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Re: [galaxy-dev] Request for showing output plots in galaxy frame
by James Taylor 26 Nov '09

26 Nov '09

PNG and JPG should already work fine as well. The only thing that may require some tweaking is to allow a choice between two output formats, but you can certainly do that using a post job hook to change what Galaxy thinks the datatype is. On Nov 26, 2009, at 11:26 AM, matthew.iyer(a)gmail.com wrote: > Would the system be able to handle PNG or JPG images too? I want to > integrate a plotting script using matplotlib and can easily follow > the examples that already exist. If I can add an option for the > user to select png or pdf output that would be ideal. > > That way the user can use PNG for just viewing the data without any > browser issues and PDF for downloading.

1 0

Removing/Hiding shared workflows/histories
by Assaf Gordon 25 Nov '09

25 Nov '09

Hello, I've finally pulled the latest changes - kudos for the history search feature - I like it a lot. Now, as usual, some usability questions: 1. How do I remove or hide or delete workflows and histories other people shared with me ? Sounds like a silly question, but it's an aspect in *my* galaxy account over which I have absolutely no control. I found no way to remove a shared workflow except asking the person who shared it with me to stop sharing it. If somebody wanted to play a trick on me, he could share hundreds of histories with me and I'll have no control over it - making it hard for me to find the actual shared histories I'm looking for (this is of course an absurd scenario, but I'm trying to make a point). The real-world scenario is that I'm the go-to guy for galaxy in our little lab, and everybody who has a problem in his history or workflow shares it with me and ask me to take a look at it. After I'm done fixing it - I don't want to see it any more. Asking to user to "unshare" the history is technically OK, but I don't think that's the way it should work. If I don't want to see a history/workflow in my galaxy account, I should be able to do it myself, without asking it from other users. 2. consistency in the workflow management screen "Workflows shared by others" appear as a link (underlined) - clicking on the does the default (and expected) action of "run workflow". "Your workflows" (mine, that is) - are not links, although they do get a rounded-box-frame when hovered upon - clicking on them does nothing. One has to pin-point the tiny triangle to run/edit/etc on my workflow. If one clicks on "Workflows"->"All Workflows" from the tools menu, then all workflows appear as clickable-links. So it's only a tiny matter of consistency. Thanks, -gordon.

2 2

Request for showing output plots in galaxy frame
by Matthew Iyer 25 Nov '09

25 Nov '09

Dear Galaxy team, My name is Matthew Iyer and I am a Bioinformatics PhD student at the University of Michigan. I am doing my thesis in Arul Chinnaiyan's cancer research lab and generally work with NGS data. I am interested in incorporating galaxy for displaying customized bar/scatter plots showing gene expression levels for many samples. I have downloaded and am successfully using a galaxy locally and I really love it. However, all of the graph display/plotting tools create images (PDF) for download. Of course, the option to download the images is important, but is it also possible to display these images in the main window? This feature would make a crucial difference for me and would create many users of galaxy in our lab. I am a python programmer myself and would be interested in contributing to this effort rather than developing this in a separate framework. I am sure that it is a simple modification to show an image in the main window. I look forward to working with you and using galaxy! Best, Matthew

3 2

Writing functional test for galaxy tools
by Vipin Thankam Sreedharan 25 Nov '09

25 Nov '09

Dear Galaxy development team, I am working with Gunnar Raetsch's group in Tuebingen and now I am writing functional test for mGene modules in our galaxy instance. Here my tools will automatically create an output directory and write all output files into that. The tool will keep most of its output files behind the galaxy screen. User will be able to see a summary file for his/her experiment. So my question is simple. Whether do you have any system to perform a functional test for such kind of situations? I would like to hear from you. Many thanks, Vipin T S

2 1

About the Database schema
by sondos seif 24 Nov '09

24 Nov '09

Dear Galaxy Team, I wanted to know If there is any schema that I can have for Galaxy's DB. Thanks in advance, -- Sondos Seif El-Din

2 1

FASTX-Toolkit v0.0.11
by Assaf Gordon 24 Nov '09

24 Nov '09

Hello, A new version of FASTX-Toolkit is available for download at http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/index.html Improvements include: * fastx_collapser can now re-collapse an already-collapsed FASTA file. you can collapse+trim+collapse without losing counts or getting error messages. * new tool: fastx_uncollapser uncollapses a FASTA file (reverse the effect of fastx_collapser). This tool can also uncollapse a tabular file with collapsed sequence-identifiers. In galaxy these are split into two separate tools: http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/galaxy.html#fasta_un… http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/galaxy.html#seqid_un… On the command line, it's the same program. * new tool: fastq quality trimmer trims a FASTQ file based on quality score cut-off. http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/galaxy.html#fastq_qu… (tool suggested by Matthew Baranski). * fastx_trimmer can now trim N bases from the end of the sequence (instead of having to specify absolute length). In Galaxy, this is a separate tool: http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/galaxy.html#fastx_tr… On the command line, it's the same program. (option suggested by Matthew Baranski). * fastx_quality_stats supports new format with statistics per-nucleotide. (so you can find avg/min/max/med quality of each nucleotide in each cycle). * Fixed several compilation errors and warnings on different platforms. Comments are welcomed, -gordon.

1 0

[hg] galaxy 3117: Rename test files for taxonomy tools and set f...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/82b63d47a0d8 changeset: 3117:82b63d47a0d8 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Nov 20 15:35:30 2009 -0500 description: Rename test files for taxonomy tools and set ftype for test's input datasets. diffstat: test-data/find_diag_hits.dat | 2 - test-data/find_diag_hits.tabular | 2 + test-data/poisson2test1.out | 5 -- test-data/poisson2test1.tabular | 5 ++ test-data/poisson2test1.txt | 5 -- test-data/poisson2test1_out.tabular | 5 ++ test-data/poisson2test2.out | 52 -------------------------- test-data/poisson2test2.tabular | 52 ++++++++++++++++++++++++++ test-data/poisson2test2.txt | 52 -------------------------- test-data/poisson2test2_out.tabular | 52 ++++++++++++++++++++++++++ test-data/t2t_report.dat | 15 ------- test-data/t2t_report.tabular | 15 +++++++ test-data/taxonomy2gi-input.tabular | 4 ++ test-data/taxonomy2gi-input.txt | 4 -- test-data/taxonomy2gi-output.tabular | 4 ++ test-data/taxonomy2gi-output.txt | 4 -- test-data/taxonomyGI.dat | 5 -- test-data/taxonomyGI.tabular | 5 ++ test-data/taxonomyGI.taxonomy | 5 ++ test-data/taxonomyGI.txt | 5 -- tools/taxonomy/example_dataset_missing_nodes.txt | 6 --- tools/taxonomy/find_diag_hits.xml | 4 +- tools/taxonomy/gi2taxonomy.xml | 4 +- tools/taxonomy/poisson2test.xml | 8 ++-- tools/taxonomy/t2t_report.xml | 4 +- 25 files changed, 159 insertions(+), 165 deletions(-) diffs (467 lines): diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/find_diag_hits.dat --- a/test-data/find_diag_hits.dat Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Primates 4 order -Homo 2 genus diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/find_diag_hits.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_diag_hits.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,2 @@ +Primates 4 order +Homo 2 genus diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test1.out --- a/test-data/poisson2test1.out Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -Acinetobacter 37 7 2.109 2.315 0.017468 0.010302 0.087342 0.051510 -Acyrthosiphon 70 21 1.549 1.612 0.060722 0.053481 0.303609 0.267406 -aedes 61 13 2.425 2.625 0.007645 0.004329 0.038223 0.021643 -Aeromonas 169 0 8.623 14.372 0.000000 0.000000 0.000000 0.000000 -anopheles 145 97 -3.217 -3.102 0.000647 0.000960 0.003234 0.004801 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poisson2test1.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,5 @@ +Acinetobacter 37 7 +Acyrthosiphon 70 21 +aedes 61 13 +Aeromonas 169 0 +anopheles 145 97 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test1.txt --- a/test-data/poisson2test1.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -Acinetobacter 37 7 -Acyrthosiphon 70 21 -aedes 61 13 -Aeromonas 169 0 -anopheles 145 97 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test1_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poisson2test1_out.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,5 @@ +Acinetobacter 37 7 2.109 2.315 0.017468 0.010302 0.087342 0.051510 +Acyrthosiphon 70 21 1.549 1.612 0.060722 0.053481 0.303609 0.267406 +aedes 61 13 2.425 2.625 0.007645 0.004329 0.038223 0.021643 +Aeromonas 169 0 8.623 14.372 0.000000 0.000000 0.000000 0.000000 +anopheles 145 97 -3.217 -3.102 0.000647 0.000960 0.003234 0.004801 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test2.out --- a/test-data/poisson2test2.out Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -Acyrthosiphon pisum 55 54 -4.303 -4.049 0.000008 0.000026 0.000438 0.001340 -Aedes aegypti 246 72 3.064 3.198 0.001093 0.000693 0.056838 0.036029 -Anopheles gambiae 337 168 -1.323 -1.307 0.092930 0.095535 1.000000 1.000000 -Apis mellifera 33 11 0.800 0.823 0.211855 0.205213 1.000000 1.000000 -Aspergillus niger 292 29 8.371 9.916 0.000000 0.000000 0.000000 0.000000 -Batrachochytrium dendrobatidis 17 14 -1.765 -1.678 0.038749 0.046690 1.000000 1.000000 -Bombyx mori 2 16 5.373 5.103 0.000000 0.000000 0.000002 0.000009 -Bos taurus 16 71 10.338 9.621 0.000000 0.000000 0.000000 0.000000 -Branchiostoma floridae 44 1 4.126 5.667 0.000018 0.000000 0.000959 0.000000 -Caenorhabditis briggsae 269 121 -0.202 -0.201 0.420141 0.420309 1.000000 1.000000 -Caenorhabditis remanei 35 29 -2.563 -2.435 0.005191 0.007450 0.269927 0.387398 -Chlamydomonas reinhardtii 85 13 3.716 4.183 0.000101 0.000014 0.005267 0.000747 -Citrus sinensis 14 2 1.568 1.780 0.058457 0.037576 1.000000 1.000000 -Culex pipiens 408 81 6.717 7.331 0.000000 0.000000 0.000000 0.000000 -Daphnia pulex 213 75 1.663 1.701 0.048160 0.044463 1.000000 1.000000 -Drosophila ananassae 3 20 5.872 5.539 0.000000 0.000000 0.000000 0.000001 -Drosophila grimshawi 14 10 -1.182 -1.134 0.118667 0.128417 1.000000 1.000000 -Drosophila pseudoobscura 28 22 -2.064 -1.967 0.019519 0.024570 1.000000 1.000000 -Drosophila willistoni 4 18 5.220 4.860 0.000000 0.000001 0.000005 0.000031 -Emiliania huxleyi 56 13 2.113 2.264 0.017321 0.011791 0.900675 0.613145 -Glycine max 4019 1831 -1.235 -1.231 0.108478 0.109251 1.000000 1.000000 -Helobdella robusta 33 1 3.496 4.684 0.000237 0.000001 0.012302 0.000073 -Homo sapiens 59 6 3.732 4.409 0.000095 0.000005 0.004933 0.000270 -Hyaloperonospora parasitica 48 10 2.201 2.389 0.013860 0.008448 0.720722 0.439307 -Hydra magnipapillata 9 65 10.697 10.120 0.000000 0.000000 0.000000 0.000000 -Medicago truncatula 62 42 -2.176 -2.096 0.014777 0.018033 0.768379 0.937696 -Mimulus guttatus 12 9 -1.224 -1.170 0.110516 0.120942 1.000000 1.000000 -Mus musculus 18 5 0.918 0.964 0.179337 0.167614 1.000000 1.000000 -Mycosphaerella fijiensis 42 7 2.472 2.755 0.006711 0.002933 0.348951 0.152533 -Nasonia vitripennis 10 12 2.443 2.277 0.007288 0.011379 0.378990 0.591708 -Nectria haematococca 67 2 4.987 6.692 0.000000 0.000000 0.000016 0.000000 -Oryza sativa 6068 2561 1.768 1.775 0.038558 0.037957 1.000000 1.000000 -Paramecium tetraurelia 749 296 1.565 1.582 0.058782 0.056837 1.000000 1.000000 -Pediculus humanus 49 40 -2.947 -2.802 0.001606 0.002538 0.083501 0.131991 -Phakopsora pachyrhizi 66 53 -3.311 -3.152 0.000464 0.000811 0.024152 0.042153 -Physcomitrella patens 304 36 7.993 9.276 0.000000 0.000000 0.000000 0.000000 -Phytophthora ramorum 174 56 2.044 2.111 0.020488 0.017390 1.000000 0.904295 -Phytophthora sojae 10 0 2.098 3.496 0.017969 0.000236 0.934412 0.012278 -Pinus taeda 0 26 7.687 8.498 0.000000 0.000000 0.000000 0.000000 -Populus balsamifera 43 4 3.281 3.916 0.000517 0.000045 0.026903 0.002339 -Pristionchus pacificus 4 14 4.349 4.025 0.000007 0.000028 0.000355 0.001481 -Rattus norvegicus 11 3 0.741 0.780 0.229238 0.217720 1.000000 1.000000 -Rhodnius prolixus 24 17 -1.516 -1.456 0.064729 0.072722 1.000000 1.000000 -Ricinus communis 75 14 3.036 3.338 0.001198 0.000422 0.062288 0.021926 -Schistosoma mansoni 80 15 3.124 3.433 0.000891 0.000298 0.046328 0.015504 -Schmidtea mediterranea 307 277 -8.853 -8.368 0.000000 0.000000 0.000000 0.000000 -Selaginella moellendorffii 27 10 0.466 0.474 0.320629 0.317714 1.000000 1.000000 -Sorghum bicolor 306 72 4.857 5.197 0.000001 0.000000 0.000031 0.000005 -Strongylocentrotus purpuratus 182 34 4.727 5.196 0.000001 0.000000 0.000059 0.000005 -Trypanosoma cruzi 23 0 3.181 5.302 0.000733 0.000000 0.038134 0.000003 -Volvox carteri 64 2 4.854 6.487 0.000001 0.000000 0.000031 0.000000 -Zea mays 583 263 -0.336 -0.335 0.368487 0.368792 1.000000 1.000000 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poisson2test2.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,52 @@ +Acyrthosiphon pisum 55 54 +Aedes aegypti 246 72 +Anopheles gambiae 337 168 +Apis mellifera 33 11 +Aspergillus niger 292 29 +Batrachochytrium dendrobatidis 17 14 +Bombyx mori 2 16 +Bos taurus 16 71 +Branchiostoma floridae 44 1 +Caenorhabditis briggsae 269 121 +Caenorhabditis remanei 35 29 +Chlamydomonas reinhardtii 85 13 +Citrus sinensis 14 2 +Culex pipiens 408 81 +Daphnia pulex 213 75 +Drosophila ananassae 3 20 +Drosophila grimshawi 14 10 +Drosophila pseudoobscura 28 22 +Drosophila willistoni 4 18 +Emiliania huxleyi 56 13 +Glycine max 4019 1831 +Helobdella robusta 33 1 +Homo sapiens 59 6 +Hyaloperonospora parasitica 48 10 +Hydra magnipapillata 9 65 +Medicago truncatula 62 42 +Mimulus guttatus 12 9 +Mus musculus 18 5 +Mycosphaerella fijiensis 42 7 +Nasonia vitripennis 10 12 +Nectria haematococca 67 2 +Oryza sativa 6068 2561 +Paramecium tetraurelia 749 296 +Pediculus humanus 49 40 +Phakopsora pachyrhizi 66 53 +Physcomitrella patens 304 36 +Phytophthora ramorum 174 56 +Phytophthora sojae 10 0 +Pinus taeda 0 26 +Populus balsamifera 43 4 +Pristionchus pacificus 4 14 +Rattus norvegicus 11 3 +Rhodnius prolixus 24 17 +Ricinus communis 75 14 +Schistosoma mansoni 80 15 +Schmidtea mediterranea 307 277 +Selaginella moellendorffii 27 10 +Sorghum bicolor 306 72 +Strongylocentrotus purpuratus 182 34 +Trypanosoma cruzi 23 0 +Volvox carteri 64 2 +Zea mays 583 263 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test2.txt --- a/test-data/poisson2test2.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -Acyrthosiphon pisum 55 54 -Aedes aegypti 246 72 -Anopheles gambiae 337 168 -Apis mellifera 33 11 -Aspergillus niger 292 29 -Batrachochytrium dendrobatidis 17 14 -Bombyx mori 2 16 -Bos taurus 16 71 -Branchiostoma floridae 44 1 -Caenorhabditis briggsae 269 121 -Caenorhabditis remanei 35 29 -Chlamydomonas reinhardtii 85 13 -Citrus sinensis 14 2 -Culex pipiens 408 81 -Daphnia pulex 213 75 -Drosophila ananassae 3 20 -Drosophila grimshawi 14 10 -Drosophila pseudoobscura 28 22 -Drosophila willistoni 4 18 -Emiliania huxleyi 56 13 -Glycine max 4019 1831 -Helobdella robusta 33 1 -Homo sapiens 59 6 -Hyaloperonospora parasitica 48 10 -Hydra magnipapillata 9 65 -Medicago truncatula 62 42 -Mimulus guttatus 12 9 -Mus musculus 18 5 -Mycosphaerella fijiensis 42 7 -Nasonia vitripennis 10 12 -Nectria haematococca 67 2 -Oryza sativa 6068 2561 -Paramecium tetraurelia 749 296 -Pediculus humanus 49 40 -Phakopsora pachyrhizi 66 53 -Physcomitrella patens 304 36 -Phytophthora ramorum 174 56 -Phytophthora sojae 10 0 -Pinus taeda 0 26 -Populus balsamifera 43 4 -Pristionchus pacificus 4 14 -Rattus norvegicus 11 3 -Rhodnius prolixus 24 17 -Ricinus communis 75 14 -Schistosoma mansoni 80 15 -Schmidtea mediterranea 307 277 -Selaginella moellendorffii 27 10 -Sorghum bicolor 306 72 -Strongylocentrotus purpuratus 182 34 -Trypanosoma cruzi 23 0 -Volvox carteri 64 2 -Zea mays 583 263 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/poisson2test2_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poisson2test2_out.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,52 @@ +Acyrthosiphon pisum 55 54 -4.303 -4.049 0.000008 0.000026 0.000438 0.001340 +Aedes aegypti 246 72 3.064 3.198 0.001093 0.000693 0.056838 0.036029 +Anopheles gambiae 337 168 -1.323 -1.307 0.092930 0.095535 1.000000 1.000000 +Apis mellifera 33 11 0.800 0.823 0.211855 0.205213 1.000000 1.000000 +Aspergillus niger 292 29 8.371 9.916 0.000000 0.000000 0.000000 0.000000 +Batrachochytrium dendrobatidis 17 14 -1.765 -1.678 0.038749 0.046690 1.000000 1.000000 +Bombyx mori 2 16 5.373 5.103 0.000000 0.000000 0.000002 0.000009 +Bos taurus 16 71 10.338 9.621 0.000000 0.000000 0.000000 0.000000 +Branchiostoma floridae 44 1 4.126 5.667 0.000018 0.000000 0.000959 0.000000 +Caenorhabditis briggsae 269 121 -0.202 -0.201 0.420141 0.420309 1.000000 1.000000 +Caenorhabditis remanei 35 29 -2.563 -2.435 0.005191 0.007450 0.269927 0.387398 +Chlamydomonas reinhardtii 85 13 3.716 4.183 0.000101 0.000014 0.005267 0.000747 +Citrus sinensis 14 2 1.568 1.780 0.058457 0.037576 1.000000 1.000000 +Culex pipiens 408 81 6.717 7.331 0.000000 0.000000 0.000000 0.000000 +Daphnia pulex 213 75 1.663 1.701 0.048160 0.044463 1.000000 1.000000 +Drosophila ananassae 3 20 5.872 5.539 0.000000 0.000000 0.000000 0.000001 +Drosophila grimshawi 14 10 -1.182 -1.134 0.118667 0.128417 1.000000 1.000000 +Drosophila pseudoobscura 28 22 -2.064 -1.967 0.019519 0.024570 1.000000 1.000000 +Drosophila willistoni 4 18 5.220 4.860 0.000000 0.000001 0.000005 0.000031 +Emiliania huxleyi 56 13 2.113 2.264 0.017321 0.011791 0.900675 0.613145 +Glycine max 4019 1831 -1.235 -1.231 0.108478 0.109251 1.000000 1.000000 +Helobdella robusta 33 1 3.496 4.684 0.000237 0.000001 0.012302 0.000073 +Homo sapiens 59 6 3.732 4.409 0.000095 0.000005 0.004933 0.000270 +Hyaloperonospora parasitica 48 10 2.201 2.389 0.013860 0.008448 0.720722 0.439307 +Hydra magnipapillata 9 65 10.697 10.120 0.000000 0.000000 0.000000 0.000000 +Medicago truncatula 62 42 -2.176 -2.096 0.014777 0.018033 0.768379 0.937696 +Mimulus guttatus 12 9 -1.224 -1.170 0.110516 0.120942 1.000000 1.000000 +Mus musculus 18 5 0.918 0.964 0.179337 0.167614 1.000000 1.000000 +Mycosphaerella fijiensis 42 7 2.472 2.755 0.006711 0.002933 0.348951 0.152533 +Nasonia vitripennis 10 12 2.443 2.277 0.007288 0.011379 0.378990 0.591708 +Nectria haematococca 67 2 4.987 6.692 0.000000 0.000000 0.000016 0.000000 +Oryza sativa 6068 2561 1.768 1.775 0.038558 0.037957 1.000000 1.000000 +Paramecium tetraurelia 749 296 1.565 1.582 0.058782 0.056837 1.000000 1.000000 +Pediculus humanus 49 40 -2.947 -2.802 0.001606 0.002538 0.083501 0.131991 +Phakopsora pachyrhizi 66 53 -3.311 -3.152 0.000464 0.000811 0.024152 0.042153 +Physcomitrella patens 304 36 7.993 9.276 0.000000 0.000000 0.000000 0.000000 +Phytophthora ramorum 174 56 2.044 2.111 0.020488 0.017390 1.000000 0.904295 +Phytophthora sojae 10 0 2.098 3.496 0.017969 0.000236 0.934412 0.012278 +Pinus taeda 0 26 7.687 8.498 0.000000 0.000000 0.000000 0.000000 +Populus balsamifera 43 4 3.281 3.916 0.000517 0.000045 0.026903 0.002339 +Pristionchus pacificus 4 14 4.349 4.025 0.000007 0.000028 0.000355 0.001481 +Rattus norvegicus 11 3 0.741 0.780 0.229238 0.217720 1.000000 1.000000 +Rhodnius prolixus 24 17 -1.516 -1.456 0.064729 0.072722 1.000000 1.000000 +Ricinus communis 75 14 3.036 3.338 0.001198 0.000422 0.062288 0.021926 +Schistosoma mansoni 80 15 3.124 3.433 0.000891 0.000298 0.046328 0.015504 +Schmidtea mediterranea 307 277 -8.853 -8.368 0.000000 0.000000 0.000000 0.000000 +Selaginella moellendorffii 27 10 0.466 0.474 0.320629 0.317714 1.000000 1.000000 +Sorghum bicolor 306 72 4.857 5.197 0.000001 0.000000 0.000031 0.000005 +Strongylocentrotus purpuratus 182 34 4.727 5.196 0.000001 0.000000 0.000059 0.000005 +Trypanosoma cruzi 23 0 3.181 5.302 0.000733 0.000000 0.038134 0.000003 +Volvox carteri 64 2 4.854 6.487 0.000001 0.000000 0.000031 0.000000 +Zea mays 583 263 -0.336 -0.335 0.368487 0.368792 1.000000 1.000000 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/t2t_report.dat --- a/test-data/t2t_report.dat Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -root root 5 -superkingdom Eukaryota 5 -kingdom Metazoa 5 -phylum Chordata 5 -subphylum Craniata 5 -superclass Gnathostomata 5 -class Mammalia 5 -superorder Euarchontoglires 4 -order Primates 4 -suborder Haplorrhini 3 -superfamily Hominoidea 3 -family Hominidae 3 -genus Homo 2 -species Homo sapiens 2 -subspecies Homo sapiens neanderthalensis 1 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/t2t_report.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t2t_report.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,15 @@ +root root 5 +superkingdom Eukaryota 5 +kingdom Metazoa 5 +phylum Chordata 5 +subphylum Craniata 5 +superclass Gnathostomata 5 +class Mammalia 5 +superorder Euarchontoglires 4 +order Primates 4 +suborder Haplorrhini 3 +superfamily Hominoidea 3 +family Hominidae 3 +genus Homo 2 +species Homo sapiens 2 +subspecies Homo sapiens neanderthalensis 1 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomy2gi-input.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy2gi-input.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,4 @@ +2 9913 +4 9646 +15 9915 +16 9771 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomy2gi-input.txt --- a/test-data/taxonomy2gi-input.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -2 9913 -4 9646 -15 9915 -16 9771 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomy2gi-output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy2gi-output.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,4 @@ +9913 9913 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n 2 +9646 9646 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria Carnivora Caniformia n Ursidae n n n Ailuropoda n Ailuropoda melanoleuca n 4 +9915 9915 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos indicus n 15 +9771 9771 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria Cetacea Mysticeti n Balaenopteridae n n n Balaenoptera n Balaenoptera musculus n 16 \ No newline at end of file diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomy2gi-output.txt --- a/test-data/taxonomy2gi-output.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -9913 9913 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n 2 -9646 9646 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria Carnivora Caniformia n Ursidae n n n Ailuropoda n Ailuropoda melanoleuca n 4 -9915 9915 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos indicus n 15 -9771 9771 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria Cetacea Mysticeti n Balaenopteridae n n n Balaenoptera n Balaenoptera musculus n 16 \ No newline at end of file diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomyGI.dat --- a/test-data/taxonomyGI.dat Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -9606 9606 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n 12583 -40674 40674 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n n n n n n n n n n n n n 410771 -63221 63221 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens Homo sapiens neanderthalensis 2286205 -9604 9604 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n n n n n 23236241 -9443 9443 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates n n n n n n n n n n 33001686 \ No newline at end of file diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomyGI.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomyGI.tabular Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,5 @@ +33001686 9443 +23236241 9604 +12583 9606 +410771 40674 +2286205 63221 diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomyGI.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomyGI.taxonomy Fri Nov 20 15:35:30 2009 -0500 @@ -0,0 +1,5 @@ +9606 9606 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n 12583 +40674 40674 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n n n n n n n n n n n n n 410771 +63221 63221 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens Homo sapiens neanderthalensis 2286205 +9604 9604 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n n n n n 23236241 +9443 9443 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates n n n n n n n n n n 33001686 \ No newline at end of file diff -r 436de91e08b0 -r 82b63d47a0d8 test-data/taxonomyGI.txt --- a/test-data/taxonomyGI.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -33001686 9443 -23236241 9604 -12583 9606 -410771 40674 -2286205 63221 diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/example_dataset_missing_nodes.txt --- a/tools/taxonomy/example_dataset_missing_nodes.txt Fri Nov 20 15:25:13 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -Species_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1 -Species_2 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 n species2 subspecies2 -Species_3 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3 -Species_4 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4 -Species_5 5 root superkingdom1 kingdom1 subkingdom1 superphylum1 n subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species5 subspecies5 - diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/find_diag_hits.xml --- a/tools/taxonomy/find_diag_hits.xml Fri Nov 20 15:25:13 2009 -0500 +++ b/tools/taxonomy/find_diag_hits.xml Fri Nov 20 15:35:30 2009 -0500 @@ -37,11 +37,11 @@ </outputs> <tests> <test> - <param name="input1" value="taxonomyGI.dat" ftype="taxonomy"/> + <param name="input1" value="taxonomyGI.taxonomy" ftype="taxonomy"/> <param name="id_col" value="1" /> <param name="rank_list" value="order,genus" /> <param name="out_format" value="counts" /> - <output name="out_file1" file="find_diag_hits.dat" ftype="tabular"/> + <output name="out_file1" file="find_diag_hits.tabular" /> </test> </tests> diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/gi2taxonomy.xml --- a/tools/taxonomy/gi2taxonomy.xml Fri Nov 20 15:25:13 2009 -0500 +++ b/tools/taxonomy/gi2taxonomy.xml Fri Nov 20 15:35:30 2009 -0500 @@ -14,10 +14,10 @@ </requirements> <tests> <test> - <param name="input" value="taxonomy2gi-input.txt"/> + <param name="input" ftype="tabular" value="taxonomy2gi-input.tabular"/> <param name="giField" value="1"/> <param name="idField" value="2"/> - <output name="out_file1" file="taxonomy2gi-output.txt"/> + <output name="out_file1" file="taxonomy2gi-output.tabular"/> </test> </tests> diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/poisson2test.xml --- a/tools/taxonomy/poisson2test.xml Fri Nov 20 15:25:13 2009 -0500 +++ b/tools/taxonomy/poisson2test.xml Fri Nov 20 15:35:30 2009 -0500 @@ -16,20 +16,20 @@ </outputs> <tests> <test> - <param name="input1" value="poisson2test1.txt"/> + <param name="input1" value="poisson2test1.tabular" ftype="tabular"/> <param name="input2" value="2" /> <param name="input3" value="3" /> <param name="input4" value="0.44" /> <param name="input5" value="0" /> - <output name="output1" file="poisson2test1.out" /> + <output name="output1" file="poisson2test1_out.tabular" /> </test> <test> - <param name="input1" value="poisson2test2.txt"/> + <param name="input1" value="poisson2test2.tabular" ftype="tabular"/> <param name="input2" value="2" /> <param name="input3" value="3" /> <param name="input4" value="0.44" /> <param name="input5" value="0" /> - <output name="output1" file="poisson2test2.out" /> + <output name="output1" file="poisson2test2_out.tabular" /> </test> </tests> <help> diff -r 436de91e08b0 -r 82b63d47a0d8 tools/taxonomy/t2t_report.xml --- a/tools/taxonomy/t2t_report.xml Fri Nov 20 15:25:13 2009 -0500 +++ b/tools/taxonomy/t2t_report.xml Fri Nov 20 15:35:30 2009 -0500 @@ -12,8 +12,8 @@ </requirements> <tests> <test> - <param name="input" value="taxonomyGI.dat" ftype="taxonomy"/> - <output name="out_file1" file="t2t_report.dat"/> + <param name="input" value="taxonomyGI.taxonomy" ftype="taxonomy"/> + <output name="out_file1" file="t2t_report.tabular"/> </test> </tests>

1 0

[hg] galaxy 3116: Data from UCSC table browser now uses hgta_tab...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/436de91e08b0 changeset: 3116:436de91e08b0 user: Kanwei Li <kanwei(a)gmail.com> date: Fri Nov 20 15:25:13 2009 -0500 description: Data from UCSC table browser now uses hgta_table for table name. Fixes #67 diffstat: tools/data_source/ucsc_tablebrowser.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r e24c2590f8af -r 436de91e08b0 tools/data_source/ucsc_tablebrowser.xml --- a/tools/data_source/ucsc_tablebrowser.xml Fri Nov 20 12:07:06 2009 -0500 +++ b/tools/data_source/ucsc_tablebrowser.xml Fri Nov 20 15:25:13 2009 -0500 @@ -19,7 +19,7 @@ <request_param galaxy_name="URL" remote_name="URL" missing="" /> <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> - <request_param galaxy_name="table" remote_name="hgta_track" missing="unknown table" /> + <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" > <data_type_translation>

1 0

[hg] galaxy 3113: Eliminate the ability to delete/undelete/purge...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5c46679d0755 changeset: 3113:5c46679d0755 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Nov 20 08:46:49 2009 -0500 description: Eliminate the ability to delete/undelete/purge users until the grid helper can access config settings. diffstat: lib/galaxy/web/controllers/admin.py | 10 +++++----- 1 files changed, 5 insertions(+), 5 deletions(-) diffs (23 lines): diff -r b9b9fe0612b9 -r 5c46679d0755 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Thu Nov 19 18:55:35 2009 -0500 +++ b/lib/galaxy/web/controllers/admin.py Fri Nov 20 08:46:49 2009 -0500 @@ -91,14 +91,14 @@ grids.GridAction( "Create new user", dict( controller='admin', action='users', operation='create' ) ) ] operations = [ - grids.GridOperation( "Manage Roles & Groups", condition=( lambda item: not item.deleted ), allow_multiple=False ) + grids.GridOperation( "Manage Roles & Groups", condition=( lambda item: not item.deleted ), allow_multiple=False ), + grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False ) ] #TODO: enhance to account for trans.app.config.allow_user_deletion here so that we can eliminate these operations if # the setting is False - operations.append( grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False ) ) - operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) - operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) - operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) + #operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) + #operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) + #operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ),

1 0

[hg] galaxy 3114: Move line count processing from set_peek() met...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f4654abcec1e changeset: 3114:f4654abcec1e user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Nov 20 11:03:41 2009 -0500 description: Move line count processing from set_peek() methods to set_meta() methods for data types since set_meta can run externally and it does line by line processing in some cases. Added new MetadataElements to the Data, Text, Sequence and Maf classes to handle setting dataset.blurb from stored metadata. Cleaned up a lot of code in the process. diffstat: lib/galaxy/datatypes/binary.py | 14 +- lib/galaxy/datatypes/data.py | 55 ++-- lib/galaxy/datatypes/genetics.py | 4 +- lib/galaxy/datatypes/images.py | 8 +- lib/galaxy/datatypes/interval.py | 15 +- lib/galaxy/datatypes/metadata.py | 5 +- lib/galaxy/datatypes/qualityscore.py | 54 +----- lib/galaxy/datatypes/sequence.py | 148 ++++++++++---- lib/galaxy/datatypes/tabular.py | 93 ++++---- lib/galaxy/datatypes/xml.py | 4 +- lib/galaxy/jobs/__init__.py | 4 +- lib/galaxy/jobs/runners/local.py | 5 +- lib/galaxy/model/__init__.py | 8 +- lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py | 8 +- test/functional/test_get_data.py | 6 +- test/functional/test_history_functions.py | 2 +- 16 files changed, 220 insertions(+), 213 deletions(-) diffs (965 lines): diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/binary.py Fri Nov 20 11:03:41 2009 -0500 @@ -18,7 +18,7 @@ class Binary( data.Data ): """Binary data""" - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = 'binary data' @@ -30,7 +30,7 @@ class Ab1( Binary ): """Class describing an ab1 binary sequence file""" file_ext = "ab1" - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: export_url = "/history_add_to?" + urlencode( {'history_id':dataset.history_id,'ext':'ab1','name':'ab1 sequence','info':'Sequence file','dbkey':dataset.dbkey} ) dataset.peek = "Binary ab1 sequence file" @@ -71,7 +71,7 @@ if os.path.exists( tmpf1bai ): os.remove( tmpf1bai ) dataset.metadata.bam_index = index_file - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: export_url = "/history_add_to?" + urlencode( {'history_id':dataset.history_id,'ext':'bam','name':'bam alignments','info':'Alignments file','dbkey':dataset.dbkey} ) dataset.peek = "Binary bam alignments file" @@ -91,7 +91,7 @@ class Binseq( Binary ): """Class describing a zip archive of binary sequence files""" file_ext = "binseq.zip" - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: zip_file = zipfile.ZipFile( dataset.file_name, "r" ) num_files = len( zip_file.namelist() ) @@ -112,7 +112,7 @@ class Scf( Binary ): """Class describing an scf binary sequence file""" file_ext = "scf" - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: export_url = "/history_add_to?" + urlencode({'history_id':dataset.history_id,'ext':'scf','name':'scf sequence','info':'Sequence file','dbkey':dataset.dbkey}) dataset.peek = "Binary scf sequence file" @@ -139,9 +139,9 @@ if binascii.b2a_hex( header ) == binascii.hexlify( '.sff' ): return True return False - except Exception, e: + except: return False - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: export_url = "/history_add_to?" + urlencode( {'history_id':dataset.history_id,'ext':'sff','name':'sff file','info':'sff file','dbkey':dataset.dbkey} ) dataset.peek = "Binary sff file" diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/data.py Fri Nov 20 11:03:41 2009 -0500 @@ -95,9 +95,6 @@ def set_meta( self, dataset, overwrite = True, **kwd ): """Unimplemented method, allows guessing of metadata from contents of file""" return True - def set_readonly_meta( self, dataset ): - """Unimplemented method, resets the readonly metadata values""" - return True def missing_meta( self, dataset, check = [], skip = [] ): """ Checks for empty metadata values, Returns True if non-optional metadata is missing @@ -114,7 +111,7 @@ if not value: return True return False - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = '' @@ -312,6 +309,11 @@ return False class Text( Data ): + file_ext = 'txt' + + """Add metadata elements""" + MetadataElement( name="data_lines", default=0, desc="Number of data lines", readonly=True, optional=True, visible=False, no_value=0 ) + def write_from_stream(self, dataset, stream): """Writes data from a stream""" # write it twice for now @@ -322,7 +324,6 @@ break os.write(fd, chunk) os.close(fd) - # rewrite the file with unix newlines fp = open(dataset.file_name, 'wt') for line in file(temp_name, "U"): @@ -344,23 +345,29 @@ def get_mime(self): """Returns the mime type of the datatype""" return 'text/plain' - def set_peek( self, dataset, line_count=None ): + def set_meta( self, dataset, **kwd ): + """ + Set the number of lines of data in dataset, + skipping all blank lines and comments. + """ + data_lines = 0 + for line in file( dataset.file_name ): + line = line.strip() + if line and not line.startswith( '#' ): + data_lines += 1 + dataset.metadata.data_lines = data_lines + def set_peek( self, dataset, line_count=None, is_multi_byte=False ): if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method - dataset.peek = get_file_peek( dataset.file_name ) + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: - dataset.blurb = "%s lines" % util.commaify( str( get_line_count( dataset.file_name ) ) ) - else: - dataset.blurb = "%s lines" % util.commaify( str( line_count ) ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def set_multi_byte_peek( self, dataset, line_count=None ): - if not dataset.dataset.purged: - # The file must exist on disk for the get_file_peek() method - dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=True ) - if line_count is None: - dataset.blurb = "%s lines" % util.commaify( str( get_line_count( dataset.file_name ) ) ) + # See if line_count is stored in the metadata + if dataset.metadata.data_lines: + dataset.blurb = "%s lines" % util.commaify( str( dataset.metadata.data_lines ) ) + else: + # Number of lines is not known ( this should not happen ), and auto-detect is + # needed to set metadata + dataset.blurb = "? lines" else: dataset.blurb = "%s lines" % util.commaify( str( line_count ) ) else: @@ -370,7 +377,7 @@ class Txtseq( Data ): """Class describing a zip archive of text sequence files""" file_ext = "txtseq.zip" - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: zip_file = zipfile.ZipFile( dataset.file_name, "r" ) num_files = len( zip_file.namelist() ) @@ -459,11 +466,3 @@ else: text = unicode( '\n'.join( lines ), 'utf-8' ) return text -def get_line_count(file_name): - """Returns the number of lines in a file that are neither null nor comments""" - count = 0 - for line in file(file_name): - line = line.strip() - if line and line[0] != '#': - count += 1 - return count diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/genetics.py Fri Nov 20 11:03:41 2009 -0500 @@ -358,7 +358,7 @@ """ file_ext="snpmatrix" - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = "Binary RGenetics file" dataset.blurb = data.nice_size( dataset.get_size() ) @@ -597,7 +597,7 @@ else: p = [] return '\n'.join(p) - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): """ expects a .pheno file in the extra_files_dir - ugh note that R is wierd and does not include the row.name in diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/images.py --- a/lib/galaxy/datatypes/images.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/images.py Fri Nov 20 11:03:41 2009 -0500 @@ -15,7 +15,7 @@ class Image( data.Data ): """Class describing an image""" - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = 'Image in %s format' % dataset.extension dataset.blurb = data.nice_size( dataset.get_size() ) @@ -51,7 +51,7 @@ """Class describing a GMAJ Applet""" file_ext = "gmaj.zip" copy_safe_peek = False - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: if hasattr( dataset, 'history_id' ): params = { @@ -102,7 +102,7 @@ class Html( data.Text ): """Class describing an html file""" file_ext = "html" - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = "HTML file" dataset.blurb = data.nice_size( dataset.get_size() ) @@ -136,7 +136,7 @@ """Class describing a LAJ Applet""" file_ext = "laj" copy_safe_peek = False - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: if hasattr( dataset, 'history_id' ): params = { diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/interval.py Fri Nov 20 11:03:41 2009 -0500 @@ -58,12 +58,18 @@ def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) - def set_peek( self, dataset, line_count=None ): + def set_peek( self, dataset, line_count=None, is_multi_byte=False ): """Set the peek and blurb text""" if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name ) + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: - dataset.blurb = "%s regions" % util.commaify( str( data.get_line_count( dataset.file_name ) ) ) + # See if line_count is stored in the metadata + if dataset.metadata.data_lines: + dataset.blurb = "%s regions" % util.commaify( str( dataset.metadata.data_lines ) ) + else: + # Number of lines is not known ( this should not happen ), and auto-detect is + # needed to set metadata + dataset.blurb = "? regions" else: dataset.blurb = "%s regions" % util.commaify( str( line_count ) ) else: @@ -884,9 +890,6 @@ """Initialize interval datatype, by adding UCSC display app""" Tabular.__init__(self, **kwd) self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) - def set_readonly_meta( self, dataset, skip=1, **kwd ): - """Resets the values of readonly metadata elements.""" - Tabular.set_readonly_meta( self, dataset, skip = skip, **kwd ) def set_meta( self, dataset, overwrite = True, **kwd ): Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 1 ) def display_peek( self, dataset ): diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/metadata.py Fri Nov 20 11:03:41 2009 -0500 @@ -89,7 +89,10 @@ return bool( self.parent._metadata.get( name, False ) ) def get_html_by_name( self, name, **kwd ): if name in self.spec: - return self.spec[name].param.get_html( value=getattr( self, name ), context=self, **kwd ) + rval = self.spec[name].param.get_html( value=getattr( self, name ), context=self, **kwd ) + if rval is None: + return self.spec[name].no_value + return rval def make_dict_copy( self, to_copy ): """Makes a deep copy of input iterable to_copy according to self.spec""" rval = {} diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/qualityscore.py --- a/lib/galaxy/datatypes/qualityscore.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/qualityscore.py Fri Nov 20 11:03:41 2009 -0500 @@ -14,23 +14,6 @@ until we know more about quality score formats """ file_ext = "qualsolid" - - def set_peek( self, dataset, line_count=None ): - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name ) - if line_count is None: - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.blurb = "%s lines, SOLiD Quality score file" % util.commaify( str( line_count ) ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - def display_peek(self, dataset): - try: - return dataset.peek - except: - return "SOLiD Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) ) def sniff( self, filename ): """ @@ -70,6 +53,7 @@ return True else: break #we found a non-empty line, but it's not a header + fh.close() except: pass return False @@ -79,23 +63,6 @@ until we know more about quality score formats """ file_ext = "qual454" - - def set_peek( self, dataset, line_count=None ): - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name ) - if line_count is None: - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.blurb = "%s lines, 454 Quality score file" % util.commaify( str( line_count ) ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - def display_peek(self, dataset): - try: - return dataset.peek - except: - return "454 Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) ) def sniff( self, filename ): """ @@ -125,6 +92,7 @@ return True else: break #we found a non-empty line, but it's not a header + fh.close() except: pass return False @@ -134,22 +102,4 @@ until we know more about quality score formats """ file_ext = "qualsolexa" - - def set_peek( self, dataset, line_count=None ): - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name ) - if line_count is None: - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.blurb = "%s lines, Solexa Quality score file" % util.commaify( str( line_count ) ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - def display_peek(self, dataset): - try: - return dataset.peek - except: - return "Solexa Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) ) - \ No newline at end of file diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/sequence.py Fri Nov 20 11:03:41 2009 -0500 @@ -17,11 +17,40 @@ class Sequence( data.Text ): """Class describing a sequence""" - def set_readonly_meta( self, dataset ): - """Resets the values of readonly metadata elements.""" - pass -class Alignment( Sequence ): + """Add metadata elements""" + MetadataElement( name="sequences", default=0, desc="Number of sequences", readonly=True, visible=False, optional=True, no_value=0 ) + + def set_meta( self, dataset, **kwd ): + """ + Set the number of sequences and the number of data lines in dataset. + """ + data_lines = 0 + sequences = 0 + for line in file( dataset.file_name ): + line = line.strip() + if line and line.startswith( '#' ): + # We don't count comment lines for sequence data types + continue + if line and line.startswith( '>' ): + sequences += 1 + data_lines +=1 + else: + data_lines += 1 + dataset.metadata.data_lines = data_lines + dataset.metadata.sequences = sequences + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + if dataset.metadata.sequences: + dataset.blurb = "%s sequences" % util.commaify( str( dataset.metadata.sequences ) ) + else: + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + +class Alignment( data.Text ): """Class describing an alignment""" """Add metadata elements""" @@ -29,16 +58,9 @@ class Fasta( Sequence ): """Class representing a FASTA sequence""" + file_ext = "fasta" - def set_peek( self, dataset ): - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name ) - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def sniff( self, filename ): """ Determines whether the file is in fasta format @@ -82,6 +104,7 @@ return True else: break #we found a non-empty line, but its not a fasta header + fh.close() except: pass return False @@ -89,14 +112,6 @@ class csFasta( Sequence ): """ Class representing the SOLID Color-Space sequence ( csfasta ) """ file_ext = "csfasta" - - def set_peek( self, dataset ): - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name ) - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' def sniff( self, filename ): """ @@ -130,6 +145,7 @@ return True else: break #we found a non-empty line, but it's not a header + fh.close() except: pass return False @@ -137,15 +153,26 @@ class Fastq ( Sequence ): """Class representing a generic FASTQ sequence""" file_ext = "fastq" - - def set_peek( self, dataset ): - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name ) - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - + + def set_meta( self, dataset, **kwd ): + """ + Set the number of sequences and the number of data lines + in dataset. + """ + data_lines = 0 + sequences = 0 + for line in file( dataset.file_name ): + line = line.strip() + if line and line.startswith( '#' ): + # We don't count comment lines for sequence data types + continue + if line and line.startswith( '@' ): + sequences += 1 + data_lines +=1 + else: + data_lines += 1 + dataset.metadata.data_lines = data_lines + dataset.metadata.sequences = sequences def sniff ( self, filename ): """ Determines whether the file is in generic fastq format @@ -178,13 +205,13 @@ """Class representing a FASTQ sequence ( the Sanger variant )""" file_ext = "fastqsanger" - try: from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) import bx.align.maf except: pass + #trying to import maf_utilities here throws an ImportError due to a circular import between jobs and tools: #from galaxy.tools.util.maf_utilities import build_maf_index_species_chromosomes #Traceback (most recent call last): @@ -223,12 +250,15 @@ species = [] species_chromosomes = {} indexes = bx.interval_index_file.Indexes() + blocks = 0 try: maf_reader = bx.align.maf.Reader( open( filename ) ) while True: pos = maf_reader.file.tell() block = maf_reader.next() - if block is None: break + if block is None: + break + blocks += 1 for c in block.components: spec = c.src chrom = None @@ -255,29 +285,30 @@ except Exception, e: #most likely a bad MAF log.debug( 'Building MAF index on %s failed: %s' % ( filename, e ) ) - return ( None, [], {} ) - return ( indexes, species, species_chromosomes ) + return ( None, [], {}, 0 ) + return ( indexes, species, species_chromosomes, blocks ) class Maf( Alignment ): """Class describing a Maf alignment""" file_ext = "maf" #Readonly and optional, users can't unset it, but if it is not set, we are generally ok; if required use a metadata validator in the tool definition + MetadataElement( name="blocks", default=0, desc="Number of blocks", readonly=True, optional=True, visible=False, no_value=0 ) MetadataElement( name="species_chromosomes", desc="Species Chromosomes", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True ) MetadataElement( name="maf_index", desc="MAF Index File", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True ) def init_meta( self, dataset, copy_from=None ): Alignment.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, **kwd ): """ Parses and sets species, chromosomes, index from MAF file. """ #these metadata values are not accessable by users, always overwrite - indexes, species, species_chromosomes = COPIED_build_maf_index_species_chromosomes( dataset.file_name ) - if indexes is None: return #this is not a MAF file - + indexes, species, species_chromosomes, blocks = COPIED_build_maf_index_species_chromosomes( dataset.file_name ) + if indexes is None: + return #this is not a MAF file dataset.metadata.species = species + dataset.metadata.blocks = blocks #only overwrite the contents if our newly determined chromosomes don't match stored chrom_file = dataset.metadata.species_chromosomes compare_chroms = {} @@ -303,17 +334,27 @@ open( chrom_file.file_name, 'wb' ).write( tmp_file.read() ) dataset.metadata.species_chromosomes = chrom_file tmp_file.close() - index_file = dataset.metadata.maf_index if not index_file: index_file = dataset.metadata.spec['maf_index'].param.new_file( dataset = dataset ) indexes.write( open( index_file.file_name, 'w' ) ) dataset.metadata.maf_index = index_file - + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + # The file must exist on disk for the get_file_peek() method + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + if dataset.metadata.blocks: + dataset.blurb = "%s blocks" % util.commaify( str( dataset.metadata.blocks ) ) + else: + # Number of blocks is not known ( this should not happen ), and auto-detect is + # needed to set metadata + dataset.blurb = "? blocks" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' def display_peek( self, dataset ): """Returns formated html of peek""" return self.make_html_table( dataset ) - def make_html_table( self, dataset, skipchars=[] ): """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] @@ -336,7 +377,6 @@ except Exception, exc: out = "Can't create peek %s" % exc return out - def sniff( self, filename ): """ Determines wether the file is in maf format @@ -368,8 +408,13 @@ except: return False -class Axt( Sequence ): +class Axt( data.Text ): """Class describing an axt alignment""" + + # gvk- 11/19/09 - This is really an alignment, but we no longer have tools that use this data type, and it is + # here simply for backward compatibility ( although it is still in the datatypes registry ). Subclassing + # from data.Text eliminates managing metadata elements inherited from the Alignemnt class. + file_ext = "axt" def sniff( self, filename ): @@ -377,10 +422,16 @@ Determines whether the file is in axt format axt alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab - at Penn State University. Each alignment block in an axt file contains three lines: a summary - line and 2 sequence lines. Blocks are separated from one another by blank lines. + at Penn State University. - The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields: + Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. + Blocks are separated from one another by blank lines. + + The summary line contains chromosomal position and size information about the alignment. It + consists of 9 required fields. + + The sequence lines contain the sequence of the primary assembly (line 2) and aligning assembly + (line 3) with inserts. Repeats are indicated by lower-case letters. For complete details see http://genome.ucsc.edu/goldenPath/help/axt.html @@ -409,10 +460,15 @@ else: return True -class Lav( Sequence ): +class Lav( data.Text ): """Class describing a LAV alignment""" + file_ext = "lav" + # gvk- 11/19/09 - This is really an alignment, but we no longer have tools that use this data type, and it is + # here simply for backward compatibility ( although it is still in the datatypes registry ). Subclassing + # from data.Text eliminates managing metadata elements inherited from the Alignemnt class. + def sniff( self, filename ): """ Determines whether the file is in lav format diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/tabular.py Fri Nov 20 11:03:41 2009 -0500 @@ -19,14 +19,12 @@ """Tab delimited data""" """Add metadata elements""" + MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 ) MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False, no_value=0 ) MetadataElement( name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] ) def init_meta( self, dataset, copy_from=None ): data.Text.init_meta( self, dataset, copy_from=copy_from ) - def set_readonly_meta( self, dataset, skip=None, **kwd ): - """Resets the values of readonly metadata elements.""" - Tabular.set_meta( self, dataset, overwrite = True, skip = skip ) def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): """ Tries to determine the number of columns as well as those columns @@ -35,15 +33,19 @@ their data type classes are responsible to determine how many invalid comment lines should be skipped. Using None for skip will cause skip to be zero, but the first line will be processed as a header. + + Items of interest: + 1. We treat 'overwrite' as always True (we always want to set tabular metadata when called). + 2. If a tabular file has no data, it will have one column of type 'str'. + 3. We used to check only the first 100 lines when setting metadata and this class's + set_peek() method read the entire file to determine the number of lines in the file. + Since metadata can now be processed on cluster nodes, we've merged the line count portion + of the set_peek() processing here, and we now check the entire contents of the file. """ - #we treat 'overwrite' as always True (we always want to set tabular metadata when called) - #if a tabular file has no data, it will have one column of type str - - num_check_lines = 100 #we will only check up to this many lines into the file - requested_skip = skip #store original skip value to check with later + # Store original skip value to check with later + requested_skip = skip if skip is None: skip = 0 - column_type_set_order = [ 'int', 'float', 'list', 'str' ] #Order to set column types in default_column_type = column_type_set_order[-1] # Default column type is lowest in list column_type_compare_order = list( column_type_set_order ) #Order to compare column types @@ -89,49 +91,47 @@ if is_column_type[column_type]( column_text ): return column_type return None - + data_lines = 0 + comment_lines = 0 column_types = [] first_line_column_types = [default_column_type] # default value is one column of type str if dataset.has_data(): #NOTE: if skip > num_check_lines, we won't detect any metadata, and will use default for i, line in enumerate( file ( dataset.file_name ) ): - line = line.rstrip('\r\n') + line = line.rstrip( '\r\n' ) if i < skip or not line or line.startswith( '#' ): - continue - - fields = line.split( '\t' ) - for field_count, field in enumerate( fields ): - if field_count >= len( column_types ): #found a previously unknown column, we append None - column_types.append( None ) - column_type = guess_column_type( field ) - if type_overrules_type( column_type, column_types[field_count] ): - column_types[field_count] = column_type - - if i == 0 and requested_skip is None: - #this is our first line, people seem to like to upload files that have a header line, but do not start with '#' (i.e. all column types would then most likely be detected as str) - #we will assume that the first line is always a header (this was previous behavior - it was always skipped) when the requested skip is None - #we only use the data from the first line if we have no other data for a column - #this is far from perfect, as: - #1,2,3 1.1 2.2 qwerty - #0 0 1,2,3 - #will detect as - #"column_types": ["int", "int", "float", "list"] - #instead of: - #"column_types": ["list", "float", "float", "str"] *** would seem to be the 'Truth' by manual observation that the first line should be included as data - #old method would have detected as: - #"column_types": ["int", "int", "str", "list"] - first_line_column_types = column_types - column_types = [ None for col in first_line_column_types ] - elif i > num_check_lines: - # We exceeded our max check lines - break - + # We'll call blank lines comments + comment_lines += 1 + else: + data_lines += 1 + fields = line.split( '\t' ) + for field_count, field in enumerate( fields ): + if field_count >= len( column_types ): #found a previously unknown column, we append None + column_types.append( None ) + column_type = guess_column_type( field ) + if type_overrules_type( column_type, column_types[field_count] ): + column_types[field_count] = column_type + if i == 0 and requested_skip is None: + # This is our first line, people seem to like to upload files that have a header line, but do not + # start with '#' (i.e. all column types would then most likely be detected as str). We will assume + # that the first line is always a header (this was previous behavior - it was always skipped). When + # the requested skip is None, we only use the data from the first line if we have no other data for + # a column. This is far from perfect, as + # 1,2,3 1.1 2.2 qwerty + # 0 0 1,2,3 + # will be detected as + # "column_types": ["int", "int", "float", "list"] + # instead of + # "column_types": ["list", "float", "float", "str"] *** would seem to be the 'Truth' by manual + # observation that the first line should be included as data. The old method would have detected as + # "column_types": ["int", "int", "str", "list"] + first_line_column_types = column_types + column_types = [ None for col in first_line_column_types ] #we error on the larger number of columns #first we pad our column_types by using data from first line if len( first_line_column_types ) > len( column_types ): for column_type in first_line_column_types[len( column_types ):]: column_types.append( column_type ) - #Now we fill any unknown (None) column_types with data from first line for i in range( len( column_types ) ): if column_types[i] is None: @@ -139,10 +139,11 @@ column_types[i] = default_column_type else: column_types[i] = first_line_column_types[i] - + # Set the discovered metadata values for the dataset + dataset.metadata.data_lines = data_lines + dataset.metadata.comment_lines = comment_lines dataset.metadata.column_types = column_types dataset.metadata.columns = len( column_types ) - def make_html_table( self, dataset, skipchars=[] ): """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] @@ -202,6 +203,10 @@ out.append( '<tr><td>' ) out.append( '%s</td></tr>' % escape( comments.pop(0) ) ) return "".join( out ) + def set_peek( self, dataset, line_count=None, is_multi_byte=False ): + data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte ) + if dataset.metadata.comment_lines: + dataset.blurb = "%s, %s comments" % ( dataset.blurb, util.commaify( str( dataset.metadata.comment_lines ) ) ) def display_peek( self, dataset ): """Returns formatted html of peek""" return self.make_html_table( dataset ) @@ -219,7 +224,6 @@ 'Superorder', 'Order', 'Suborder', 'Superfamily', 'Family', 'Subfamily', 'Tribe', 'Subtribe', 'Genus', 'Subgenus', 'Species', 'Subspecies' ] - def make_html_table( self, dataset, skipchars=[] ): """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] @@ -317,6 +321,7 @@ count += 1 if count == 5: return True + fh.close() if count < 5 and count > 0: return True except: diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/datatypes/xml.py Fri Nov 20 11:03:41 2009 -0500 @@ -10,10 +10,10 @@ class BlastXml( data.Text ): """NCBI Blast XML Output data""" file_ext = "blastxml" - def set_peek( self, dataset ): + def set_peek( self, dataset, is_multi_byte=False ): """Set the peek and blurb text""" if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name ) + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) dataset.blurb = 'NCBI Blast XML data' else: dataset.peek = 'file does not exist' diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Fri Nov 20 11:03:41 2009 -0500 @@ -549,12 +549,12 @@ try: assert context.get( 'line_count', None ) is not None if ( not dataset.datatype.composite_type and dataset.dataset.is_multi_byte() ) or self.tool.is_multi_byte: - dataset.set_multi_byte_peek( line_count=context['line_count'] ) + dataset.set_peek( line_count=context['line_count'], is_multi_byte=True ) else: dataset.set_peek( line_count=context['line_count'] ) except: if ( not dataset.datatype.composite_type and dataset.dataset.is_multi_byte() ) or self.tool.is_multi_byte: - dataset.set_multi_byte_peek() + dataset.set_peek( is_multi_byte=True ) else: dataset.set_peek() try: diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/jobs/runners/local.py Fri Nov 20 11:03:41 2009 -0500 @@ -101,10 +101,9 @@ job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - #run the metadata setting script here - #this is terminatable when output dataset/job is deleted - #so that long running set_meta()s can be cancelled without having to reboot the server + #this is terminate-able when output dataset/job is deleted + #so that long running set_meta()s can be canceled without having to reboot the server if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and self.app.config.set_metadata_externally and job_wrapper.output_paths: external_metadata_script = job_wrapper.setup_external_metadata( output_fnames = job_wrapper.get_output_fnames(), set_extension = True, diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/model/__init__.py Fri Nov 20 11:03:41 2009 -0500 @@ -537,17 +537,13 @@ def is_multi_byte( self ): """Data consists of multi-byte characters""" return self.dataset.is_multi_byte() - def set_peek( self ): - return self.datatype.set_peek( self ) - def set_multi_byte_peek( self ): - return self.datatype.set_multi_byte_peek( self ) + def set_peek( self, is_multi_byte=False ): + return self.datatype.set_peek( self, is_multi_byte=is_multi_byte ) def init_meta( self, copy_from=None ): return self.datatype.init_meta( self, copy_from=copy_from ) def set_meta( self, **kwd ): self.clear_associated_files( metadata_safe = True ) return self.datatype.set_meta( self, **kwd ) - def set_readonly_meta( self, **kwd ): - return self.datatype.set_readonly_meta( self, **kwd ) def missing_meta( self, **kwd ): return self.datatype.missing_meta( self, **kwd ) def as_display_type( self, type, **kwd ): diff -r 5c46679d0755 -r f4654abcec1e lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Fri Nov 20 08:46:49 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Fri Nov 20 11:03:41 2009 -0500 @@ -227,17 +227,13 @@ def get_mime( self ): """Returns the mime type of the data""" return datatypes_registry.get_mimetype_by_extension( self.extension.lower() ) - def set_peek( self ): - return self.datatype.set_peek( self ) - def set_multi_byte_peek( self ): - return self.datatype.set_multi_byte_peek( self ) + def set_peek( self, is_multi_byte=False ): + return self.datatype.set_peek( self, is_multi_byte=is_multi_byte ) def init_meta( self, copy_from=None ): return self.datatype.init_meta( self, copy_from=copy_from ) def set_meta( self, **kwd ): self.clear_associated_files( metadata_safe = True ) return self.datatype.set_meta( self, **kwd ) - def set_readonly_meta( self, **kwd ): - return self.datatype.set_readonly_meta( self, **kwd ) def missing_meta( self, **kwd ): return self.datatype.missing_meta( self, **kwd ) def as_display_type( self, type, **kwd ): diff -r 5c46679d0755 -r f4654abcec1e test/functional/test_get_data.py --- a/test/functional/test_get_data.py Fri Nov 20 08:46:49 2009 -0500 +++ b/test/functional/test_get_data.py Fri Nov 20 11:03:41 2009 -0500 @@ -294,7 +294,7 @@ .first() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( 'qualscores.qualsolid', hid=str( hda.hid ) ) - self.check_history_for_string( '2.5 Kb, format: <span class="qualsolid">qualsolid</span>, database: \? Info: uploaded file' ) + self.check_history_for_string( '48 lines, format: <span class="qualsolid">qualsolid</span>, database: \? Info: uploaded file' ) self.check_metadata_for_string( 'Change data type value="qualsolid" selected="yes">qualsolid' ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_0090_upload_file( self ): @@ -312,7 +312,7 @@ .first() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( 'qualscores.qual454', hid=str( hda.hid ) ) - self.check_history_for_string( '5.6 Kb, format: <span class="qual454">qual454</span>, database: \?' ) + self.check_history_for_string( '49 lines, format: <span class="qual454">qual454</span>, database: \?' ) self.check_metadata_for_string( 'Change data type value="qual454" selected="yes">qual454' ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_0095_upload_file( self ): @@ -483,7 +483,7 @@ .first() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( 'shrimp_cs_test1.csfasta', hid=str( hda.hid ) ) - self.check_history_for_string( '162.6 Kb, format: <span class="csfasta">csfasta</span>, <td>>2_14_26_F3,-1282216.0</td>' ) + self.check_history_for_string( '2,500 sequences, format: <span class="csfasta">csfasta</span>, <td>>2_14_26_F3,-1282216.0</td>' ) self.check_metadata_for_string( 'value="shrimp_cs_test1.csfasta" value="\?" Change data type value="csfasta" selected="yes"' ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_0140_upload_file( self ): diff -r 5c46679d0755 -r f4654abcec1e test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Fri Nov 20 08:46:49 2009 -0500 +++ b/test/functional/test_history_functions.py Fri Nov 20 11:03:41 2009 -0500 @@ -737,7 +737,7 @@ deleted_history_ids=deleted_history_ids ) sa_session.refresh( history6 ) if len( history6.datasets ) != 2: - raise AssertionError, "Copying hda1 to the current history failed" + raise AssertionError, "Copying hda1 to the current history failed, history 6 has %d datasets, but should have 2" % len( history6.datasets ) # Test copying 1 hda to another history self.new_history( name=urllib.quote( 'copy history items - 2' ) ) history7 = sa_session.query( galaxy.model.History ) \

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