attr("value",g)}else{if(b!=""){c.attr("value",b)}else{c.attr("value","?")}}})})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0! ){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text(k)}else{j=$("<input type='text'></input>").attr({value:k,size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){l.text(o);if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus()}); \ No newline at end of file +$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmen! u(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function replace_big_select_inputs(){$("select[name=dbkey]").each(function(){var a=$(this);if(a! .find("option").length<20){return}var b=a.attr("value");var c=$("<inpu t type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",a.attr("name"));c.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var f=[];var e={};a.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}f.push(h);e[h]=g;e[g]=g;if(g==b){c.attr("value",h)}});if(c.attr("value")==""){c.attr("value","Click to Search or Select")}var d={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};c.autocomplete(f,d);a.replaceWith(c);c.parents("form").submit(function(){var h=c.attr("value");var g=e[h];if(g!==null&&g!==undefined){c.attr("value",g)}else{if(b!=""){c.attr("value",b)}else{c.attr("value","?")}}})})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-activ! e").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text(k)}else{j=$("<input type='text'></input>").attr({value:k,size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){l.text(o);if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus()}); \ No newline at end of file

1 0

[hg] galaxy 3624: Add additional tests to FASTQ Quality Trimmer ...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/58ba6fbe22b3 changeset: 3624:58ba6fbe22b3 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Apr 09 11:35:02 2010 -0400 description: Add additional tests to FASTQ Quality Trimmer tool diffstat: test-data/sanger_full_range_empty_reads.fastqsanger | 8 ++++++ tools/fastq/fastq_trimmer_by_quality.py | 11 ++++++-- tools/fastq/fastq_trimmer_by_quality.xml | 26 +++++++++++++++++++++ 3 files changed, 42 insertions(+), 3 deletions(-) diffs (90 lines): diff -r ac044bb17d24 -r 58ba6fbe22b3 test-data/sanger_full_range_empty_reads.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_empty_reads.fastqsanger Fri Apr 09 11:35:02 2010 -0400 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) + ++ + +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) + ++ + diff -r ac044bb17d24 -r 58ba6fbe22b3 tools/fastq/fastq_trimmer_by_quality.py --- a/tools/fastq/fastq_trimmer_by_quality.py Fri Apr 09 11:29:26 2010 -0400 +++ b/tools/fastq/fastq_trimmer_by_quality.py Fri Apr 09 11:35:02 2010 -0400 @@ -55,6 +55,12 @@ if len ( args ) != 2: parser.error( "Need to specify an input file and an output file" ) + if options.window_size < 1: + parser.error( 'You must specify a strictly positive window size' ) + + if options.window_step < 1: + parser.error( 'You must specify a strictly positive step size' ) + #determine an exhaustive list of window indexes that can be excluded from aggregation exclude_window_indexes = [] last_exclude_indexes = [] @@ -76,7 +82,6 @@ out = fastqWriter( open( args[1], 'wb' ), format = options.format ) action = ACTION_METHODS[ options.aggregation_action ] - window_step = abs( options.window_step ) num_reads = None num_reads_excluded = 0 @@ -93,7 +98,7 @@ if exclude_and_compare( action, quality_list[ lwindow_position:lwindow_position + options.window_size ], options.score_comparison, options.quality_score, exclude_window_indexes ): fastq_read = fastq_read.slice( lwindow_position, None ) break - lwindow_position += window_step + lwindow_position += options.window_step else: rwindow_position = len( quality_list ) #right position of window while True: @@ -105,7 +110,7 @@ if exclude_and_compare( action, quality_list[ lwindow_position:rwindow_position ], options.score_comparison, options.quality_score, exclude_window_indexes ): fastq_read = fastq_read.slice( None, rwindow_position ) break - rwindow_position -= window_step + rwindow_position -= options.window_step if options.keep_zero_length or len( fastq_read ): out.write( fastq_read ) else: diff -r ac044bb17d24 -r 58ba6fbe22b3 tools/fastq/fastq_trimmer_by_quality.xml --- a/tools/fastq/fastq_trimmer_by_quality.xml Fri Apr 09 11:29:26 2010 -0400 +++ b/tools/fastq/fastq_trimmer_by_quality.xml Fri Apr 09 11:35:02 2010 -0400 @@ -94,6 +94,32 @@ <param name="quality_score" value="1"/> <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> </test> + <test> +  + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="keep_zero_length" value="true" /> + <param name="trim_ends" value="53"/> + <param name="window_size" value="1"/> + <param name="step_size" value="1"/> + <param name="exclude_count" value="0"/> + <param name="aggregation_action" value="min"/> + <param name="score_comparison" value=">="/> + <param name="quality_score" value="999"/> + <output name="output_file" file="sanger_full_range_empty_reads.fastqsanger" /> + </test> + <test> +  + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="keep_zero_length"/> + <param name="trim_ends" value="53"/> + <param name="window_size" value="1"/> + <param name="step_size" value="1"/> + <param name="exclude_count" value="0"/> + <param name="aggregation_action" value="min"/> + <param name="score_comparison" value=">="/> + <param name="quality_score" value="999"/> + <output name="output_file" file="empty_file.dat" /> + </test> </tests> <help> This tool allows you to trim the ends of reads based upon the aggregate value of quality scores found within a sliding window; a sliding window of size 1 is equivalent to 'simple' trimming of the ends.

1 0

[hg] galaxy 3623: Fix Test framework's handling of boolean and m...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ac044bb17d24 changeset: 3623:ac044bb17d24 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Apr 09 11:29:26 2010 -0400 description: Fix Test framework's handling of boolean and multiple select checkboxes and radio buttons. diffstat: test/base/twilltestcase.py | 22 +++++++--------------- 1 files changed, 7 insertions(+), 15 deletions(-) diffs (55 lines): diff -r ab319f94495c -r ac044bb17d24 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Apr 08 16:21:53 2010 -0400 +++ b/test/base/twilltestcase.py Fri Apr 09 11:29:26 2010 -0400 @@ -1000,24 +1000,21 @@ break # To help with debugging a tool, print out the form controls when the test fails print "form '%s' contains the following controls ( note the values )" % f.name - control_names = [] - hidden_control_names = [] # cannot change these, so ignore or many complex page tool tests will fail + controls = {} hc_prefix = '<HiddenControl(' for i, control in enumerate( f.controls ): print "control %d: %s" % ( i, str( control ) ) - if hc_prefix in str(control): - hidden_control_names.append(control.name) # cannot do much with these - else: + if not hc_prefix in str( control ): try: #check if a repeat element needs to be added if control.name not in kwd and control.name.endswith( '_add' ): #control name doesn't exist, could be repeat repeat_startswith = control.name[0:-4] - if repeat_startswith and not [ c_name for c_name in control_names if c_name.startswith( repeat_startswith ) ] and [ c_name for c_name in kwd.keys() if c_name.startswith( repeat_startswith ) ]: + if repeat_startswith and not [ c_name for c_name in controls.keys() if c_name.startswith( repeat_startswith ) ] and [ c_name for c_name in kwd.keys() if c_name.startswith( repeat_startswith ) ]: tc.submit( control.name ) return self.submit_form( form_no=form_no, button=button, **kwd ) # Check for refresh_on_change attribute, submit a change if required - if 'refresh_on_change' in control.attrs.keys(): + if hasattr( control, 'attrs' ) and 'refresh_on_change' in control.attrs.keys(): changed = False item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] #For DataToolParameter, control.value is the HDA id, but kwd contains the filename. This loop gets the filename/label for the selected values. for value in kwd[ control.name ]: @@ -1040,19 +1037,14 @@ except Exception, e: log.debug( "In submit_form, continuing, but caught exception: %s" % str( e ) ) continue - control_names.append( control.name ) + controls[ control.name ] = control # No refresh_on_change attribute found in current form, so process as usual for control_name, control_value in kwd.items(): - if control_name in hidden_control_names: + if control_name not in controls: continue # these cannot be handled safely - cause the test to barf out if not isinstance( control_value, list ): control_value = [ control_value ] - try: - control = f.find_control( name=control_name ) - except: - # This assumes we always want the first control of the given name, - # which may not be ideal... - control = f.find_control( name=control_name, nr=0 ) + control = controls[ control_name ] control.clear() if control.is_of_kind( "text" ): tc.fv( f.name, control.name, ",".join( control_value ) )

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