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[hg] galaxy 3425: Bug fixes to LCA tool
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c0192e97a79a changeset: 3425:c0192e97a79a user: gua110 date: Mon Feb 22 16:22:12 2010 -0500 description: Bug fixes to LCA tool diffstat: test-data/lca_input2.taxonomy | 4 + test-data/lca_input3.taxonomy | 100 +++++++++++++++++++++++++++++++++++++++++ test-data/lca_output2.taxonomy | 1 + test-data/lca_output3.taxonomy | 40 ++++++++++++++++ tools/taxonomy/lca.py | 49 +++++++++++++------ tools/taxonomy/lca.xml | 24 +++++++-- 6 files changed, 195 insertions(+), 23 deletions(-) diffs (308 lines): diff -r 9d9f0dfeeebf -r c0192e97a79a test-data/lca_input2.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lca_input2.taxonomy Mon Feb 22 16:22:12 2010 -0500 @@ -0,0 +1,4 @@ +read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1 1 2 3 4 +read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 subgenus2 species2 subspecies2 1 2 3 4 +read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3 1 X Y Z +read_2 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4 1 X Y Z diff -r 9d9f0dfeeebf -r c0192e97a79a test-data/lca_input3.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lca_input3.taxonomy Mon Feb 22 16:22:12 2010 -0500 @@ -0,0 +1,100 @@ +IA_1-79371 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604065 +IA_1-84488 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604065 +IA_1-270826 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-285361 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-93958 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-99821 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-144417 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-278966 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-314709 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-324951 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-27817 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604153 +IA_1-95255 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604181 +IA_1-104173 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-135979 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-139090 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-139090 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-139090 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-144996 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-160446 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-160446 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-160446 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-160446 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-160446 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-160446 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-160446 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-160446 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-161439 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-216231 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-237681 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-250166 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-254274 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-254274 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-27817 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-29000 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-291427 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-291427 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-293054 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-293054 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-296315 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-296315 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus +IA_1-310974 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-310974 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-311282 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-311282 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-322295 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n +IA_1-42600 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-45102 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-45102 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-48105 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-48105 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-57254 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-61975 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-61975 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-66943 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-68288 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-82334 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-95526 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 diff -r 9d9f0dfeeebf -r c0192e97a79a test-data/lca_output2.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lca_output2.taxonomy Mon Feb 22 16:22:12 2010 -0500 @@ -0,0 +1,1 @@ +read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n 1 2 3 4 diff -r 9d9f0dfeeebf -r c0192e97a79a test-data/lca_output3.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lca_output3.taxonomy Mon Feb 22 16:22:12 2010 -0500 @@ -0,0 +1,40 @@ +IA_1-104173 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-135979 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-139090 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-144417 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-144996 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-160446 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-161439 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-190855 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-205154 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-216231 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-236286 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-237681 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-250166 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-254274 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-270826 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-27817 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604153 +IA_1-278966 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-285361 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-29000 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-291427 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-293054 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-296315 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-310974 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-311282 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-314709 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-324951 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-42600 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-45102 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-48105 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-57254 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-61975 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-66943 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-68288 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-79371 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604065 +IA_1-82334 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-84488 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604065 +IA_1-93958 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-95255 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604181 +IA_1-95526 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-99821 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 diff -r 9d9f0dfeeebf -r c0192e97a79a tools/taxonomy/lca.py --- a/tools/taxonomy/lca.py Mon Feb 22 13:56:51 2010 -0500 +++ b/tools/taxonomy/lca.py Mon Feb 22 16:22:12 2010 -0500 @@ -42,6 +42,16 @@ except: stop_err("Syntax error: Use correct syntax: program infile outfile") + fin = open(sys.argv[1],'r') + for j, line in enumerate( fin ): + elems = line.strip().split('\t') + if len(elems) < 24: + stop_err("The format of the input dataset is incorrect. Taxonomy datatype should contain at least 24 columns.") + if j > 30: + break + cols = range(1,len(elems)) + fin.close() + group_col = 0 tmpfile = tempfile.NamedTemporaryFile() @@ -68,11 +78,11 @@ remaining_vals = [] skipped_lines = 0 fout = open(outfile, "w") - cols = range(1,25) block_valid = False + for ii, line in enumerate( file( tmpfile.name )): - if line and not line.startswith( '#' ): + if line and not line.startswith( '#' ) and len(line.split('\t')) >= 24: #Taxonomy datatype should have at least 24 columns line = line.rstrip( '\r\n' ) try: fields = line.split("\t") @@ -95,14 +105,11 @@ corresponding aggregate values into the output file. This works due to the sort on group_col we've applied to the data above. """ - out_list = ['']*25 + out_list = ['']*24 out_list[0] = str(prev_item) out_list[1] = str(prev_vals[0][0]) out_list[2] = str(prev_vals[1][0]) - try: - out_list[24] = str(prev_vals[23][0]) - except: - pass + for k, col in enumerate(cols): if col >= 3 and col < 24: if len(set(prev_vals[k])) == 1: @@ -113,11 +120,17 @@ out_list[k+1] = 'n' k += 1 + j = 0 + while True: + try: + out_list.append(str(prev_vals[23+j][0])) + j += 1 + except: + break + if rank_bound == 0: print >>fout, '\t'.join(out_list).strip() - #print 'n'*( 24 - rank_bound ) else: - #print '\t'.join(out_list[rank_bound:24]) if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ): print >>fout, '\t'.join(out_list).strip() @@ -144,15 +157,11 @@ skipped_lines += 1 # Handle the last grouped value - out_list = ['']*25 + out_list = ['']*24 out_list[0] = str(prev_item) out_list[1] = str(prev_vals[0][0]) out_list[2] = str(prev_vals[1][0]) - try: - out_list[24] = str(prev_vals[23][0]) - except: - pass - + for k, col in enumerate(cols): if col >= 3 and col < 24: if len(set(prev_vals[k])) == 1: @@ -163,11 +172,17 @@ out_list[k+1] = 'n' k += 1 + j = 0 + while True: + try: + out_list.append(str(prev_vals[23+j][0])) + j += 1 + except: + break + if rank_bound == 0: print >>fout, '\t'.join(out_list).strip() else: - #print ''.join(out_list[rank_bound:24]) - #print 'n'*( 24 - rank_bound ) if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ): print >>fout, '\t'.join(out_list).strip() diff -r 9d9f0dfeeebf -r c0192e97a79a tools/taxonomy/lca.xml --- a/tools/taxonomy/lca.xml Mon Feb 22 13:56:51 2010 -0500 +++ b/tools/taxonomy/lca.xml Mon Feb 22 16:22:12 2010 -0500 @@ -1,4 +1,4 @@ -<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.0"> +<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1"> <description></description> <command interpreter="python"> lca.py $input1 $out_file1 $rank_bound @@ -34,11 +34,23 @@ <data format="taxonomy" name="out_file1" metadata_source="input1" /> </outputs> <tests> - <test> - <param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/> - <param name="rank_bound" value="0" /> - <output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/> - </test> + <test> + <param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/> + <param name="rank_bound" value="0" /> + <output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/> + </test> + <test> + <param name="input1" value="lca_input2.taxonomy" ftype="taxonomy"/> + <param name="rank_bound" value="7" /> + <output name="out_file1" file="lca_output2.taxonomy" ftype="taxonomy"/> + </test> + +  + <test> + <param name="input1" value="lca_input3.taxonomy" ftype="taxonomy"/> + <param name="rank_bound" value="10" /> + <output name="out_file1" file="lca_output3.taxonomy" ftype="taxonomy"/> + </test> </tests> <help>

1 0

[hg] galaxy 3424: Annotations for published items: (1) added ann...
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9d9f0dfeeebf changeset: 3424:9d9f0dfeeebf user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 22 13:56:51 2010 -0500 description: Annotations for published items: (1) added annotations to pages; (2) added annotation column to all published item grids; (3) refactored annotation code out of base controller and into its own mixin. diffstat: lib/galaxy/model/__init__.py | 3 + lib/galaxy/model/mapping.py | 13 ++++- lib/galaxy/model/migrate/versions/0040_page_annotations.py | 42 ++++++++++++++ lib/galaxy/web/base/controller.py | 8 ++- lib/galaxy/web/controllers/dataset.py | 2 +- lib/galaxy/web/controllers/history.py | 3 +- lib/galaxy/web/controllers/page.py | 24 +++++-- lib/galaxy/web/controllers/root.py | 2 +- lib/galaxy/web/controllers/workflow.py | 3 +- lib/galaxy/web/framework/helpers/grids.py | 39 ++++++++++-- 10 files changed, 118 insertions(+), 21 deletions(-) diffs (351 lines): diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Feb 22 09:21:42 2010 -0500 +++ b/lib/galaxy/model/__init__.py Mon Feb 22 13:56:51 2010 -0500 @@ -1567,6 +1567,9 @@ class WorkflowStepAnnotationAssociation( object ): pass +class PageAnnotationAssociation( object ): + pass + class UserPreference ( object ): def __init__( self, name=None, value=None ): self.name = name diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Feb 22 09:21:42 2010 -0500 +++ b/lib/galaxy/model/mapping.py Mon Feb 22 13:56:51 2010 -0500 @@ -814,6 +814,12 @@ Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "annotation", TEXT, index=True) ) + +PageAnnotationAssociation.table = Table( "page_annotation_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "annotation", TEXT, index=True) ) # User tables. @@ -1304,7 +1310,8 @@ latest_revision=relation( PageRevision, post_update=True, primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ), lazy=False ), - tags=relation(PageTagAssociation, order_by=PageTagAssociation.table.c.id, backref="pages") + tags=relation(PageTagAssociation, order_by=PageTagAssociation.table.c.id, backref="pages"), + annotations=relation( PageAnnotationAssociation, order_by=PageAnnotationAssociation.table.c.id, backref="pages" ) ) ) # Set up proxy so that @@ -1377,6 +1384,10 @@ properties=dict( workflow_step=relation( WorkflowStep ), user=relation( User ) ) ) +assign_mapper( context, PageAnnotationAssociation, PageAnnotationAssociation.table, + properties=dict( page=relation( Page ), user=relation( User ) ) + ) + assign_mapper( context, UserPreference, UserPreference.table, properties = {} ) diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/model/migrate/versions/0040_page_annotations.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0040_page_annotations.py Mon Feb 22 13:56:51 2010 -0500 @@ -0,0 +1,42 @@ +""" +Migration script to (a) create tables for annotating pages. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +PageAnnotationAssociation_table = Table( "page_annotation_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "annotation", TEXT, index=True) ) + +def upgrade(): + print __doc__ + metadata.reflect() + + # Create history_annotation_association table. + try: + PageAnnotationAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Creating page_annotation_association table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # Drop page_annotation_association table. + try: + PageAnnotationAssociation_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping page_annotation_association table failed: %s" % str( e ) ) + \ No newline at end of file diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Mon Feb 22 09:21:42 2010 -0500 +++ b/lib/galaxy/web/base/controller.py Mon Feb 22 13:56:51 2010 -0500 @@ -41,6 +41,10 @@ item_class = None return item_class +Root = BaseController + +class UsesAnnotations: + """ Mixin for getting and setting item annotations. """ def get_item_annotation_str( self, db_session, user, item ): """ Returns a user's annotation string for an item. """ annotation_obj = self.get_item_annotation_obj( db_session, user, item ) @@ -67,6 +71,8 @@ annotation_assoc = annotation_assoc.filter_by( stored_workflow=item ) elif item.__class__ == model.WorkflowStep: annotation_assoc = annotation_assoc.filter_by( workflow_step=item ) + elif item.__class__ == model.Page: + annotation_assoc = annotation_assoc.filter_by( page=item ) return annotation_assoc.first() def add_item_annotation( self, trans, item, annotation ): @@ -89,8 +95,6 @@ # Set annotation. annotation_assoc.annotation = annotation return True - -Root = BaseController class SharableItemSecurity: """ Mixin for handling security for sharable items. """ diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Mon Feb 22 09:21:42 2010 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Mon Feb 22 13:56:51 2010 -0500 @@ -110,7 +110,7 @@ # a user relation. return query.select_from( model.HistoryDatasetAssociation.table.join( model.History.table ) ).filter( model.History.user == trans.user ) -class DatasetInterface( BaseController, UsesHistoryDatasetAssociation ): +class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssociation ): stored_list_grid = HistoryDatasetAssociationListGrid() diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Feb 22 09:21:42 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Feb 22 13:56:51 2010 -0500 @@ -128,6 +128,7 @@ use_async = True columns = [ NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.History, model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) @@ -146,7 +147,7 @@ # A public history is published, has a slug, and is not deleted. return query.filter( self.model_class.published == True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) -class HistoryController( BaseController, Sharable, UsesHistory ): +class HistoryController( BaseController, Sharable, UsesAnnotations, UsesHistory ): @web.expose def index( self, trans ): return "" diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Mon Feb 22 09:21:42 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Mon Feb 22 13:56:51 2010 -0500 @@ -45,7 +45,7 @@ ] operations = [ grids.DisplayByUsernameAndSlugGridOperation( "View", allow_multiple=False ), - grids.GridOperation( "Edit name/id", allow_multiple=False, url_args=dict( action='edit') ), + grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit') ), grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Delete" ), @@ -63,6 +63,7 @@ default_filter = dict( title="All", username="All" ) columns = [ grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced"), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) @@ -70,7 +71,7 @@ columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], + cols_to_filter=[ columns[0], columns[1], columns[2], columns[3] ], key="free-text-search", visible=False, filterable="standard" ) ) def build_initial_query( self, session ): @@ -285,7 +286,7 @@ # Default behavior: _BaseHTMLProcessor.unknown_endtag( self, tag ) -class PageController( BaseController, Sharable, UsesHistory, UsesStoredWorkflow, UsesHistoryDatasetAssociation ): +class PageController( BaseController, Sharable, UsesAnnotations, UsesHistory, UsesStoredWorkflow, UsesHistoryDatasetAssociation ): _page_list = PageListGrid() _all_published_list = PageAllPublishedGrid() @@ -385,7 +386,7 @@ @web.expose @web.require_login( "create pages" ) - def edit( self, trans, id, page_title="", page_slug="" ): + def edit( self, trans, id, page_title="", page_slug="", page_annotation="" ): """ Create a new page """ @@ -395,7 +396,7 @@ page = session.query( model.Page ).get( id ) user = trans.user assert page.user == user - page_title_err = page_slug_err = "" + page_title_err = page_slug_err = page_annotation_err = "" if trans.request.method == "POST": if not page_title: page_title_err = "Page name is required" @@ -403,17 +404,24 @@ page_slug_err = "Page id is required" elif not VALID_SLUG_RE.match( page_slug ): page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character" - elif page_slug == page.slug or trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): + elif page_slug != page.slug and trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): page_slug_err = "Page id must be unique" + elif not page_annotation: + page_annotation_err = "Page annotation is required" else: page.title = page_title page.slug = page_slug + page_annotation = sanitize_html( page_annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans, page, page_annotation ) session.flush() # Redirect to page list. return trans.response.send_redirect( web.url_for( action='list' ) ) else: page_title = page.title page_slug = page.slug + page_annotation = self.get_item_annotation_str( trans.sa_session, trans.get_user(), page ) + if not page_annotation: + page_annotation = "" return trans.show_form( web.FormBuilder( web.url_for( id=encoded_id ), "Edit page attributes", submit_text="Submit" ) .add_text( "page_title", "Page title", value=page_title, error=page_title_err ) @@ -422,7 +430,9 @@ public links to this page. A default is generated from the page title, but can be edited. This field must contain only lowercase letters, numbers, and - the '-' character.""" ), + the '-' character.""" ) + .add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err, + help="A description of or notes about the page. Annotation is shown alongside published pages."), template="page/create.mako" ) @web.expose diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Feb 22 09:21:42 2010 -0500 +++ b/lib/galaxy/web/controllers/root.py Mon Feb 22 13:56:51 2010 -0500 @@ -10,7 +10,7 @@ log = logging.getLogger( __name__ ) -class RootController( BaseController, UsesHistory ): +class RootController( BaseController, UsesHistory, UsesAnnotations ): @web.expose def default(self, trans, target1=None, target2=None, **kwd): diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Mon Feb 22 09:21:42 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Mon Feb 22 13:56:51 2010 -0500 @@ -60,6 +60,7 @@ use_async = True columns = [ grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.StoredWorkflow, model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) @@ -78,7 +79,7 @@ # A public workflow is published, has a slug, and is not deleted. return query.filter( self.model_class.published==True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) -class WorkflowController( BaseController, Sharable, UsesStoredWorkflow ): +class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnnotations ): stored_list_grid = StoredWorkflowListGrid() published_list_grid = StoredWorkflowAllPublishedGrid() diff -r 8d77e3acf653 -r 9d9f0dfeeebf lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Feb 22 09:21:42 2010 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Feb 22 13:56:51 2010 -0500 @@ -1,6 +1,7 @@ from galaxy.model import * from galaxy.model.orm import * +from galaxy.web.base import controller from galaxy.web.framework.helpers import iff from galaxy.tags.tag_handler import TagHandler from galaxy.web import url_for @@ -341,22 +342,46 @@ elif column_filter: query = query.filter( self.get_filter( user, column_filter ) ) return query + def get_filter( self, user, column_filter ): - """ Returns a SQLAlchemy criterion derived from column_filter. """ - model_class_key_field = getattr( self.model_class, self.key ) - + """ Returns a SQLAlchemy criterion derived from column_filter. """ if isinstance( column_filter, basestring ): - return func.lower( model_class_key_field ).like( "%" + column_filter.lower() + "%" ) + return self.get_single_filter( user, column_filter ) elif isinstance( column_filter, list ): clause_list = [] for filter in column_filter: - clause_list.append( func.lower( model_class_key_field ).like( "%" + filter.lower() + "%" ) ) + clause_list.append( self.get_single_filter( user, filter ) ) return and_( *clause_list ) - + + def get_single_filter( self, user, a_filter ): + """ Returns a SQLAlchemy criterion derived for a single filter. Single filter is the most basic filter--usually a string--and cannot be a list. """ + model_class_key_field = getattr( self.model_class, self.key ) + return func.lower( model_class_key_field ).like( "%" + a_filter.lower() + "%" ) + +class OwnerAnnotationColumn( TextColumn, controller.UsesAnnotations ): + """ Column that displays and filters item owner's annotations. """ + def __init__( self, col_name, key, model_class, model_annotation_association_class, filterable ): + GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable ) + self.sortable = False + self.model_annotation_association_class = model_annotation_association_class + + def get_value( self, trans, grid, item ): + """ Returns item annotation. """ + annotation = self.get_item_annotation_str( trans.sa_session, item.user, item ) + return iff( annotation, annotation, "" ) + + def get_single_filter( self, user, a_filter ): + """ Filter by annotation and annotation owner. """ + return self.model_class.annotations.any( + and_( func.lower( self.model_annotation_association_class.annotation ).like( "%" + a_filter.lower() + "%" ), + # TODO: not sure why, to filter by owner's annotations, we have to do this rather than + # 'self.model_class.user==self.model_annotation_association_class.user' + self.model_annotation_association_class.table.c.user_id==self.model_class.table.c.user_id ) ) + class CommunityTagsColumn( TextColumn ): """ Column that supports community tags. """ def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): - GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable) + GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable ) self.model_tag_association_class = model_tag_association_class # Tags cannot be sorted. self.sortable = False

1 0

[hg] galaxy 3423: Fix for displaying datasets in the bx browser.
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8d77e3acf653 changeset: 3423:8d77e3acf653 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Feb 22 09:21:42 2010 -0500 description: Fix for displaying datasets in the bx browser. diffstat: lib/galaxy/datatypes/interval.py | 2 +- lib/galaxy/datatypes/tabular.py | 2 -- 2 files changed, 1 insertions(+), 3 deletions(-) diffs (24 lines): diff -r 94741c94de0a -r 8d77e3acf653 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Mon Feb 22 08:12:03 2010 -0500 +++ b/lib/galaxy/datatypes/interval.py Mon Feb 22 09:21:42 2010 -0500 @@ -54,7 +54,7 @@ """Initialize interval datatype, by adding UCSC display apps""" Tabular.__init__(self, **kwd) self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) - self.add_display_app ( 'main', 'BX', 'as_bx_display_file', 'bx_links' ) + self.add_display_app ( 'main', 'BX', 'as_ucsc_display_file', 'bx_links' ) def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) diff -r 94741c94de0a -r 8d77e3acf653 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Mon Feb 22 08:12:03 2010 -0500 +++ b/lib/galaxy/datatypes/tabular.py Mon Feb 22 09:21:42 2010 -0500 @@ -214,8 +214,6 @@ return open( dataset.file_name ) def as_ucsc_display_file( self, dataset, **kwd ): return open( dataset.file_name ) - def as_bx_display_file( self, dataset, **kwd ): - return open( dataset.file_name ) class Taxonomy( Tabular ): def __init__(self, **kwd):

1 0

[hg] galaxy 3422: Make anchor ID/name editable in pages.
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/94741c94de0a changeset: 3422:94741c94de0a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 22 08:12:03 2010 -0500 description: Make anchor ID/name editable in pages. diffstat: templates/page/editor.mako | 3 ++- 1 files changed, 2 insertions(+), 1 deletions(-) diffs (13 lines): diff -r 831bbcccc4b2 -r 94741c94de0a templates/page/editor.mako --- a/templates/page/editor.mako Mon Feb 22 07:43:12 2010 -0500 +++ b/templates/page/editor.mako Mon Feb 22 08:12:03 2010 -0500 @@ -138,7 +138,8 @@ // Set input elt class, value. var attribute_input = $(".wym_href"); attribute_input.addClass("wym_id").removeClass("wym_href"); - attribute_input.val( attribute_input.attr('id') ); + if (selected) + attribute_input.val( $(selected).attr('id') ); // Remove link. $(this).remove();

1 0

[hg] galaxy 3421: Pack script.
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/831bbcccc4b2 changeset: 3421:831bbcccc4b2 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 22 07:43:12 2010 -0500 description: Pack script. diffstat: static/scripts/packed/galaxy.panels.js | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (8 lines): diff -r 47aa31eb9cb6 -r 831bbcccc4b2 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Mon Feb 22 07:42:07 2010 -0500 +++ b/static/scripts/packed/galaxy.panels.js Mon Feb 22 07:43:12 2010 -0500 @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(i){$("#DD-helper").show()}).bind("dragen! 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1 0

[hg] galaxy 3420: Added functionality for creating links on page...
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/47aa31eb9cb6 changeset: 3420:47aa31eb9cb6 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 22 07:42:07 2010 -0500 description: Added functionality for creating links on pages: (1) existing links are editable and (2) can create in-page, named anchors. diffstat: static/scripts/galaxy.panels.js | 5 ++- templates/page/editor.mako | 64 ++++++++++++++++++++++++++++++++-------- 2 files changed, 54 insertions(+), 15 deletions(-) diffs (119 lines): diff -r 1e23f73647bb -r 47aa31eb9cb6 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js Fri Feb 19 17:54:44 2010 -0500 +++ b/static/scripts/galaxy.panels.js Mon Feb 22 07:42:07 2010 -0500 @@ -165,7 +165,7 @@ } ); }; -function show_modal( title, body, buttons, extra_buttons ) { +function show_modal( title, body, buttons, extra_buttons, init_fn ) { if ( title ) { $( ".dialog-box" ).find( ".title" ).html( title ); $( ".dialog-box" ).find( ".unified-panel-header" ).show(); @@ -200,6 +200,9 @@ $("#overlay").show(); $(".dialog-box-container").fadeIn() } + if ( init_fn ) { + init_fn(); + } }; function show_in_overlay( options ) { diff -r 1e23f73647bb -r 47aa31eb9cb6 templates/page/editor.mako --- a/templates/page/editor.mako Fri Feb 19 17:54:44 2010 -0500 +++ b/templates/page/editor.mako Mon Feb 22 07:42:07 2010 -0500 @@ -126,6 +126,25 @@ var sStamp = wym.uniqueStamp(); var selected = wym.selected(); + // Swap out URL attribute for id/name attribute in link creation to enable anchor creation in page. + function set_link_id() + { + // When "set link id" link clicked, update UI. + $('#set_link_id').click( function() + { + // Set label. + $("#link_attribute_label").text("ID/Name"); + + // Set input elt class, value. + var attribute_input = $(".wym_href"); + attribute_input.addClass("wym_id").removeClass("wym_href"); + attribute_input.val( attribute_input.attr('id') ); + + // Remove link. + $(this).remove(); + }); + } + // LINK DIALOG if ( dialogType == WYMeditor.DIALOG_LINK ) { if(selected) { @@ -134,28 +153,45 @@ jQuery(wym._options.titleSelector).val(jQuery(selected).attr(WYMeditor.TITLE)); jQuery(wym._options.altSelector).val(jQuery(selected).attr(WYMeditor.ALT)); } + // Get current URL, title. + var curURL, curTitle; + if (selected) + { + curURL = $(selected).attr("href"); + if (curURL == undefined) + curURL = ""; + curTitle = $(selected).attr("title"); + if (curTitle == undefined) + curTitle = ""; + } show_modal( - "Link", - "<div><div><label>URL</label><br><input type='text' class='wym_href' value='' size='40' /></div>" - + "<div><label>Title</label><br><input type='text' class='wym_title' value='' size='40' /></div><div>", + "Create Link", + "<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='" + curURL + "' size='40' /></div>" + + "<div><label>Title</label><br><input type='text' class='wym_title' value='" + curTitle + "' size='40' /></div><div>", { "Make link": function() { var sUrl = jQuery(wym._options.hrefSelector).val(); - if(sUrl.length > 0) { - - wym._exec(WYMeditor.CREATE_LINK, sStamp); - - jQuery("a[href=" + sStamp + "]", wym._doc.body) - .attr(WYMeditor.HREF, sUrl) - .attr(WYMeditor.TITLE, jQuery(wym._options.titleSelector).val()); - + sUrl = ( sUrl ? sUrl : "" ); + var sName = $(".wym_id").val(); + sName = ( sName ? sName : "" ); + if ( (sUrl.length > 0) || (sName.length > 0) ) { + // Create link. + wym._exec(WYMeditor.CREATE_LINK, sStamp); + + var link = jQuery("a[href=" + sStamp + "]", wym._doc.body); + link.attr(WYMeditor.HREF, sUrl); + link.attr(WYMeditor.TITLE, jQuery(wym._options.titleSelector).val()); + if (sName.length > 0) + link.attr("id", sName); } hide_modal(); }, - "Cancel:": function() { + "Cancel": function() { hide_modal(); } - } + }, + {}, + set_link_id ); return; } @@ -668,7 +704,7 @@ ##"Embed Page": function() { ## editor.dialog(Galaxy.DIALOG_EMBED_PAGE); ##} - }); + }); }); </script> </%def>

1 0

[hg] galaxy 3419: trackster:
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1e23f73647bb changeset: 3419:1e23f73647bb user: Kanwei Li <kanwei(a)gmail.com> date: Fri Feb 19 17:54:44 2010 -0500 description: trackster: - Refactor - Focus on new browser text - Fixed linetrack bug when switching chroms diffstat: static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 152 +++++++++++++++++------------------- templates/tracks/browser.mako | 13 +- templates/tracks/new_browser.mako | 2 +- 4 files changed, 83 insertions(+), 86 deletions(-) diffs (313 lines): diff -r 879432079138 -r 1e23f73647bb static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Fri Feb 19 14:34:25 2010 -0500 +++ b/static/scripts/packed/trackster.js Fri Feb 19 17:54:44 2010 -0500 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_! img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tr! acks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a. track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[a]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");var d=[];var c=$("#viewport > div").sort(function(g,f){return b.indexOf($(g).attr("id"))>b.indexOf($(f).attr("id"))});$("#viewport > div").remove();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.ma! x(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.con! tent_div=$("<div class='track-content'>");this.container_div=$("<div>< /div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_! element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height)}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.ad! dClass("line-track");this.dataset_id=a;this.prefs={min_value:undefined ,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){this.data_queue={};this.data_cache=new Cache(CACHED_DATA);var a=this,b=a.view.tracks.indexOf(a);a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d.length===0||d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");if(a.prefs.min_value===undefined||a.prefs.max_value===undefined){a.prefs.min_value=d! .min;a.prefs.max_value=d.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;if($("#linetrack_"+b+"_minval").length===0){var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)}a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(this.vertical_range===undefined){! return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canva s>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top:0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f}}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("<div></div>").addClass("form-row");var e="track_"+j+"_minval",g="track_"+j+"_maxval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("<input></input>").attr("id",e).val(b),d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("! <input></input>").attr("id",g).val(f);return a.append(h).append(i).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_o! ffset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};thi s.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.adClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=th! is,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!=! =undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(this.inc_slo ts[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slots[this.v! iew.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></canvas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.view.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.bloc! ks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{ if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.length;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.ceil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P);p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e=$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);! return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.prefs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color! ;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A") .width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file +var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_! img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tr! acks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a. track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[a]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");var d=[];var c=$("#viewport > div").sort(function(g,f){return b.indexOf($(g).attr("id"))>b.indexOf($(f).attr("id"))});$("#viewport > div").remove();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.ma! x(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.con! tent_div=$("<div class='track-content'>");this.container_div=$("<div>< /div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d.length===0||d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");b(d);a.draw()}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.! high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden! =true;this.container_div.addClass("label-track")};$.extend(LabelTrack. prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:fu! nction(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(d){if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=d.min;a.prefs.max_value=d.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;! if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer: this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution,},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(this.vertical_range===undefined){return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canvas>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top:0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f}}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("<div></div>").addClass("form-row");var e="track_"+j+"_! minval",g="track_"+j+"_maxval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("<input></input>").attr("id",e).val(b),d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(i).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px! =100;this.container_div.addClass("feature-track");this.dataset_id=a;th is.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;this.init_each({indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){a.values=b;a.calc_slots();a.slots=a.zo_slots})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},! function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(this.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)! *h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;wh ile(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slots[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></can! vas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.view.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.blocks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.le! ngth;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.c eil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P);p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e=$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.p! refs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(! Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l. uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file diff -r 879432079138 -r 1e23f73647bb static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Feb 19 14:34:25 2010 -0500 +++ b/static/scripts/trackster.js Fri Feb 19 17:54:44 2010 -0500 @@ -198,6 +198,39 @@ this.content_div = $("<div class='track-content'>"); this.container_div = $("<div></div>").addClass('track').append( this.header_div ).append( this.content_div ); this.parent_element.append( this.container_div ); + }, + init_each: function(params, success_fn) { + var track = this; + track.data_queue = {}; + track.tile_cache.clear(); + track.data_cache.clear(); + track.content_div.css( "height", "30px" ); + track.content_div.text(DATA_LOADING); + track.container_div.removeClass("nodata error pending"); + + if (track.view.chrom) { + $.getJSON( data_url, params, function ( data ) { + if (!data || data == "error") { + track.container_div.addClass("error"); + track.content_div.text(DATA_ERROR); + } else if (data.length === 0 || data == "no data") { + track.container_div.addClass("nodata"); + track.content_div.text(DATA_NONE); + } else if (data == "pending") { + track.container_div.addClass("pending"); + track.content_div.text(DATA_PENDING); + setTimeout(function() { track.init(); }, 5000); + } else { + track.content_div.text(""); + track.content_div.css( "height", track.height_px + "px" ); + success_fn(data); + track.draw(); + } + }); + } else { + track.container_div.addClass("nodata"); + track.content_div.text(DATA_NONE); + } } }); @@ -233,9 +266,7 @@ if (this.left_offset) { left -= this.left_offset; } - cached.css( { - left: left - }); + cached.css({ left: left }); // Our responsibility to move the element to the new parent parent_element.append( cached ); this.max_height = Math.max( this.max_height, cached.height() ); @@ -252,7 +283,7 @@ if ( tile_element ) { track.tile_cache.set(key, tile_element); track.max_height = Math.max( track.max_height, tile_element.height() ); - track.content_div.css( "height", track.max_height ); + track.content_div.css( "height", track.max_height + "px"); } } }, 50); @@ -289,7 +320,6 @@ var LineTrack = function ( name, dataset_id, indexer, prefs ) { this.track_type = "LineTrack"; - this.tile_cache = new Cache(CACHED_TILES_LINE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -297,61 +327,42 @@ this.height_px = 100; this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; + this.data_cache = new Cache(CACHED_DATA); + this.tile_cache = new Cache(CACHED_TILES_LINE); this.prefs = { 'min_value': undefined, 'max_value': undefined }; if (prefs.min_value !== undefined) { this.prefs.min_value = prefs.min_value; } if (prefs.max_value !== undefined) { this.prefs.max_value = prefs.max_value; } }; $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { - this.data_queue = {}; - this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of - // asynchronous calls var track = this, track_id = track.view.tracks.indexOf(track); - track.content_div.text(DATA_LOADING); - track.container_div.removeClass("nodata error pending"); - $.getJSON( data_url, { stats: true, indexer: track.indexer, + track.vertical_range = undefined; + this.init_each({ stats: true, indexer: track.indexer, chrom: track.view.chrom, low: null, high: null, - dataset_id: track.dataset_id }, function ( data ) { - if (!data || data == "error") { - track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); - } else if (data.length === 0 || data == "no data") { - track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); - } else if (data == "pending") { - track.container_div.addClass("pending"); - track.content_div.text(DATA_PENDING); - setTimeout(function() { track.init(); }, 5000); - } else { - track.content_div.text(""); - track.content_div.css( "height", track.height_px + "px" ); - - if (track.prefs.min_value === undefined || track.prefs.max_value === undefined) { - track.prefs.min_value = data.min; - track.prefs.max_value = data.max; - - // Update the config - $('#track_' + track_id + '_minval').val(track.prefs.min_value); - $('#track_' + track_id + '_maxval').val(track.prefs.max_value); - } - track.vertical_range = track.prefs.max_value - track.prefs.min_value; - - // Draw y-axis labels if necessary - if ( $('#linetrack_' + track_id + '_minval').length === 0) { - var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); - var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); - - max_label.css({ position: "relative", top: "25px" }); - max_label.prependTo(track.container_div); - - min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); - min_label.prependTo(track.container_div); - } - - track.draw(); + dataset_id: track.dataset_id }, function(data) { + if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { + track.prefs.min_value = data.min; + track.prefs.max_value = data.max; + // Update the config + $('#track_' + track_id + '_minval').val(track.prefs.min_value); + $('#track_' + track_id + '_maxval').val(track.prefs.max_value); } + track.vertical_range = track.prefs.max_value - track.prefs.min_value; + + // Draw y-axis labels if necessary + $('#linetrack_' + track_id + '_minval').remove(); + $('#linetrack_' + track_id + '_maxval').remove(); + + var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); + var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); + + max_label.css({ position: "relative", top: "25px" }); + max_label.prependTo(track.container_div); + + min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); + min_label.prependTo(track.container_div); }); }, get_data: function( resolution, position ) { @@ -362,9 +373,9 @@ if (!track.data_queue[key]) { track.data_queue[key] = true; - $.getJSON( data_url, { indexer: this.indexer, chrom: this.view.chrom, - low: low, high: high, dataset_id: this.dataset_id, - resolution: this.view.resolution }, function ( data ) { + $.getJSON( data_url, { "indexer": this.indexer, "chrom": this.view.chrom, + "low": low, "high": high, "dataset_id": this.dataset_id, + "resolution": this.view.resolution, }, function (data) { track.data_cache.set(key, data); delete track.data_queue[key]; track.draw(); @@ -392,7 +403,7 @@ top: 0, left: ( tile_low - this.view.low ) * w_scale }); - + canvas.get(0).width = Math.ceil( tile_length * w_scale ); canvas.get(0).height = this.height_px; var ctx = canvas.get(0).getContext("2d"), @@ -462,7 +473,6 @@ var FeatureTrack = function ( name, dataset_id, indexer, prefs ) { this.track_type = "FeatureTrack"; - this.tile_cache = new Cache(CACHED_TILES_FEATURE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -480,7 +490,9 @@ this.inc_slots = {}; this.data_queue = {}; this.s_e_by_tile = {}; + this.tile_cache = new Cache(CACHED_TILES_FEATURE); this.data_cache = new Cache(20); + this.prefs = { 'block_color': 'black', 'label_color': 'black' }; if (prefs.block_color !== undefined) { this.prefs.block_color = prefs.block_color; } if (prefs.label_color !== undefined) { this.prefs.label_color = prefs.label_color; } @@ -489,33 +501,15 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { var track = this; - track.content_div.text(DATA_LOADING); - track.container_div.removeClass("nodata error pending"); - $.getJSON( data_url, { indexer: track.indexer, low: track.view.max_low, - high: track.view.max_high, dataset_id: track.dataset_id, - chrom: track.view.chrom }, function ( data ) { - if (data == "error") { - track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); - } else if (data.length === 0 || data == "no data") { - track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); - } else if (data == "pending") { - track.container_div.adClass("pending"); - track.content_div.text(DATA_PENDING); - setTimeout(function() { track.init(); }, 5000); - } else { - track.content_div.text(""); - track.content_div.css( "height", track.height_px + "px" ); - track.values = data; - track.calc_slots(); - track.slots = track.zo_slots; - track.draw(); - } + this.init_each({ indexer: track.indexer, low: track.view.max_low, + high: track.view.max_high, dataset_id: track.dataset_id, + chrom: track.view.chrom }, function (data) { + track.values = data; + track.calc_slots(); + track.slots = track.zo_slots; }); }, get_data: function( low, high ) { - // console.log("getting: ", low, high); var track = this, key = low + '_' + high; @@ -523,7 +517,7 @@ track.data_queue[key] = true; $.getJSON( data_url, { indexer: track.indexer, chrom: track.view.chrom, low: low, high: high, dataset_id: track.dataset_id, - include_blocks: true }, function ( data ) { + include_blocks: true }, function (data) { track.data_cache.set(key, data); // console.log("datacache", track.data_cache.get(key)); delete track.data_queue[key]; diff -r 879432079138 -r 1e23f73647bb templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri Feb 19 14:34:25 2010 -0500 +++ b/templates/tracks/browser.mako Fri Feb 19 17:54:44 2010 -0500 @@ -107,8 +107,10 @@ error: function() { alert( "Couldn't create new browser" ) }, success: function(form_html) { show_modal("New Track Browser", form_html, { + "Cancel": function() { window.location = "/"; }, "Continue": continue_fn }); + $("#new-title").focus(); } }); %endif @@ -292,7 +294,7 @@ track.init(); } } - // view.redraw(); + view.redraw(); }); }); @@ -301,8 +303,9 @@ var track_id = track.track_id, label = $('<label for="track_' + track_id + 'title">' + track.name + '</label>'), title = $('<div class="historyItemTitle"></div>'), - del_icon = $('<a style="display:block; float:right" href="#" class="icon-button delete" />'), - edit_icon = $('<a style="display:block; float:right" href="#" class="icon-button edit" />'), + icon_div = $('<div class="historyItemButtons"></div>'); + del_icon = $('<a href="#" class="icon-button delete" />'), + edit_icon = $('<a href="#" class="icon-button edit" />'), body = $('<div class="historyItemBody"></div>'), checkbox = $('<input type="checkbox" checked="checked"></input>').attr("id", "track_" + track_id + "title"), li = $('<li class="sortable"></li>').attr("id", "track_" + track_id), @@ -318,8 +321,8 @@ view.remove_track(track); view.update_options(); }); - - title.append(label).append(del_icon).append(edit_icon); + icon_div.append(edit_icon).append(del_icon); + title.append(label).prepend(icon_div); if (track.gen_options) { editable.append(track.gen_options(track_id)).appendTo(body); } diff -r 879432079138 -r 1e23f73647bb templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako Fri Feb 19 14:34:25 2010 -0500 +++ b/templates/tracks/new_browser.mako Fri Feb 19 17:54:44 2010 -0500 @@ -2,7 +2,7 @@ <div class="form-row"> <label for="title">Browser name:</label> <div class="form-row-input"> - <input type="text" name="title" id="new-title" value="Unnamed Browser"></input> + <input type="text" name="title" id="new-title" value="Unnamed"></input> </div> <div style="clear: both;"></div> </div>

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[hg] galaxy 3418: Fix MySQL_python static egg on OS X
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/879432079138 changeset: 3418:879432079138 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Feb 19 14:34:25 2010 -0500 description: Fix MySQL_python static egg on OS X diffstat: eggs.ini | 2 +- scripts/scramble/scripts/MySQL_python.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diffs (24 lines): diff -r 68eaeb1b1d69 -r 879432079138 eggs.ini --- a/eggs.ini Fri Feb 19 11:29:25 2010 -0500 +++ b/eggs.ini Fri Feb 19 14:34:25 2010 -0500 @@ -71,7 +71,7 @@ bx_python = http://bitbucket.org/james_taylor/bx-python/get/3b9d30e47619.bz2 Cheetah = http://pypi.python.org/packages/source/C/Cheetah/Cheetah-2.2.2.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz -MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz +MySQL_python = http://downloads.sourceforge.net/project/mysql-python/mysql-python/1.2.2/My… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz pexpect = http://pypi.python.org/packages/source/p/pexpect/pexpect-2.4.tar.gz psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz ftp://ftp-archives.postgresql.org/pub/source/v8.2.6/postgresql-8.2.6.tar.bz2 diff -r 68eaeb1b1d69 -r 879432079138 scripts/scramble/scripts/MySQL_python.py --- a/scripts/scramble/scripts/MySQL_python.py Fri Feb 19 11:29:25 2010 -0500 +++ b/scripts/scramble/scripts/MySQL_python.py Fri Feb 19 14:34:25 2010 -0500 @@ -80,7 +80,7 @@ CONFIGURE += "CXXFLAGS='-O -g -isysroot /Developer/SDKs/MacOSX10.4u.sdk -arch i386 -arch ppc' " CONFIGURE += "LDFLAGS='-arch i386 -arch ppc' " CONFIGURE += "LD='gcc -mmacosx-version-min=10.4 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -nostartfiles -arch i386 -arch ppc' " - CONFIGURE += "./configure --prefix=%s/mysql --disable-dependency-tracking --without-server --without-uca --without-libwrap " %os.getcwd() + CONFIGURE += "./configure --prefix=%s/mysql --disable-dependency-tracking --disable-shared --without-server --without-uca --without-libwrap " %os.getcwd() CONFIGURE += "--without-extra-tools --without-openssl --without-yassl --without-docs --without-man --without-bench --enable-thread-safe-client" else: CONFIGURE = "CFLAGS='-fPIC' ./configure --prefix=%s/mysql --disable-shared --without-server --without-uca --without-libwrap " %os.getcwd()

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[hg] galaxy 3417: Fix bug so that, when a user submits edits to ...
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/68eaeb1b1d69 changeset: 3417:68eaeb1b1d69 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 19 11:29:25 2010 -0500 description: Fix bug so that, when a user submits edits to a page's attributes, he is redicted to his page list. diffstat: lib/galaxy/web/controllers/page.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (14 lines): diff -r d995557d383b -r 68eaeb1b1d69 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Fri Feb 19 10:01:33 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Fri Feb 19 11:29:25 2010 -0500 @@ -409,8 +409,8 @@ page.title = page_title page.slug = page_slug session.flush() - # Display the management page - return trans.response.send_redirect( web.url_for( action='index' ) ) + # Redirect to page list. + return trans.response.send_redirect( web.url_for( action='list' ) ) else: page_title = page.title page_slug = page.slug

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Re: [galaxy-dev] Sqlite to MYSQL conversion in galaxy
by Roy Weckiewicz 23 Feb '10

23 Feb '10

Hi Nate, Sorry I had an empty database set the first time (which was giving me the revision error): Part of my problem has been trying to convert the db from sqlite to mysql -- the closest I got using scripts was 40 tables in the database: datasetdataset_permissionsdefault_history_permissions default_user_permissionseventform_definition_currentgalaxy_group galaxy_sessiongalaxy_session_to_historygalaxy_usergroup_role_association historyhistory_dataset_associationhistory_user_share_association implicitly_converted_dataset_associationjobjob_external_output_metadata job_parameterjob_to_input_datasetjob_to_output_datasetlibrarylibrary_dataset library_dataset_dataset_association library_dataset_dataset_association_permissionslibrary_dataset_permissions library_folderlibrary_folder_permissionslibrary_permissionsmetadata_file migrate_versionrolestored_workflowstored_workflow_menu_entry stored_workflow_user_share_connectionuser_group_association user_role_associationvalidation_errorworkflowworkflow_step workflow_step_connection When I try to run it linked to the above database I get the following error: galaxy.model.migrate.check DEBUG 2010-02-19 13:42:18,987 MySQL_python egg successfully loaded for mysql dialect Traceback (most recent call last): File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py", line 102, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest ) ) Exception: Your database has version '22' but this code expects version '39'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. So when I try to run the manage_db.sh I get: 22 -> 23... Migration script to add columns for tracking whether pages are deleted and publicly accessible. Traceback (most recent call last): File "./scripts/manage_db.py", line 45, in <module> main( repository='lib/galaxy/model/migrate', url=db_url ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py", line 349, in _migrate schema.runchange(ver, change, changeset.step) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/script/py.py", line 101, in run func() File "lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py", line 20, in upgrade Page_table = Table( "page", metadata, autoload=True ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1265, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py", line 1664, in reflecttable sql = self._show_create_table(connection, table, charset) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py", line 1835, in _show_create_table raise exc.NoSuchTableError(full_name) sqlalchemy.exc.NoSuchTableError: page I guess my problem all along is not having the full table schema for use in mySQL. Rgds, Roy Weckiewicz On Fri, Feb 19, 2010 at 1:33 PM, Nate Coraor <nate(a)bx.psu.edu> wrote: > Roy Weckiewicz wrote: > >> Thanks again Nate, >> >> I just tried the one you sent me - it seems I just have a database >> revision issue: >> >> Traceback (most recent call last): >> File >> "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py", >> line 61, in app_factory >> app = UniverseApplication( global_conf = global_conf, **kwargs ) >> File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py", >> line 28, in __init__ >> create_or_verify_database( db_url, self.config.database_engine_options >> ) >> File >> "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py", >> line 72, in create_or_verify_database >> raise Exception( "Your database is older than hg revision >> 1464:c7acaa1bb88f and will need to be updated manually" ) >> Exception: Your database is older than hg revision 1464:c7acaa1bb88f and >> will need to be updated manually >> > > Hi Roy, > > Is this the database you converted from sqlite? Does it include the > 'migrate_version' table? Could you paste the output of 'SHOW TABLES;'? > > Thanks, > > >> >> Rgds, >> >> >> Roy Weckiewicz >> >> >> On Fri, Feb 19, 2010 at 1:28 PM, Nate Coraor <nate(a)bx.psu.edu <mailto: >> nate(a)bx.psu.edu>> wrote: >> >> Roy Weckiewicz wrote: >> >> What's strange is that eventhough the file name on the egg is >> MySQL*fat-ucs2.egg the error still reports the file in question >> as MySQL*fat.egg -- I've tried renaming the egg to match the >> original file, but it didn't seem to make a difference. >> Furthermore, when I run.sh, the program will create a directory >> in home called .python-eggs/ containing the _MySQL.so file, >> among other things - Will I have to add a different URL to the >> eggs.ini to keep it from re-downloading the old file? >> >> >> Ah, sorry, that egg relies on some uncommitted patches. I've >> rebuilt it using a clean checkout, could you try this one instead?: >> >> >> http://www.bx.psu.edu/~nate/galaxy/MySQL_python-1.2.2_5.0.67_static-py2.5-m… >> >> Thanks, >> --nate >> >> >> >> >> -- >> Roy Weckiewicz >> Texas A&M University >> > > -- Roy Weckiewicz Texas A&M University

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