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

[hg] galaxy 3662: forgot rgcaco - stretch lines_diff
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6be8d5818087 changeset: 3662:6be8d5818087 user: fubar: ross Lazarus at gmail period com date: Thu Apr 15 21:41:50 2010 -0400 description: forgot rgcaco - stretch lines_diff diffstat: tools/rgenetics/rgCaCo.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 92ce16e0e37e -r 6be8d5818087 tools/rgenetics/rgCaCo.xml --- a/tools/rgenetics/rgCaCo.xml Thu Apr 15 21:20:04 2010 -0400 +++ b/tools/rgenetics/rgCaCo.xml Thu Apr 15 21:41:50 2010 -0400 @@ -31,7 +31,7 @@ </param> <param name='name' value='rgCaCotest1' /> <output name='out_file1' file='rgCaCotest1_CaCo.xls' ftype='tabular' compare='diff' /> - <output name='logf' file='rgCaCotest1_CaCo_log.txt' ftype='txt' compare='diff' lines_diff='19' /> + <output name='logf' file='rgCaCotest1_CaCo_log.txt' ftype='txt' compare='diff' lines_diff='20' /> <output name='gffout' file='rgCaCotest1_CaCo_topTable.gff' ftype='gff' compare='diff' /> </test> </tests>

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[hg] galaxy 3661: Less blather from rgGRR and new functional tes...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/92ce16e0e37e changeset: 3661:92ce16e0e37e user: fubar: ross Lazarus at gmail period com date: Thu Apr 15 21:20:04 2010 -0400 description: Less blather from rgGRR and new functional test output files to match Stretch lines_diff even further to accomodate an older version of plink for functional tests diffstat: lib/galaxy/datatypes/genetics.py | 24 +- test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 21 +- test-data/rgtestouts/rgGRR/rgGRRtest1.html | 32 +- test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 517 +------ test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 1560 +++++++++++----------- test-data/smallwgaP.xls | 103 + tools/rgenetics/rgGLM.xml | 2 +- tools/rgenetics/rgGRR.py | 8 +- tools/rgenetics/rgGRR.xml | 2 +- tools/rgenetics/rgQC.xml | 2 +- 10 files changed, 967 insertions(+), 1304 deletions(-) diffs (2456 lines): diff -r ed5535c4d48e -r 92ce16e0e37e lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Thu Apr 15 15:58:08 2010 -0400 +++ b/lib/galaxy/datatypes/genetics.py Thu Apr 15 21:20:04 2010 -0400 @@ -86,8 +86,6 @@ site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - if base_url.startswith( 'https://' ): - base_url = base_url.replace( 'https', 'http', 1 ) display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) display_url = urllib.quote_plus( display_url ) # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) @@ -264,7 +262,7 @@ stored in extra files path """ - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="rgenetics", + MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", readonly=True, set_in_upload=True) composite_type = 'auto_primary_file' @@ -290,27 +288,15 @@ """ cannot do this until we are setting metadata """ - guessmt = {'.log':'text/plain','.ped':'text/plain', '.map':'text/plain','.out':'text/plain','.in':'text/plain'} - def fix(oldpath,newbase): - old,e = os.path.splitext(oldpath) - head,rest = os.path.split(old) - newpath = os.path.join(head,newbase) - newpath = '%s%s' % (newpath,e) - if oldpath <> newpath: - shutil.move(oldpath,newpath) - return newpath bn = dataset.metadata.base_name efp = dataset.extra_files_path flist = os.listdir(efp) - proper_base = bn - rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Composite %s contains the following files:<p/><ul>' % (dataset.name,dataset.name)] + rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name,dataset.name)] for i,fname in enumerate(flist): - newpath = fix(os.path.join(efp,fname),proper_base) - sfname = os.path.split(newpath)[-1] + sfname = os.path.split(fname)[-1] f,e = os.path.splitext(fname) - mt = guessmt.get(e,'application/binary') - rval.append( '<li><a href="%s" mimetype="%s">%s</a></li>' % ( sfname, mt, sfname) ) - rval.append( '</ul></html>' ) + rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) ) + rval.append( '</ul></body></html>' ) f = file(dataset.file_name,'w') f.write("\n".join( rval )) f.write('\n') diff -r ed5535c4d48e -r 92ce16e0e37e test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt --- a/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Thu Apr 15 15:58:08 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Thu Apr 15 21:20:04 2010 -0400 @@ -1,22 +1,13 @@ -Reading genotypes for 40 subjects and 25 markers -Calculating 780 pairs, updating every 78 pairs... +Reading genotypes for 40 subjects and 5 markers +Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec -0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec -0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec -0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec -0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec -0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec -0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec -0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec -0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec -T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19 +Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17 -Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15 +Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 +Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 780 pairs are available of 780 Outliers: 0 diff -r ed5535c4d48e -r 92ce16e0e37e test-data/rgtestouts/rgGRR/rgGRRtest1.html --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.html Thu Apr 15 15:58:08 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Thu Apr 15 21:20:04 2010 -0400 @@ -9,7 +9,7 @@ </head> <body> <div class="document"> -<h4><div>Output from rgGRR.py run at 25/03/2010 21:01:24<br> +<h4><div>Output from rgGRR.py run at 15/04/2010 13:12:45<br> </h4> If you need to rerun this analysis, the command line was <pre>'/opt/galaxy/tools/rgenetics/rgGRR.py' '/opt/galaxy/test-data/tinywga' 'tinywga' '/opt/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/opt/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6'</pre> @@ -18,43 +18,25 @@ <li><a href="rgGRRtest1_table.xls">Mean by SD alleles shared - 780 rows</a></li> <li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li> <li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> -</ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 25 markers +</ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 5 markers -Calculating 780 pairs, updating every 78 pairs... +Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec - -0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec - -0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec - -0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec - -0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec - -0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec - -0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec - -0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec - -0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec - -T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19 +Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17 +Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 -Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15 +Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 diff -r ed5535c4d48e -r 92ce16e0e37e test-data/rgtestouts/rgGRR/rgGRRtest1.svg --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Thu Apr 15 15:58:08 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Thu Apr 15 21:20:04 2010 -0400 @@ -5,9 +5,9 @@ xmlns="http://www.w3.org/2000/svg" version="1.2" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()"> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/checkbox_and_radiobutton.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/helper_functions.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/timer.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/checkbox_and_radiobutton.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/helper_functions.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/timer.js"/> <script type="text/ecmascript"> <![CDATA[ var checkBoxes = new Array(); @@ -247,492 +247,99 @@  <g style="fill:black; stroke:none" font-size="18" font-family="Arial"> - <text x="425" y="-30">rgGRRtest1 (40 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1.200000 0.577350 0.469098 0.077804 25 5 -101_1 12_1 1.200000 0.577350 0.469098 -0.467230 25 5 -101_1 12_2 1.200000 0.577350 0.469098 -0.467230 25 5 -101_1 12_3 1.200000 0.577350 1.071833 -0.655899 25 5 -101_1 13_1 1.200000 0.577350 -0.133637 -0.504142 25 5 -101_1 13_2 1.200000 0.577350 -0.255930 0.042025 25 5 -101_1 13_3 1.200000 0.577350 1.071832 -0.655899 25 5 -101_1 1334_1 1.200000 0.577350 -0.133636 0.045908 25 5 -101_1 1334_10 1.200000 0.577350 -0.334548 -0.566551 25 5 -101_1 1334_11 1.200000 0.577350 -0.937282 0.679102 25 5 -101_1 1334_12 1.200000 0.577350 -0.334548 -0.007823 25 5 -101_1 1334_13 1.200000 0.577350 -0.133636 -0.504142 25 5 -101_1 1334_2 1.200000 0.577350 -0.736370 1.194476 25 5 -101_1 1340_1 1.200000 0.577350 -0.535459 -0.084293 25 5 -101_1 1340_10 1.200000 0.577350 -0.535459 -0.084293 25 5 -101_1 1340_11 1.200000 0.577350 -0.133636 -0.504142 25 5 -101_1 1340_12 1.200000 0.577350 0.469098 -0.467231 25 5 -101_1 1340_2 1.200000 0.577350 0.469098 -0.467231 25 5 -101_1 1340_9 1.200000 0.577350 -2.142751 0.999931 25 5 -101_1 1341_1 1.200000 0.577350 0.163363 -0.455013 25 5 -101_1 1341_11 1.200000 0.577350 -0.334549 0.481281 25 5 -101_1 1341_12 1.200000 0.577350 -0.937282 -0.925605 25 5 -101_1 1341_13 1.200000 0.577350 -0.736371 0.779435 25 5 -101_1 1341_14 1.200000 0.577350 -0.736371 0.779435 25 5 -101_1 1341_2 1.200000 0.577350 -0.736371 0.779435 25 5 -101_1 1344_1 1.200000 0.577350 -0.535459 0.413356 25 5 -101_1 1344_12 1.200000 0.577350 0.469098 -0.467231 25 5 -101_1 1344_13 1.200000 0.577350 0.469098 -0.467231 25 5 -101_1 1345_12 1.200000 0.577350 -0.736370 -0.774446 25 5 -101_2 101_3 1.200000 0.577350 0.236040 -0.228179 25 5 -101_2 105_1 1.200000 0.577350 0.670010 -0.504142 25 5 -101_2 105_2 1.200000 0.577350 0.943250 -0.598443 25 5 -101_2 105_3 1.200000 0.577350 1.136125 -0.693367 25 5 -101_2 112_1 1.200000 0.577350 -0.599751 0.780517 25 5 -101_2 112_2 1.200000 0.577350 -0.792626 0.696771 25 5 -101_2 112_3 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_2 117_1 1.200000 0.577350 0.171750 0.062100 25 5 -101_2 117_2 1.200000 0.577350 0.557499 -0.483424 25 5 -101_2 117_3 1.200000 0.577350 0.557499 0.042491 25 5 -101_2 12_1 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 12_2 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 12_3 1.200000 0.577350 1.136124 -0.693367 25 5 -101_2 13_1 1.200000 0.577350 -0.021126 -0.483423 25 5 -101_2 13_2 1.200000 0.577350 -0.255930 0.042025 25 5 -101_2 13_3 1.200000 0.577350 1.136124 -0.693367 25 5 -101_2 1334_1 1.200000 0.577350 -0.021125 0.042491 25 5 -101_2 1334_10 1.200000 0.577350 -0.214001 -0.528970 25 5 -101_2 1334_11 1.200000 0.577350 -0.792626 0.696771 25 5 -101_2 1334_12 1.200000 0.577350 -0.214001 0.002982 25 5 -101_2 1334_13 1.200000 0.577350 -0.021126 -0.483424 25 5 -101_2 1334_2 1.200000 0.577350 -0.599751 1.178851 25 5 -101_2 1340_1 1.200000 0.577350 -0.406876 -0.057030 25 5 -101_2 1340_10 1.200000 0.577350 -0.406876 -0.057030 25 5 -101_2 1340_11 1.200000 0.577350 -0.021126 -0.483424 25 5 -101_2 1340_12 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 1340_2 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 1340_9 1.200000 0.577350 -1.949876 1.086115 25 5 -101_2 1341_1 1.200000 0.577350 0.268187 -0.455013 25 5 -101_2 1341_11 1.200000 0.577350 -0.214002 0.471641 25 5 -101_2 1341_12 1.200000 0.577350 -0.792626 -0.816040 25 5 -101_2 1341_13 1.200000 0.577350 -0.599751 0.780517 25 5 -101_2 1341_14 1.200000 0.577350 -0.599751 0.780517 25 5 -101_2 1341_2 1.200000 0.577350 -0.599751 0.780517 25 5 -101_2 1344_1 1.200000 0.577350 -0.406876 0.418047 25 5 -101_2 1344_12 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 1344_13 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 1345_12 1.200000 0.577350 -0.599751 -0.693367 25 5 -101_3 105_1 1.200000 0.577350 -1.540017 1.879362 25 5 -101_3 105_2 1.200000 0.577350 0.171750 -0.460872 25 5 -101_3 105_3 1.200000 0.577350 -0.792627 -0.242861 25 5 -101_3 112_1 1.200000 0.577350 -0.599750 0.780517 25 5 -101_3 112_2 1.200000 0.577350 -0.792626 2.157894 25 5 -101_3 112_3 1.200000 0.577350 -0.021126 -0.483423 25 5 -101_3 117_1 1.200000 0.577350 -0.599751 1.178851 25 5 -101_3 117_2 1.200000 0.577350 1.329000 -0.816040 25 5 -101_3 117_3 1.200000 0.577350 0.171750 0.062100 25 5 -101_3 12_1 1.200000 0.577350 2.486250 -2.592124 25 5 -101_3 12_2 1.200000 0.577350 2.486250 -2.592124 25 5 -101_3 12_3 1.200000 0.577350 1.136124 -0.693367 25 5 -101_3 13_1 1.200000 0.577350 1.521875 -0.969866 25 5 -101_3 13_2 1.200000 0.577350 -0.255930 0.546459 25 5 -101_3 13_3 1.200000 0.577350 1.136125 -0.693367 25 5 -101_3 1334_1 1.200000 0.577350 -0.021126 -0.483424 25 5 -101_3 1334_10 1.200000 0.577350 -0.599750 -0.693367 25 5 -101_3 1334_11 1.200000 0.577350 -0.792626 2.157894 25 5 -101_3 1334_12 1.200000 0.577350 -0.599751 0.345553 25 5 -101_3 1334_13 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_3 1334_2 1.200000 0.577350 -0.985501 1.388993 25 5 -101_3 1340_1 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_3 1340_10 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_3 1340_11 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_3 1340_12 1.200000 0.577350 -0.599750 -0.693367 25 5 -101_3 1340_2 1.200000 0.577350 -0.599751 0.345552 25 5 -101_3 1340_9 1.200000 0.577350 -0.406876 1.948414 25 5 -101_3 1341_1 1.200000 0.577350 -1.339106 0.413355 25 5 -101_3 1341_11 1.200000 0.577350 -1.371251 1.881413 25 5 -101_3 1341_12 1.200000 0.577350 -1.564126 0.158748 25 5 -101_3 1341_13 1.200000 0.577350 -0.599750 0.780517 25 5 -101_3 1341_14 1.200000 0.577350 -0.599750 0.780517 25 5 -101_3 1341_2 1.200000 0.577350 -0.599750 0.780517 25 5 -101_3 1344_1 1.200000 0.577350 -0.792626 2.157893 25 5 -101_3 1344_12 1.200000 0.577350 -0.599751 0.345552 25 5 -101_3 1344_13 1.200000 0.577350 -0.599751 0.345552 25 5 -101_3 1345_12 1.200000 0.577350 -1.371251 0.327238 25 5 -105_1 105_2 1.200000 0.577350 -1.155984 0.612530 25 5 -105_1 105_3 1.200000 0.577350 -0.936806 0.621689 25 5 -105_1 112_1 1.200000 0.577350 -1.540017 1.127651 25 5 -105_1 112_2 1.200000 0.577350 -0.133636 1.738452 25 5 -105_1 112_3 1.200000 0.577350 -1.339105 0.859974 25 5 -105_1 117_1 1.200000 0.577350 0.067275 0.991299 25 5 -105_1 117_2 1.200000 0.577350 -1.138194 0.991299 25 5 -105_1 117_3 1.200000 0.577350 -0.736371 0.779434 25 5 -105_1 12_1 1.200000 0.577350 -1.540017 1.879362 25 5 -105_1 12_2 1.200000 0.577350 -1.540017 1.879362 25 5 -105_1 12_3 1.200000 0.577350 -0.535459 0.859974 25 5 -105_1 13_1 1.200000 0.577350 -1.740928 1.738452 25 5 -105_1 13_2 1.200000 0.577350 -1.094517 0.648831 25 5 -105_1 13_3 1.200000 0.577350 -0.937282 0.679103 25 5 -105_1 1334_1 1.200000 0.577350 -0.937283 1.102364 25 5 -105_1 1334_10 1.200000 0.577350 -1.138194 0.991300 25 5 -105_1 1334_11 1.200000 0.577350 -0.133636 1.738452 25 5 -105_1 1334_12 1.200000 0.577350 -1.138194 0.991300 25 5 -105_1 1334_13 1.200000 0.577350 -0.937282 0.213207 25 5 -105_1 1334_2 1.200000 0.577350 -1.540016 1.879362 25 5 -105_1 1340_1 1.200000 0.577350 -1.339106 0.859974 25 5 -105_1 1340_10 1.200000 0.577350 -1.339106 0.859974 25 5 -105_1 1340_11 1.200000 0.577350 -0.937282 0.213207 25 5 -105_1 1340_12 1.200000 0.577350 -0.334548 -0.566551 25 5 -105_1 1340_2 1.200000 0.577350 0.469098 -0.467231 25 5 -105_1 1340_9 1.200000 0.577350 -2.946397 2.337655 25 5 -105_1 1341_1 1.200000 0.577350 0.582657 -0.481725 25 5 -105_1 1341_11 1.200000 0.577350 0.469098 0.077804 25 5 -105_1 1341_12 1.200000 0.577350 -0.535459 1.268636 25 5 -105_1 1341_13 1.200000 0.577350 -1.540017 1.127651 25 5 -105_1 1341_14 1.200000 0.577350 -1.540017 1.127651 25 5 -105_1 1341_2 1.200000 0.577350 -1.540017 1.127651 25 5 -105_1 1344_1 1.200000 0.577350 0.268187 1.397944 25 5 -105_1 1344_12 1.200000 0.577350 0.469098 -0.467231 25 5 -105_1 1344_13 1.200000 0.577350 0.469098 -0.467231 25 5 -105_1 1345_12 1.200000 0.577350 -0.334549 1.325597 25 5 -105_2 105_3 1.200000 0.577350 0.722984 0.122716 25 5 -105_2 112_1 1.200000 0.577350 -0.021126 0.507014 25 5 -105_2 112_2 1.200000 0.577350 -0.214001 0.471641 25 5 -105_2 112_3 1.200000 0.577350 0.943249 -0.598443 25 5 -105_2 117_1 1.200000 0.577350 0.750376 -0.528970 25 5 -105_2 117_2 1.200000 0.577350 1.521875 -0.969866 25 5 -105_2 117_3 1.200000 0.577350 1.521875 -0.969867 25 5 -105_2 12_1 1.200000 0.577350 0.364625 -0.460872 25 5 -105_2 12_2 1.200000 0.577350 0.364625 -0.460872 25 5 -105_2 12_3 1.200000 0.577350 0.943251 -0.598443 25 5 -105_2 13_1 1.200000 0.577350 -0.214002 -0.528970 25 5 -105_2 13_2 1.200000 0.577350 0.163363 0.111360 25 5 -105_2 13_3 1.200000 0.577350 0.943249 -0.598444 25 5 -105_2 1334_1 1.200000 0.577350 1.328999 -0.816040 25 5 -105_2 1334_10 1.200000 0.577350 0.364624 -0.460872 25 5 -105_2 1334_11 1.200000 0.577350 -0.214001 0.471641 25 5 -105_2 1334_12 1.200000 0.577350 -0.021126 0.042491 25 5 -105_2 1334_13 1.200000 0.577350 0.943249 -0.598443 25 5 -105_2 1334_2 1.200000 0.577350 -0.792626 1.101688 25 5 -105_2 1340_1 1.200000 0.577350 0.557499 -0.483424 25 5 -105_2 1340_10 1.200000 0.577350 0.557499 -0.483424 25 5 -105_2 1340_11 1.200000 0.577350 0.943249 -0.598443 25 5 -105_2 1340_12 1.200000 0.577350 1.907625 -1.394354 25 5 -105_2 1340_2 1.200000 0.577350 1.521875 -0.969866 25 5 -105_2 1340_9 1.200000 0.577350 -1.371251 1.163511 25 5 -105_2 1341_1 1.200000 0.577350 1.272743 -0.774447 25 5 -105_2 1341_11 1.200000 0.577350 0.364624 0.524595 25 5 -105_2 1341_12 1.200000 0.577350 -0.599751 -0.693367 25 5 -105_2 1341_13 1.200000 0.577350 -0.021126 0.507014 25 5 -105_2 1341_14 1.200000 0.577350 -0.021126 0.507014 25 5 -105_2 1341_2 1.200000 0.577350 -0.021126 0.507014 25 5 -105_2 1344_1 1.200000 0.577350 0.171750 0.062100 25 5 -105_2 1344_12 1.200000 0.577350 1.521875 -0.969866 25 5 -105_2 1344_13 1.200000 0.577350 1.521875 -0.969866 25 5 -105_2 1345_12 1.200000 0.577350 -0.406876 -0.598443 25 5 -105_3 112_1 1.200000 0.577350 0.943249 -0.057030 25 5 -105_3 112_2 1.200000 0.577350 -0.406876 -0.057030 25 5 -105_3 112_3 1.200000 0.577350 0.750375 -0.528970 25 5 -105_3 117_1 1.200000 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+rs16823529 1 3161070 1.000 0.000000 0.534 0.272621 0.541 0.266883 1.000 0.000000 +rs12075867 1 3161113 1.000 0.000000 0.191 0.719422 0.193 0.713768 1.000 0.000000 +rs2817148 1 3161293 1.000 0.000000 0.009 2.050269 0.006 2.244583 1.000 0.000000 +rs2651891 1 3163073 1.000 0.000000 0.009 2.050269 0.006 2.244583 1.000 0.000000 +rs16823551 1 3164773 1.000 0.000000 0.005 2.260982 0.004 2.447453 1.000 0.000000 +rs10157420 1 3169654 1.000 0.000000 0.413 0.383840 0.432 0.364919 1.000 0.000000 +rs6424069 1 3170187 1.000 0.000000 0.004 2.354381 0.003 2.495257 1.000 0.000000 + diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgGLM.xml --- a/tools/rgenetics/rgGLM.xml Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgGLM.xml Thu Apr 15 21:20:04 2010 -0400 @@ -68,7 +68,7 @@ <param name='maf' value='0.0' /> <param name='logistic' value='0' /> <output name='out_file1' file='rgGLMtest1_GLM.xls' ftype='tabular' compare="diff" /> - <output name='logf' file='rgGLMtest1_GLM_log.txt' ftype='txt' compare="diff" lines_diff='33'/> + <output name='logf' file='rgGLMtest1_GLM_log.txt' ftype='txt' compare="diff" lines_diff='36'/> <output name='gffout' file='rgGLMtest1_GLM_topTable.gff' compare="diff" ftype='gff' /> </test> </tests> diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgGRR.py --- a/tools/rgenetics/rgGRR.py Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgGRR.py Thu Apr 15 21:20:04 2010 -0400 @@ -639,7 +639,7 @@ skip = set() ndone = 0 ## How many have been done so far - logf.write('Calculating %d pairs, updating every %d pairs...\n' % (tot, nprog)) + logf.write('Calculating %d pairs...\n' % (tot)) logf.write('Estimated time is %2.2f to %2.2f seconds ...\n' % (estimatedTimeFast, estimatedTimeSlow)) t1sum = 0 @@ -695,10 +695,6 @@ for s2 in xrange(s1+1, nSubjects): if s2 in emptyRows: continue - if nprog and ndone % nprog == 0 and ndone > 1: - dur = time.time() - started - pct = float(ndone)/tot*100.0 - logf.write('%f sec at pair %d of %d (%3.2f%%): %f marker*pairs/sec\n' % (dur, ndone, tot, pct, ndone/dur*nrsSamples)) t1s = time.time() (fid2,iid2,did2,mid2,sex2,phe2,iid2,d_sid2,m_sid2) = scache.setdefault(s2, ped.getSubject(s2)) @@ -848,9 +844,7 @@ continue outliers = [(scalefactor*int(abs(x[3]))+ int(abs(x[2])),x) for x in outliers] # decorate outliers.sort() - logf.write('### outliers after decorated sort=%s' % outliers) outliers.reverse() # largest deviation first - logf.write('### outliers after decorated sort=%s' % outliers) outliers = [x[1] for x in outliers] # undecorate nrows = len(outliers) truncated = 0 diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgGRR.xml --- a/tools/rgenetics/rgGRR.xml Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgGRR.xml Thu Apr 15 21:20:04 2010 -0400 @@ -29,7 +29,7 @@ <param name='n' value='100' /> <param name='Z' value='6' /> <output name='out_file1' file='rgtestouts/rgGRR/rgGRRtest1.html' ftype='html' compare="diff" lines_diff='30'> - <extra_files type="file" name='Log_rgGRRtest1.txt' value="rgtestouts/rgGRR/Log_rgGRRtest1.txt" compare="diff" lines_diff="30"/> + <extra_files type="file" name='Log_rgGRRtest1.txt' value="rgtestouts/rgGRR/Log_rgGRRtest1.txt" compare="diff" lines_diff="70"/> <extra_files type="file" name='rgGRRtest1.svg' value="rgtestouts/rgGRR/rgGRRtest1.svg" compare="diff" lines_diff="1000" /> <extra_files type="file" name='rgGRRtest1_table.xls' value="rgtestouts/rgGRR/rgGRRtest1_table.xls" compare="diff" lines_diff="100" /> </output> diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgQC.xml Thu Apr 15 21:20:04 2010 -0400 @@ -27,7 +27,7 @@ <composite_data value='tinywga.fam' /> </param> <param name='out_prefix' value='rgQCtest1' /> - <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='250'> + <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='260'> <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="diff" lines_diff="2600"/> <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="10"/> <extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" />

1 0

[hg] galaxy 3660: Decouple the Galaxy specific foms stuff ( addr...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ed5535c4d48e changeset: 3660:ed5535c4d48e user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Apr 15 15:58:08 2010 -0400 description: Decouple the Galaxy specific foms stuff ( address, etc ) from the User Preferences page. diffstat: lib/galaxy/web/controllers/user.py | 122 ++++++++++------- templates/user/index.mako | 6 +- templates/user/info.mako | 207 ++++++---------------------- templates/webapps/community/user/info.mako | 9 + templates/webapps/galaxy/user/info.mako | 122 +++++++++++++++++ 5 files changed, 252 insertions(+), 214 deletions(-) diffs (651 lines): diff -r 1dc7e6c15272 -r ed5535c4d48e lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Thu Apr 15 12:33:28 2010 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu Apr 15 15:58:08 2010 -0400 @@ -297,6 +297,8 @@ def __validate_username( self, trans, username, user=None ): # User names must be at least four characters in length and contain only lower-case # letters, numbers, and the '-' character. + if username in [ 'None', None, '' ]: + return None if user and user.username == username: return None if len( username ) < 4: @@ -323,17 +325,14 @@ error = self.__validate_username( trans, username ) if not error: if webapp == 'galaxy': - # TODO: the user controller must be decoupled from the model, so this import causes problems. - # The get_all_forms method is used only if Galaxy is the webapp, so it needs to be re-worked - # so that it can be imported with no problems if the controller is not 'galaxy'. from galaxy.web.controllers.forms import get_all_forms if len( get_all_forms( trans, filter=dict( deleted=False ), form_type=trans.app.model.FormDefinition.types.USER_INFO ) ): if not params.get( 'user_info_select', False ): - return 'Select the user type and the user information' + return "Select the user's type and information" return error - def __user_info_ui(self, trans, user=None, **kwd): + def __user_info_ui( self, trans, user=None, **kwd ): ''' This method creates the user type select box & user information form widgets and is called during user registration and editing user information. @@ -342,14 +341,12 @@ show a selectbox containing all the forms, then the user can select the one that fits the user's description the most ''' - # TODO: the user controller must be decoupled from the model, so this import causes problems. - # The get_all_forms method is used only if Galaxy is the webapp, so it needs to be re-worked - # so that it can be imported with no problems if the controller is not 'galaxy'. from galaxy.web.controllers.forms import get_all_forms params = util.Params( kwd ) # get all the user information forms - user_info_forms = get_all_forms( trans, filter=dict(deleted=False), - form_type=trans.app.model.FormDefinition.types.USER_INFO ) + user_info_forms = get_all_forms( trans, + filter=dict( deleted=False ), + form_type=trans.app.model.FormDefinition.types.USER_INFO ) user_info_select = None if user: if user.values: @@ -398,19 +395,15 @@ information, public user name, reset password & other user information obtained during registration ''' - # TODO: the user controller must be decoupled from the model, so this import causes problems. - # The get_all_forms method is used only if Galaxy is the webapp, so it needs to be re-worked - # so that it can be imported with no problems if the controller is not 'galaxy'. - from galaxy.web.controllers.forms import get_all_forms params = util.Params( kwd ) user_id = params.get( 'user_id', None ) + webapp = params.get( 'webapp', 'galaxy' ) if user_id: user = trans.sa_session.query( trans.app.model.User ).get( int( user_id ) ) else: user = trans.user if not user: - # TODO: handle this without the deprecated exception. - raise "In show_info, we don't have a valid user" + raise AssertionError, "The user id (%s) is not valid" % str( user_id ) email = util.restore_text( params.get( 'email', user.email ) ) # Do not sanitize passwords, so take from kwd # instead of params ( which were sanitized ) @@ -423,38 +416,55 @@ admin_view = util.string_as_bool( params.get( 'admin_view', False ) ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - user_info_select, user_info_form, widgets = self.__user_info_ui( trans, user, **kwd ) - # user's addresses - show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) - if show_filter == 'All': - addresses = [address for address in user.addresses] - elif show_filter == 'Deleted': - addresses = [address for address in user.addresses if address.deleted] + if webapp == 'galaxy': + from galaxy.web.controllers.forms import get_all_forms + user_info_select, user_info_form, widgets = self.__user_info_ui( trans, user, **kwd ) + # user's addresses + show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) + if show_filter == 'All': + addresses = [address for address in user.addresses] + elif show_filter == 'Deleted': + addresses = [address for address in user.addresses if address.deleted] + else: + addresses = [address for address in user.addresses if not address.deleted] + user_info_forms = get_all_forms( trans, + filter=dict( deleted=False ), + form_type=trans.app.model.FormDefinition.types.USER_INFO ) + return trans.fill_template( '/webapps/galaxy/user/info.mako', + user=user, + email=email, + current=current, + password=password, + confirm=confirm, + username=username, + user_info_select=user_info_select, + user_info_forms=user_info_forms, + user_info_form=user_info_form, + widgets=widgets, + addresses=addresses, + show_filter=show_filter, + admin_view=admin_view, + webapp=webapp, + message=message, + status=status ) else: - addresses = [address for address in user.addresses if not address.deleted] - user_info_forms = get_all_forms( trans, filter=dict(deleted=False), - form_type=trans.app.model.FormDefinition.types.USER_INFO ) - return trans.fill_template( '/user/info.mako', - user=user, - email=email, - current=current, - password=password, - confirm=confirm, - username=username, - user_info_select=user_info_select, - user_info_forms=user_info_forms, - user_info_form=user_info_form, - widgets=widgets, - addresses=addresses, - show_filter=show_filter, - admin_view=admin_view, - message=message, - status=status ) + return trans.fill_template( '/webapps/community/user/info.mako', + user=user, + email=email, + current=current, + password=password, + confirm=confirm, + username=username, + admin_view=False, + webapp=webapp, + message=message, + status=status ) @web.expose def edit_info( self, trans, **kwd ): params = util.Params( kwd ) user_id = params.get( 'user_id', None ) admin_view = util.string_as_bool( params.get( 'admin_view', False ) ) + webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) if user_id: @@ -467,11 +477,12 @@ username = util.restore_text( params.get( 'username', '' ) ).lower() # validate the new values error = self.__validate_email( trans, email, user ) - if not error: + if not error and username: error = self.__validate_username( trans, username, user ) if error: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=error, status='error') ) # The user's private role name must match the user's login ( email ) @@ -484,15 +495,17 @@ trans.sa_session.add_all( ( user, private_role ) ) trans.sa_session.flush() message = 'The login information has been updated with the changes' - if admin_view: + if webapp == 'galaxy' and admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', user_id=user.id, admin_view=admin_view, + webapp=webapp, message=message, status='done' ) ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=message, status='done') ) # Change password @@ -502,27 +515,30 @@ password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) # When from the user perspective, validate the current password - if not admin_view: + if not webapp == 'galaxy' and not admin_view: # Do not sanitize passwords, so get from kwd and not params # ( which were sanitized ). current = kwd.get( 'current', '' ) if not trans.user.check_password( current ): return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message='Invalid current password', status='error') ) # validate the new values error = self.__validate_password( trans, password, confirm ) if error: - if admin_view: + if webapp == 'galaxy' and admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, user_id=user.id, admin_view=admin_view, message=error, status='error' ) ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=error, status='error') ) # save new password @@ -531,40 +547,46 @@ trans.sa_session.flush() trans.log_event( "User change password" ) message = 'The password has been changed.' - if admin_view: + if webapp == 'galaxy' and admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, user_id=user.id, admin_view=admin_view, message=message, status='done' ) ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=message, status='done') ) - # Edit user information + # Edit user information - webapp MUST BE 'galaxy' elif params.get( 'edit_user_info_button', False ): self.__save_user_info(trans, user, "show_info", new_user=False, **kwd) message = "The user information has been updated with the changes." if admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, user_id=user.id, admin_view=admin_view, message=message, status='done' ) ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=message, status='done') ) else: - if admin_view: + if webapp == 'galaxy' and admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, user_id=user.id, admin_view=admin_view ) ) return trans.response.send_redirect( web.url_for( controller='user', - action='show_info' ) ) + action='show_info', + webapp=webapp ) ) @web.expose def reset_password( self, trans, email=None, webapp='galaxy', **kwd ): message = util.restore_text( kwd.get( 'message', '' ) ) diff -r 1dc7e6c15272 -r ed5535c4d48e templates/user/index.mako --- a/templates/user/index.mako Thu Apr 15 12:33:28 2010 -0400 +++ b/templates/user/index.mako Thu Apr 15 15:58:08 2010 -0400 @@ -10,8 +10,10 @@ <p>You are currently logged in as ${trans.user.email}.</p> <ul> %if webapp == 'galaxy': - <li><a href="${h.url_for( action='show_info' )}">${_('Manage your information')}</a></li> - <li><a href="${h.url_for( action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> + <li><a href="${h.url_for( controller='user', action='show_info' )}">${_('Manage your information')}</a></li> + <li><a href="${h.url_for( controller='user', action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> + %else: + <li><a href="${h.url_for( controller='user', action='show_info', webapp='community' )}">${_('Manage your information')}</a></li> %endif </ul> %else: diff -r 1dc7e6c15272 -r ed5535c4d48e templates/user/info.mako --- a/templates/user/info.mako Thu Apr 15 12:33:28 2010 -0400 +++ b/templates/user/info.mako Thu Apr 15 15:58:08 2010 -0400 @@ -1,176 +1,59 @@ <%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -%if message: - ${render_msg( message, status )} -%endif - -<h2>Manage User Information</h2> -%if not admin_view: - <ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='user', action='index')}"> - <span>User preferences</span></a> - </li> - </ul> -%endif - -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#user_info" ).submit(); - } - }); -}); -</script> - -<div class="toolForm"> - <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">Login Information</div> - <div class="form-row"> - <label>Email address:</label> - <input type="text" name="email" value="${email}" size="40"/> - </div> - <div class="form-row"> - <label>Public user name:</label> - <input type="text" name="username" size="40" value="${username}"/> - <div class="toolParamHelp" style="clear: both;"> - Your user name is an optional identifier that will be used to generate addresses for information - you share publicly. User names must be at least four characters in length and contain only lower-case - letters, numbers, and the '-' character. +<%def name="render_user_info()"> + <h2>Manage User Information</h2> + %if not admin_view: + <ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='user', action='index' )}"> + <span>User preferences</span></a> + </li> + </ul> + %endif + <div class="toolForm"> + <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">Login Information</div> + <div class="form-row"> + <label>Email address:</label> + <input type="text" name="email" value="${email}" size="40"/> </div> - </div> - <div class="form-row"> - <input type="submit" name="login_info_button" value="Save"/> - </div> - </form> -</div> -<p></p> -<div class="toolForm"> - <form name="change_password" id="change_password" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">Change Password</div> - %if not admin_view: <div class="form-row"> - <label>Current Password:</label> - <input type="password" name="current" value="${current}" size="40"/> + <label>Public user name:</label> + <input type="text" name="username" size="40" value="${username}"/> + <div class="toolParamHelp" style="clear: both;"> + Your user name is an optional identifier that will be used to generate addresses for information + you share publicly. User names must be at least four characters in length and contain only lower-case + letters, numbers, and the '-' character. + </div> </div> - %endif - <div class="form-row"> - <label>New Password:</label> - <input type="password" name="password" value="${password}" size="40"/> - </div> - <div class="form-row"> - <label>Confirm:</label> - <input type="password" name="confirm" value="${confirm}" size="40"/> - </div> - <div class="form-row"> - <input type="submit" name="change_password_button" value="Save"/> - </div> - </form> -</div> -%if user.values or user_info_forms: - <p></p> - <div class="toolForm"> - <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">User information</div> - %if user_info_select: - <div class="form-row"> - <label>User type:</label> - ${user_info_select.get_html()} - </div> - %endif - - %for field in widgets: - <div class="form-row"> - <label>${field['label']}:</label> - ${field['widget'].get_html()} - <div class="toolParamHelp" style="clear: both;"> - ${field['helptext']} - </div> - <div style="clear: both"></div> - </div> - %endfor - %if not user_info_select: - <input type="hidden" name="user_info_select" value="${user_info_form.id}"/> - %endif - <div class="form-row"> - <input type="submit" name="edit_user_info_button" value="Save"/> + <input type="hidden" name="webapp" value="${webapp}" size="40"/> + <input type="submit" name="login_info_button" value="Save"/> </div> </form> </div> -%endif -<p></p> -<div class="toolForm"> - <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">User Addresses</div> - <div class="toolFormBody"> - %if user.addresses: + <p></p> + <div class="toolForm"> + <form name="change_password" id="change_password" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">Change Password</div> + %if not admin_view: <div class="form-row"> - <div class="grid-header"> - ##<span class="title">Filter:</span> - %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): - %if i > 0: - <span>|</span> - %endif - %if show_filter == filter: - <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}"><b>${filter}</b></a></span> - %else: - <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}">${filter}</a></span> - %endif - %endfor + <label>Current Password:</label> + <input type="password" name="current" value="${current}" size="40"/> </div> - </div> - <table class="grid"> - <tbody> - %for index, address in enumerate(addresses): - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td> - <div class="form-row"> - <label>${address.desc}:</label> - ${address.get_html()} - </div> - <div class="form-row"> - <ul class="manage-table-actions"> - <li> - %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', admin_view=admin_view, address_id=address.id, user_id=user.id )}"> - <span>Edit</span></a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"> - <span>Delete</span></a> - %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"> - <span>Undelete</span></a> - %endif - - </li> - </ul> - </div> - </td> - </tr> - %endfor - </tbody> - </table> %endif <div class="form-row"> - <input type="submit" value="Add a new address"> + <label>New Password:</label> + <input type="password" name="password" value="${password}" size="40"/> </div> - </div> - </form> -</div> + <div class="form-row"> + <label>Confirm:</label> + <input type="password" name="confirm" value="${confirm}" size="40"/> + </div> + <div class="form-row"> + <input type="hidden" name="webapp" value="${webapp}" size="40"/> + <input type="submit" name="change_password_button" value="Save"/> + </div> + </form> + </div> +</%def> diff -r 1dc7e6c15272 -r ed5535c4d48e templates/webapps/community/user/info.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/user/info.mako Thu Apr 15 15:58:08 2010 -0400 @@ -0,0 +1,9 @@ +<%inherit file="/base.mako"/> +<%namespace file="/user/info.mako" import="render_user_info" /> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +${render_user_info()} diff -r 1dc7e6c15272 -r ed5535c4d48e templates/webapps/galaxy/user/info.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/galaxy/user/info.mako Thu Apr 15 15:58:08 2010 -0400 @@ -0,0 +1,122 @@ +<%inherit file="/base.mako"/> +<%namespace file="/user/info.mako" import="render_user_info" /> +<%namespace file="/message.mako" import="render_msg" /> + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#user_info" ).submit(); + } + }); +}); +</script> + +%if message: + ${render_msg( message, status )} +%endif + +${render_user_info()} + +%if user.values or user_info_forms: + <p></p> + <div class="toolForm"> + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">User information</div> + %if user_info_select: + <div class="form-row"> + <label>User type:</label> + ${user_info_select.get_html()} + </div> + %endif + %for field in widgets: + <div class="form-row"> + <label>${field['label']}:</label> + ${field['widget'].get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + %if not user_info_select: + <input type="hidden" name="user_info_select" value="${user_info_form.id}"/> + %endif + + <div class="form-row"> + <input type="submit" name="edit_user_info_button" value="Save"/> + </div> + </form> + </div> + <p></p> +%endif + +<div class="toolForm"> + <p></p> + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">User Addresses</div> + <div class="toolFormBody"> + %if user.addresses: + <div class="form-row"> + <div class="grid-header"> + %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): + %if i > 0: + <span>|</span> + %endif + %if show_filter == filter: + <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}"><b>${filter}</b></a></span> + %else: + <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}">${filter}</a></span> + %endif + %endfor + </div> + </div> + <table class="grid"> + <tbody> + %for index, address in enumerate(addresses): + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td> + <div class="form-row"> + <label>${address.desc}:</label> + ${address.get_html()} + </div> + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + %if not address.deleted: + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', admin_view=admin_view, address_id=address.id, user_id=user.id )}"><span>Edit</span></a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"><span>Delete</span></a> + %else: + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"><span>Undelete</span></a> + %endif + </li> + </ul> + </div> + </td> + </tr> + %endfor + </tbody> + </table> + %endif + <div class="form-row"> + <input type="submit" value="Add a new address"> + </div> + </div> + </form> + <p></p> +</div>

1 0

[hg] galaxy 3659: Have fastq set_meta() only skip counting 'comm...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1dc7e6c15272 changeset: 3659:1dc7e6c15272 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Apr 15 12:33:28 2010 -0400 description: Have fastq set_meta() only skip counting 'comment lines' when they are before any sequences. This is still not properly determining sequence counts in cases where line wrapping occurs; quality score lines can start with e.g. '#' and '@'. diffstat: lib/galaxy/datatypes/sequence.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r df40eae8e86b -r 1dc7e6c15272 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Apr 15 11:10:57 2010 -0400 +++ b/lib/galaxy/datatypes/sequence.py Thu Apr 15 12:33:28 2010 -0400 @@ -163,7 +163,7 @@ seq_counter = 0 # blocks should be 4 lines long for line in file( dataset.file_name ): line = line.strip() - if line and line.startswith( '#' ): + if line and line.startswith( '#' ) and not sequences: # We don't count comment lines for sequence data types continue if line and line.startswith( '@' ):

1 0

[hg] galaxy 3658: changes to help text
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/df40eae8e86b changeset: 3658:df40eae8e86b user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Apr 15 11:10:57 2010 -0400 description: changes to help text diffstat: tools/samtools/pileup_parser.xml | 10 +++++----- 1 files changed, 5 insertions(+), 5 deletions(-) diffs (48 lines): diff -r 33eab99a2df5 -r df40eae8e86b tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Thu Apr 15 10:51:51 2010 -0400 +++ b/tools/samtools/pileup_parser.xml Thu Apr 15 11:10:57 2010 -0400 @@ -93,7 +93,7 @@ <param name="type_select" value="ten"/> <param name="qv_cutoff" value="20" /> <param name="cvrg_cutoff" value="3" /> - <param name="snps_only" value="Yes"/> + <param name="snps_only" value="Yes"/>q <param name="interval" value="Yes" /> <param name="diff" value="No" /> <param name="qc_base" value="Yes" /> @@ -183,7 +183,7 @@ 2 Position (1-based) 3 Reference base at that position 4 Coverage (# reads aligning over that position) - 5 Bases within reads where (see Galaxy wiki for more info) + 5 Bases within reads 6 Quality values (phred33 scale, see Galaxy wiki for more) **Ten column pileup** @@ -210,7 +210,7 @@ 6 SNP quality 7 Maximum mapping quality 8 Coverage (# reads aligning over that position) - 9 Bases within reads where (see Galaxy wiki for more info) + 9 Bases within reads 10 Quality values (phred33 scale, see Galaxy wiki for more) @@ -255,7 +255,7 @@ 2 Position (1-based) 3 Reference base at that position 4 Coverage (# reads aligning over that position) - 5 Bases within reads where (see Galaxy wiki for more info) + 5 Bases within reads where 6 Quality values (phred33 scale, see Galaxy wiki for more) 7 Number of A variants 8 Number of C variants @@ -289,7 +289,7 @@ 3 End position (1-based) 4 Reference base at that position 5 Coverage (# reads aligning over that position) - 6 Bases within reads where (see Galaxy wiki for more info) + 6 Bases within reads 7 Quality values (phred33 scale, see Galaxy wiki for more) 8 Number of A variants 9 Number of C variants

1 0

[hg] galaxy 3657: Small fixes to rgGRR and rgManQQ
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/33eab99a2df5 changeset: 3657:33eab99a2df5 user: fubar: ross Lazarus at gmail period com date: Thu Apr 15 10:51:51 2010 -0400 description: Small fixes to rgGRR and rgManQQ Prevent default base_name overwriting real base_name in root.py Revert to prevent infotrack being requested - even the latest release of Haploview 4.2 is busted and fails to create any images when creating the infotrack - this only happens in headless mode and seems to be an upstream bug in a java library. No sign of a fix despite multiple pleas to the Haploview authors... Allow https in ucsc genome graphs - suggestion from Assaf Gordon - thanks. Fixes to creation of html page for rgenetics composite datatypes related to base_name problems traced to root.py when user tries to autodetect on the metadata edit page diffstat: lib/galaxy/web/controllers/root.py | 2 +- test-data/rgtestouts/rgManQQ/Allelep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R | 52 ++++++++------ test-data/rgtestouts/rgManQQ/rgManQQtest1.html | 10 +-- tools/rgenetics/rgGRR.py | 66 +----------------- tools/rgenetics/rgHaploView.py | 1 + tools/rgenetics/rgHaploView.xml | 2 +- tools/rgenetics/rgManQQ.py | 14 ++-- tools/rgenetics/rgManQQ.xml | 2 +- tools/rgenetics/rgQC.py | 3 +- tools/rgenetics/rgtest_one_tool.sh | 5 +- tools/rgenetics/rgutils.py | 63 +++++++++++++++++- 13 files changed, 115 insertions(+), 105 deletions(-) diffs (453 lines): diff -r 6f43a97e7908 -r 33eab99a2df5 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Apr 15 10:35:31 2010 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Apr 15 10:51:51 2010 -0400 @@ -314,7 +314,7 @@ return trans.show_error_message( "This dataset is currently being used as input or output. You cannot change metadata until the jobs have completed or you have canceled them." ) for name, spec in data.metadata.spec.items(): # We need to be careful about the attributes we are resetting - if name not in [ 'name', 'info', 'dbkey' ]: + if name not in [ 'name', 'info', 'dbkey', 'base_name' ]: if spec.get( 'default' ): setattr( data.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) if trans.app.config.set_metadata_externally: diff -r 6f43a97e7908 -r 33eab99a2df5 test-data/rgtestouts/rgManQQ/Allelep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Allelep_manhattan.png has changed diff -r 6f43a97e7908 -r 33eab99a2df5 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png has changed diff -r 6f43a97e7908 -r 33eab99a2df5 test-data/rgtestouts/rgManQQ/rgManQQtest1.R --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Thu Apr 15 10:35:31 2010 -0400 +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Thu Apr 15 10:51:51 2010 -0400 @@ -22,7 +22,7 @@ manhattan = function(chrom=NULL,offset=NULL,pvals=NULL, title=NULL, max.y="max", - suggestiveline=0, genomewide=T, size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL,grey=F) { + suggestiveline=0, genomewide=T, size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL,grey=0) { if (annotate & is.null(SNPlist)) stop("You requested annotation but provided no SNPlist!") genomewideline=NULL # was genomewideline=-log10(5e-8) @@ -43,10 +43,8 @@ lastbase=0 chrlist = unique(d$CHR) nchr = length(chrlist) # may be any number? - print(paste('## manhattan got chrlist=',chrlist,'nchr',nchr)) for (x in c(1:nchr)) { i = chrlist[x] # need the chrom number - may not == index - print(paste('## manhattan got chrlist=',chrlist,'nchr',nchr,'x=',x,'i=',i)) if (x == 1) { # first time d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP } else { @@ -63,8 +61,9 @@ } if (max.y=="max") maxy=ceiling(max(d$logp)) else maxy=max.y - if (maxy<8) maxy=8 - + maxy = max(maxy,1.1*genomewideline) + # if (maxy<8) maxy=8 + # only makes sense if genome wide is assumed - we could have a fine mapping region? if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ] plot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR)) @@ -76,11 +75,13 @@ plot=plot + opts(title=title) plot=plot+opts( panel.background=theme_blank(), - panel.grid.minor=theme_blank(), axis.text.x=theme_text(size=size.x.labels, colour="grey50"), axis.text.y=theme_text(size=size.y.labels, colour="grey50"), axis.ticks=theme_segment(colour=NA) ) + #plot = plot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank()) + #plot = plot + opts(panel.grid.major=theme_blank()) + if (suggestiveline) plot=plot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3)) if (genomewideline) plot=plot+geom_hline(yintercept=genomewideline,colour="red") plot @@ -107,44 +108,51 @@ if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) plot } - - -#rs Chr Offset Genop log10Genop Armitagep log10Armitagep Allelep log10Allelep Domp log10Domp -#rs3094315 1 792429 1.000 0.000000 0.122 0.912574 0.152 0.817871 1.000 0.000000 -# eg for testing -# this function needs column numbers so galaxy tool is easy to drive - rgqqMan = function(infile="/opt/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), - title="rgManQQtest1",outprefix="rgManQQtest1") { - d = read.table(infile,head=T,sep=' ') - print(paste('###',length(d[,1]),'values read from',infile,'read - now running plots',sep=' ')) +title="rgManQQtest1",grey=0) { +rawd = read.table(infile,head=T,sep=' ') +dn = names(rawd) +cc = dn[chromcolumn] +oc = dn[offsetcolumn] +nams = c(cc,oc) +plen = length(rawd[,1]) +doreorder=1 +print(paste('###',plen,'values read from',infile,'read - now running plots',sep=' ')) +if (plen > 0) { for (pvalscolumn in pvalscolumns) { if (pvalscolumn > 0) { - cname = names(d)[pvalscolumn] + cname = names(rawd)[pvalscolumn] mytitle = paste('p=',cname,', ',title,sep='') myfname = chartr(' ','_',cname) - myqqplot = qq(d[,pvalscolumn],title=mytitle) + myqqplot = qq(rawd[,pvalscolumn],title=mytitle) print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { + if (doreorder) { + rawd = rawd[do.call(order,rawd[nams]),] + # mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according… + # in case not yet ordered + doreorder = 0 + } print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) - mymanplot= manhattan(chrom=d[,chromcolumn],offset=d[,offsetcolumn],pvals=d[,pvalscolumn],title=mytitle) + mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) ggsave(file=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) } else { print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn, - 'Cannot parse - no manhattan plot possible')) + 'so no Manhattan plot - supply both chromosome and offset as numerics for Manhattan plots if required')) } - ggsave(file=paste(myfname,"qqplot.png",sep='_'),myqqplot,w=5,h=5,dpi=100) + ggsave(file=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=8,height=11,dpi=100) } else { print(paste('pvalue column =',pvalscolumn,'Cannot parse it so no plots possible')) } } # for pvalscolumn + } else { print('## Problem - no values available to plot - was there really a chromosome and offset column?') } } rgqqMan() # execute with defaults as substituted -#R script autogenerated by rgenetics/rgutils.py on 25/03/2010 21:01:09 +#R script autogenerated by rgenetics/rgutils.py on 15/04/2010 09:56:14 diff -r 6f43a97e7908 -r 33eab99a2df5 test-data/rgtestouts/rgManQQ/rgManQQtest1.html --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.html Thu Apr 15 10:35:31 2010 -0400 +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.html Thu Apr 15 10:51:51 2010 -0400 @@ -38,24 +38,16 @@ [1] "## manhattan on Armitagep starting 2 3 6" -[1] "## manhattan got chrlist= 1 nchr 1" - -[1] "## manhattan got chrlist= 1 nchr 1 x= 1 i= 1" - [1] "## manhattan plot on Armitagep done" [1] "## qqplot on Allelep done" [1] "## manhattan on Allelep starting 2 3 8" -[1] "## manhattan got chrlist= 1 nchr 1" - -[1] "## manhattan got chrlist= 1 nchr 1 x= 1 i= 1" - [1] "## manhattan plot on Allelep done" </pre> -<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgManQQ.py run at 25/03/2010 21:01:19</h3> +<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgManQQ.py run at 15/04/2010 09:56:23</h3> </div></body></html> diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgGRR.py --- a/tools/rgenetics/rgGRR.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgGRR.py Thu Apr 15 10:51:51 2010 -0400 @@ -63,7 +63,8 @@ except NameError: from Sets import Set as set -from rgutils import timenow,pruneLD,plinke +from rgutils import timenow,pruneLD,plinke,openOrMakeLDreduced + import plinkbinJZ @@ -1002,61 +1003,6 @@ svg.close() return newfiles,explanations,repOut -def makeOpenLDR(ldreduced=None,basename=None,newfpath=None,plinke='plink'): - """we stow a thin ldreduced version of the primary file in the files_path for future runs - if none there yet - ugh the --thin option will happily return zero snps if only a few - """ - ped = None - loglines = [] - ldbedname = '%s.bed' % ldreduced - ldpedname = '%s.ped' % ldreduced - bedname = '%s.bed' % basename - pedname = '%s.ped' % basename - ldbedfn = os.path.join(newfpath,ldbedname) - ldpedfn = os.path.join(newfpath,ldpedname) - bedfn = os.path.join(newfpath,bedname) - pedfn = os.path.join(newfpath,pedname) - bmap = os.path.join(newfpath,'%s.bim' % basename) - pmap = os.path.join(newfpath,'%s.map' % basename) - if os.path.exists(ldbedfn): # joy. already done - ped = plinkbinJZ.BPed(os.path.splitext(ldbedfn)[0]) - ped.parse(quick=True) - elif os.path.exists(ldpedfn): # why bother - for completeness I guess - ped = plinkbinJZ.LPed(os.path.splitext(ldbedfn)[0]) - ped.parse() - elif os.path.exists(bedfn): # run ld prune and thin and save these for next time - nsnp = len(open(bmap,'r').readlines()) - if nsnp > 100: # if 9 snps --thin 0.1 will happily return 0 snps - plinktasks = [['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], - ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s_INDEP' % (basename, basename)], - ['--bfile %s_INDEP --thin 0.1 --make-bed --out %s' % (basename,ldreduced)]] - else: # no thin stage - plinktasks = [['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], - ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s' % (basename, ldreduced)]] - # subset of ld independent markers for eigenstrat and other requirements - vclbase = [plinke,'--noweb'] - loglines = pruneLD(plinktasks=plinktasks,cd=newfpath,vclbase = vclbase) - ped = plinkbinJZ.BPed(os.path.splitext(ldbedfn)[0]) - ped.parse(quick=True) - elif pedname and os.path.exists(pedfn): # screw it - return a bed - quicker to process - nsnp = len(open(pmap,'r').readlines()) - if nsnp > 100: - plinktasks = [['--file',basename,'--make-bed','--out',basename], - ['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], - ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s_INDEP' % (basename, basename)], - ['--bfile %s_INDEP --thin 0.1 --recode --out %s' % (bedname,ldreduced),]] - else: # no thin step - plinktasks = [['--file',basename,'--make-bed','--out',basename], - ['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], - ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s' % (basename, ldreduced)]] - - # subset of ld independent markers for eigenstrat and other requirements - vclbase = [plinke,'--noweb'] - loglines = pruneLD(plinktasks=plinktasks,cd=newfpath,vclbase = vclbase) - ped = plinkbinJZ.BPed(os.path.splitext(ldbedfn)[0]) - ped.parse(quick=True) - return ped,loglines - def doIBS(n=100): """parse parameters from galaxy expect 'input pbed path' 'basename' 'outpath' 'title' 'logpath' 'n' @@ -1078,6 +1024,7 @@ ts = '%s%s' % (string.punctuation,string.whitespace) ptran = string.maketrans(ts,'_'*len(ts)) inpath = sys.argv[1] + ldpath = os.path.split(inpath)[0] basename = sys.argv[2] outhtml = sys.argv[3] newfilepath = sys.argv[4] @@ -1095,14 +1042,13 @@ pass logf = file(logpath,'w') efp,ibase_name = os.path.split(inpath) # need to use these for outputs in files_path - ldreduced = '%s_INDEP_THIN' % ibase_name # we store ld reduced and thinned data - ped,loglines = makeOpenLDR(ldreduced=ldreduced,basename=ibase_name,newfpath=efp,plinke=plinke) + ped,loglines = openOrMakeLDreduced(basename,ldpath,plinke) if ped == None: - print >> sys.stderr, '## doIBSpy problem - cannot open %s or %s - cannot run' % (bedname,pedname) + print >> sys.stderr, '## doIBSpy problem - cannot open %s or %s - cannot run' % (ldreduced,basename) sys.exit(1) if len(loglines) > 0: logf.write('### first time for this input file - log from creating an ld reduced and thinned data set:\n') - logf.write('\n'.join(loglines)) + logf.write(''.join(loglines)) logf.write('\n') newfiles,explanations,repOut = doIBSpy(ped=ped,basename=basename,outdir=newfilepath, logf=logf,nrsSamples=n,title=title,pdftoo=0,Zcutoff=Zcutoff) diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgHaploView.py --- a/tools/rgenetics/rgHaploView.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgHaploView.py Thu Apr 15 10:51:51 2010 -0400 @@ -84,6 +84,7 @@ outfpath = sys.argv[12] infotrack = False # note that otherwise this breaks haploview in headless mode #infotrack = sys.argv[13] == 'info' + # this fails in headless mode as at april 2010 with haploview 4.2 tagr2 = sys.argv[14] or '0.8' hmpanels = sys.argv[15] # eg "['CEU','YRI']" if hmpanels: diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgHaploView.xml --- a/tools/rgenetics/rgHaploView.xml Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgHaploView.xml Thu Apr 15 10:51:51 2010 -0400 @@ -53,7 +53,7 @@ <param name="infoTrack" type="select" label="Add Hapmap information track to image" help="Refseq genes and snp density can be added to the plot if desired for orientation" > - <option value="info">Add Information track (Not available - awaiting fix from Haploview authors)</option> + <option value="info">Add Information track (DISABLED! Awaiting fix from Haploview authors)</option> <option value="noinfo" selected="True">No Information track</option> </param> diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgManQQ.py --- a/tools/rgenetics/rgManQQ.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgManQQ.py Thu Apr 15 10:51:51 2010 -0400 @@ -129,27 +129,27 @@ cc = dn[chromcolumn] oc = dn[offsetcolumn] nams = c(cc,oc) -plen = length(d[,1]) -doreorder=True +plen = length(rawd[,1]) +doreorder=1 print(paste('###',plen,'values read from',infile,'read - now running plots',sep=' ')) if (plen > 0) { for (pvalscolumn in pvalscolumns) { if (pvalscolumn > 0) { - cname = names(d)[pvalscolumn] + cname = names(rawd)[pvalscolumn] mytitle = paste('p=',cname,', ',title,sep='') myfname = chartr(' ','_',cname) - myqqplot = qq(d[,pvalscolumn],title=mytitle) + myqqplot = qq(rawd[,pvalscolumn],title=mytitle) print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { if (doreorder) { - d = rawd[do.call(order,rawd[nams]),] + rawd = rawd[do.call(order,rawd[nams]),] # mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according… # in case not yet ordered - doreorder = False + doreorder = 0 } print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) - mymanplot= manhattan(chrom=d[,chromcolumn],offset=d[,offsetcolumn],pvals=d[,pvalscolumn],title=mytitle,grey=grey) + mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) ggsave(file=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) } diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgManQQ.xml --- a/tools/rgenetics/rgManQQ.xml Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgManQQ.xml Thu Apr 15 10:51:51 2010 -0400 @@ -37,7 +37,7 @@ <test> <param name='i' value='smallwgaP.xls' ftype='tabular' > </param> - <param name='name' value='rgManQQ_test1' /> + <param name='name' value='rgManQQtest1' /> <param name='pval_col' value='5,7' /> <param name='chrom_col' value='1' /> <param name='offset_col' value='2' /> diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgQC.py --- a/tools/rgenetics/rgQC.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgQC.py Thu Apr 15 10:51:51 2010 -0400 @@ -1264,8 +1264,7 @@ plinktasks = [['--freq',],['--hwe 0.0', '--missing','--hardy'], ['--mendel',],['--check-sex',]] vclbase = [options.plinke,'--noweb','--out',basename,'--bfile',bfn,'--mind','1.0','--geno','1.0','--maf','0.0'] - runPlink(bfn = bfn,ofn = ofn,logf=plogf,plinktasks=plinktasks,cd=newfpath, - vclbase=vclbase) + runPlink(logf=plogf,plinktasks=plinktasks,cd=newfpath, vclbase=vclbase) plinktasks = [['--bfile',bfn,'--indep-pairwise 40 20 0.5','--out %s' % basename], ['--bfile',bfn,'--extract %s.prune.in --make-bed --out ldp_%s' % (basename, basename)], ['--bfile ldp_%s --het --out %s' % (basename,basename)]] diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgtest_one_tool.sh --- a/tools/rgenetics/rgtest_one_tool.sh Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgtest_one_tool.sh Thu Apr 15 10:51:51 2010 -0400 @@ -6,11 +6,12 @@ *) esac GALAXYROOT=`pwd` +PATHTOGALAXY='/opt/galaxy' # whatever echo "using $GALAXYROOT" # change this as needed for your local install INPATH="${GALAXYROOT}/test-data" BINPATH="${GALAXYROOT}/tool-data/rg/bin" -TOOLPATH="${GALAXYROOT}/tools/rgenetics" +TOOLPATH="${PATHTOGALAXY}/tools/rgenetics" OROOT="${GALAXYROOT}/test-data/rgtestouts" NORMALOROOT="${GALAXYROOT}/test-data" case "$1" in @@ -67,6 +68,8 @@ echo "now doing $TOOL" OUTPATH="$OROOT/$TOOL" rm -rf $OUTPATH/* +cmd="$TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6'" +echo "Doing $cmd" python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6' # rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" #'$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgutils.py --- a/tools/rgenetics/rgutils.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgutils.py Thu Apr 15 10:51:51 2010 -0400 @@ -4,7 +4,7 @@ # released under the LGPL # -import subprocess, os, sys, time, tempfile,string +import subprocess, os, sys, time, tempfile,string,plinkbinJZ galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> @@ -279,3 +279,64 @@ rsdict = dict(zip(rslist,rslist)) mfile.close() return markers,snpcols,rslist,rsdict + +def openOrMakeLDreduced(basename,newfpath,plinke): + """ move out of the way - highly specific plink function to create or open + an ld reduced and thinned data set for one of the ibs/grr methods.. + this should be part of the plinkJZ stuff - or bought in here maybe + """ + ldr = '%s_INDEP_THIN' % basename # we store ld reduced and thinned data + ldreduced = os.path.join(newfpath,ldr) + ped = None + loglines = [] + vclbase = [] + ldbedname = '%s.bed' % ldreduced + ldpedname = '%s.ped' % ldreduced + bedname = '%s.bed' % basename + pedname = '%s.ped' % basename + ldbedfn = os.path.join(newfpath,ldbedname) + ldpedfn = os.path.join(newfpath,ldpedname) + bedfn = os.path.join(newfpath,bedname) + pedfn = os.path.join(newfpath,pedname) + bmap = os.path.join(newfpath,'%s.bim' % basename) + pmap = os.path.join(newfpath,'%s.map' % basename) + if os.path.exists(ldbedfn): # joy. already done + ped = plinkbinJZ.BPed(ldreduced) + ped.parse(quick=True) + return ped,loglines + if os.path.exists(ldpedfn): # why bother - for completeness I guess + ped = plinkbinJZ.LPed(ldreduced) + ped.parse() + return ped,loglines + if os.path.exists(bedfn): # run ld prune and thin and save these for next time + nsnp = len(open(bmap,'r').readlines()) + plinktasks = [['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], + ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s_INDEP' % (basename, basename)]] + if nsnp < 100: # if 9 snps --thin 0.1 will happily return 0 snps + plinktasks += [['--bfile %s_INDEP --make-bed --out %s' % (basename,ldreduced)],] + else: # thin rather than copy + plinktasks += [['--bfile',basename,'--extract %s.prune.in --make-bed --out %s' % (basename, ldreduced)]] + # subset of ld independent markers for eigenstrat and other requirements + vclbase = [plinke,'--noweb'] + loglines = pruneLD(plinktasks=plinktasks,cd=newfpath,vclbase = vclbase) + ped = plinkbinJZ.BPed(ldreduced) + return ped,loglines + if pedname and os.path.exists(pedfn): # screw it - return a bed - quicker to process + nsnp = len(open(pmap,'r').readlines()) + if nsnp > 100: + plinktasks = [['--file',basename,'--make-bed','--out',basename], + ['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], + ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s_INDEP' % (basename, basename)], + ['--bfile %s_INDEP --thin 0.1 --recode --out %s' % (bedname,ldreduced),]] + else: # no thin step + plinktasks = [['--file',basename,'--make-bed','--out',basename], + ['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], + ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s' % (basename, ldreduced)]] + + # subset of ld independent markers for eigenstrat and other requirements + vclbase = [plinke,'--noweb'] + loglines = pruneLD(plinktasks=plinktasks,cd=newfpath,vclbase = vclbase) + ped = plinkbinJZ.BPed(os.path.splitext(ldbedfn)[0]) + ped.parse(quick=True) + return ped,loglines +

1 0

[hg] galaxy 3656: Fix parameter name bug in grid ajaxing that wa...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6f43a97e7908 changeset: 3656:6f43a97e7908 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Apr 15 10:35:31 2010 -0400 description: Fix parameter name bug in grid ajaxing that was introduced by a change in the default settings (hg diff) in JQuery 1.4 diffstat: templates/grid_base.mako | 10 +++++++--- 1 files changed, 7 insertions(+), 3 deletions(-) diffs (27 lines): diff -r 4ee481a4b235 -r 6f43a97e7908 templates/grid_base.mako --- a/templates/grid_base.mako Thu Apr 15 10:06:40 2010 -0400 +++ b/templates/grid_base.mako Thu Apr 15 10:35:31 2010 -0400 @@ -42,7 +42,11 @@ <%def name="grid_javascripts()"> ${h.js("jquery.autocomplete", "autocomplete_tagging" )} - <script type="text/javascript"> + <script type="text/javascript"> + // This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are + // not appended to the identifier of a nested array. + jQuery.ajaxSettings.traditional = true; + ## TODO: generalize and move into galaxy.base.js $(document).ready(function() { init_grid_elements(); @@ -461,8 +465,8 @@ operation = operation.toLowerCase(); // Update URL args. - url_args['operation'] = operation; - url_args['id'] = item_ids; + url_args["operation"] = operation; + url_args["id"] = item_ids; // If operation cannot be performed asynchronously, redirect to location. Otherwise do operation. var no_async = ( async_ops[operation] === undefined || async_ops[operation] === null);

1 0

[hg] galaxy 3655: Drop the unique constraint on the username col...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4ee481a4b235 changeset: 3655:4ee481a4b235 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Apr 15 10:06:40 2010 -0400 description: Drop the unique constraint on the username colum in the Community model's galaxy_user table, and fix a bug theat kept users from being logged in immediately after registering in the Community Space. diffstat: lib/galaxy/web/controllers/user.py | 14 +++++++-- lib/galaxy/webapps/community/model/mapping.py | 3 +- lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py | 2 +- 3 files changed, 12 insertions(+), 7 deletions(-) diffs (64 lines): diff -r b402fca44934 -r 4ee481a4b235 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Wed Apr 14 17:51:36 2010 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu Apr 15 10:06:40 2010 -0400 @@ -118,11 +118,14 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) referer = kwd.get( 'referer', trans.request.referer ) - if not refresh_frames and webapp == 'galaxy': - if trans.app.config.require_login: - refresh_frames = [ 'masthead', 'history', 'tools' ] + if not refresh_frames: + if webapp == 'galaxy': + if trans.app.config.require_login: + refresh_frames = [ 'masthead', 'history', 'tools' ] + else: + refresh_frames = [ 'masthead', 'history' ] else: - refresh_frames = [ 'masthead', 'history' ] + refresh_frames = [ 'masthead' ] error = '' if not trans.app.config.allow_user_creation and not trans.user_is_admin(): error = 'User registration is disabled. Please contact your Galaxy administrator for an account.' @@ -162,6 +165,9 @@ action='users', message='Created new user account (%s)' % user.email, status='done' ) ) + else: + # Must be logging into the community space webapp + trans.handle_user_login( user, webapp ) if not error: redirect_url = referer if error: diff -r b402fca44934 -r 4ee481a4b235 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py Wed Apr 14 17:51:36 2010 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Thu Apr 15 10:06:40 2010 -0400 @@ -44,7 +44,7 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "email", TrimmedString( 255 ), nullable=False ), - Column( "username", String( 255 ), index=True, unique=True, default=False ), + Column( "username", String( 255 ), index=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), Column( "deleted", Boolean, index=True, default=False ), @@ -193,7 +193,6 @@ def init( file_path, url, engine_options={}, create_tables=False ): """Connect mappings to the database""" - log.debug("###In init, file_path: %s" % str( file_path )) # Connect dataset to the file path Tool.file_path = file_path # Load the appropriate db module diff -r b402fca44934 -r 4ee481a4b235 lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py --- a/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Wed Apr 14 17:51:36 2010 -0400 +++ b/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Thu Apr 15 10:06:40 2010 -0400 @@ -21,7 +21,7 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "email", TrimmedString( 255 ), nullable=False ), - Column( "username", String( 255 ), index=True, unique=True, default=False ), + Column( "username", String( 255 ), index=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), Column( "deleted", Boolean, index=True, default=False ),

1 0

[hg] galaxy 3654: Remove tags from dataset's 'Edit Attributes' f...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b402fca44934 changeset: 3654:b402fca44934 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Wed Apr 14 17:51:36 2010 -0400 description: Remove tags from dataset's 'Edit Attributes' form. diffstat: templates/dataset/edit_attributes.mako | 20 ++------------------ 1 files changed, 2 insertions(+), 18 deletions(-) diffs (41 lines): diff -r 6e0fc1622959 -r b402fca44934 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Wed Apr 14 15:16:03 2010 -0400 +++ b/templates/dataset/edit_attributes.mako Wed Apr 14 17:51:36 2010 -0400 @@ -4,12 +4,12 @@ <%def name="title()">${_('Edit Dataset Attributes')}</%def> <%def name="stylesheets()"> - ${h.css( "base", "autocomplete_tagging" )} + ${h.css( "base" )} </%def> <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )} + ${h.js( "galaxy.base" )} </%def> <%def name="datatype( dataset, datatypes )"> @@ -52,22 +52,6 @@ <div style="clear: both"></div> </div> %if trans.get_user() is not None: - <%namespace file="../tagging_common.mako" import="render_individual_tagging_element" /> - <div class="form-row"> - <label> - Tags: - </label> - <div style="float: left; width: 295px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px"> - <style> - .tag-area { - border: none; - } - </style> - ${render_individual_tagging_element(user=trans.get_user(), tagged_item=data, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="30")} - </div> - <div style="clear: both"></div> - <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div> - </div> <div class="form-row"> <label> Annotation / Notes:

1 0

[hg] galaxy 3653: Allow non-admin users that have the LIBRARY_MO...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6e0fc1622959 changeset: 3653:6e0fc1622959 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Apr 14 15:16:03 2010 -0400 description: Allow non-admin users that have the LIBRARY_MODIFY permission to delete / undelete library items as well as display / hide deleted library items. diffstat: lib/galaxy/web/controllers/library_admin.py | 74 -------------------------- lib/galaxy/web/controllers/library_common.py | 78 ++++++++++++++++++++++++++++ templates/library/common/browse_library.mako | 30 +++++----- templates/library/common/library_info.mako | 8 +- test/base/twilltestcase.py | 12 ++-- test/functional/test_library_features.py | 27 ++++++--- test/functional/test_library_security.py | 3 +- 7 files changed, 122 insertions(+), 110 deletions(-) diffs (388 lines): diff -r 1486617bfae8 -r 6e0fc1622959 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Wed Apr 14 14:09:01 2010 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Wed Apr 14 15:16:03 2010 -0400 @@ -161,77 +161,3 @@ action='browse_libraries', message=util.sanitize_text( message ), status='done' ) ) - @web.expose - @web.require_admin - def delete_library_item( self, trans, library_id, item_id, item_type, **kwd ): - # This action will handle deleting all types of library items. State is saved for libraries and - # folders ( i.e., if undeleted, the state of contents of the library or folder will remain, so previously - # deleted / purged contents will have the same state ). When a library or folder has been deleted for - # the amount of time defined in the cleanup_datasets.py script, the library or folder and all of its - # contents will be purged. The association between this method and the cleanup_datasets.py script - # enables clean maintenance of libraries and library dataset disk files. This is also why the item_types - # are not any of the associations ( the cleanup_datasets.py script handles everything ). - show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) - item_types = { 'library': trans.app.model.Library, - 'folder': trans.app.model.LibraryFolder, - 'library_dataset': trans.app.model.LibraryDataset } - if item_type not in item_types: - message = 'Bad item_type specified: %s' % str( item_type ) - status = 'error' - else: - if item_type == 'library_dataset': - item_desc = 'Dataset' - else: - item_desc = item_type.capitalize() - library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) ) - library_item.deleted = True - trans.sa_session.add( library_item ) - trans.sa_session.flush() - message = util.sanitize_text( "%s '%s' has been marked deleted" % ( item_desc, library_item.name ) ) - status = 'done' - if item_type == 'library': - return self.browse_libraries( trans, message=message, status=status ) - else: - return trans.response.send_redirect( web.url_for( controller='library_common', - action='browse_library', - cntrller='library_admin', - id=library_id, - show_deleted=show_deleted, - message=message, - status=status ) ) - @web.expose - @web.require_admin - def undelete_library_item( self, trans, library_id, item_id, item_type, **kwd ): - # This action will handle undeleting all types of library items - show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) - item_types = { 'library': trans.app.model.Library, - 'folder': trans.app.model.LibraryFolder, - 'library_dataset': trans.app.model.LibraryDataset } - if item_type not in item_types: - message = 'Bad item_type specified: %s' % str( item_type ) - status = ERROR - else: - if item_type == 'library_dataset': - item_desc = 'Dataset' - else: - item_desc = item_type.capitalize() - library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) ) - if library_item.purged: - message = '%s %s has been purged, so it cannot be undeleted' % ( item_desc, library_item.name ) - status = ERROR - else: - library_item.deleted = False - trans.sa_session.add( library_item ) - trans.sa_session.flush() - message = util.sanitize_text( "%s '%s' has been marked undeleted" % ( item_desc, library_item.name ) ) - status = SUCCESS - if item_type == 'library': - return self.browse_libraries( trans, message=message, status=status ) - else: - return trans.response.send_redirect( web.url_for( controller='library_common', - action='browse_library', - cntrller='library_admin', - id=library_id, - show_deleted=show_deleted, - message=message, - status=status ) ) diff -r 1486617bfae8 -r 6e0fc1622959 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Wed Apr 14 14:09:01 2010 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Wed Apr 14 15:16:03 2010 -0400 @@ -1733,6 +1733,84 @@ show_deleted=show_deleted, message=util.sanitize_text( message ), status=status ) ) + @web.expose + def delete_library_item( self, trans, cntrller, library_id, item_id, item_type, **kwd ): + # This action will handle deleting all types of library items. State is saved for libraries and + # folders ( i.e., if undeleted, the state of contents of the library or folder will remain, so previously + # deleted / purged contents will have the same state ). When a library or folder has been deleted for + # the amount of time defined in the cleanup_datasets.py script, the library or folder and all of its + # contents will be purged. The association between this method and the cleanup_datasets.py script + # enables clean maintenance of libraries and library dataset disk files. This is also why the item_types + # are not any of the associations ( the cleanup_datasets.py script handles everything ). + show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) + item_types = { 'library': trans.app.model.Library, + 'folder': trans.app.model.LibraryFolder, + 'library_dataset': trans.app.model.LibraryDataset } + if item_type not in item_types: + message = 'Bad item_type specified: %s' % str( item_type ) + status = 'error' + else: + if item_type == 'library_dataset': + item_desc = 'Dataset' + else: + item_desc = item_type.capitalize() + library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) ) + library_item.deleted = True + trans.sa_session.add( library_item ) + trans.sa_session.flush() + message = util.sanitize_text( "%s '%s' has been marked deleted" % ( item_desc, library_item.name ) ) + status = 'done' + if item_type == 'library': + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_libraries', + message=message, + status=status ) ) + else: + return trans.response.send_redirect( web.url_for( controller='library_common', + action='browse_library', + cntrller=cntrller, + id=library_id, + show_deleted=show_deleted, + message=message, + status=status ) ) + @web.expose + def undelete_library_item( self, trans, cntrller, library_id, item_id, item_type, **kwd ): + # This action will handle undeleting all types of library items + show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) + item_types = { 'library': trans.app.model.Library, + 'folder': trans.app.model.LibraryFolder, + 'library_dataset': trans.app.model.LibraryDataset } + if item_type not in item_types: + message = 'Bad item_type specified: %s' % str( item_type ) + status = ERROR + else: + if item_type == 'library_dataset': + item_desc = 'Dataset' + else: + item_desc = item_type.capitalize() + library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) ) + if library_item.purged: + message = '%s %s has been purged, so it cannot be undeleted' % ( item_desc, library_item.name ) + status = ERROR + else: + library_item.deleted = False + trans.sa_session.add( library_item ) + trans.sa_session.flush() + message = util.sanitize_text( "%s '%s' has been marked undeleted" % ( item_desc, library_item.name ) ) + status = SUCCESS + if item_type == 'library': + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_libraries', + message=message, + status=status ) ) + else: + return trans.response.send_redirect( web.url_for( controller='library_common', + action='browse_library', + cntrller=cntrller, + id=library_id, + show_deleted=show_deleted, + message=message, + status=status ) ) # ---- Utility methods ------------------------------------------------------- diff -r 1486617bfae8 -r 6e0fc1622959 templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Wed Apr 14 14:09:01 2010 -0400 +++ b/templates/library/common/browse_library.mako Wed Apr 14 15:16:03 2010 -0400 @@ -232,11 +232,11 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> %endif - %if cntrller in [ 'library_admin', 'requests_admin' ]: + %if cntrller == 'library_admin' or can_modify: %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: - <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> + <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> %endif %endif </div> @@ -328,11 +328,11 @@ %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_manage ): <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif - %if cntrller in [ 'library_admin', 'requests_admin' ]: + %if cntrller == 'library_admin' or can_modify: %if not library.deleted and not folder.deleted: - <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a> + <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a> %elif not library.deleted and folder.deleted and not folder.purged: - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a> %endif %endif </div> @@ -435,6 +435,12 @@ %if not library.deleted: %if cntrller == 'library_admin' or can_modify: <a class="action-button" href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> + %if show_deleted: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a> + %endif %endif %if ( cntrller == 'library_admin' or can_modify ) and not library.info_association: <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> @@ -446,16 +452,8 @@ %if cntrller == 'library_admin' or can_manage: <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif - %if cntrller == 'library_admin': - <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> - %if show_deleted: - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a> - %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a> - %endif - %endif - %elif cntrller == 'library_admin' and not library.purged: - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a> + %elif ( cntrller == 'library_admin' or can_modify ) and not library.purged: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a> %elif library.purged: <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">This data library has been purged</a> %endif diff -r 1486617bfae8 -r 6e0fc1622959 templates/library/common/library_info.mako --- a/templates/library/common/library_info.mako Wed Apr 14 14:09:01 2010 -0400 +++ b/templates/library/common/library_info.mako Wed Apr 14 15:16:03 2010 -0400 @@ -37,11 +37,11 @@ %if cntrller == 'library_admin' or can_manage: <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif - %if cntrller == 'library_admin': - <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> + %if cntrller == 'library_admin' or can_modify: + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> %endif - %elif cntrller == 'library_admin' and not library.purged: - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Undelete this data library</a> + %elif ( cntrller == 'library_admin' or can_modify ) and not library.purged: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Undelete this data library</a> %elif library.purged: <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">This data library has been purged</a> %endif diff -r 1486617bfae8 -r 6e0fc1622959 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Apr 14 14:09:01 2010 -0400 +++ b/test/base/twilltestcase.py Wed Apr 14 15:16:03 2010 -0400 @@ -2014,11 +2014,11 @@ errmsg += 'Unpacked archive remains in: %s\n' % tmpd raise AssertionError( errmsg ) shutil.rmtree( tmpd ) - def delete_library_item( self, library_id, item_id, item_name, item_type='library_dataset' ): + def delete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ): """Mark a library item as deleted""" self.home() - self.visit_url( "%s/library_admin/delete_library_item?library_id=%s&item_id=%s&item_type=%s" \ - % ( self.url, library_id, item_id, item_type ) ) + self.visit_url( "%s/library_common/delete_library_item?cntrller=%s&library_id=%s&item_id=%s&item_type=%s" \ + % ( self.url, cntrller, library_id, item_id, item_type ) ) if item_type == 'library_dataset': item_desc = 'Dataset' else: @@ -2026,11 +2026,11 @@ check_str = "%s '%s' has been marked deleted" % ( item_desc, item_name ) self.check_page_for_string( check_str ) self.home() - def undelete_library_item( self, library_id, item_id, item_name, item_type='library_dataset' ): + def undelete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ): """Mark a library item as deleted""" self.home() - self.visit_url( "%s/library_admin/undelete_library_item?library_id=%s&item_id=%s&item_type=%s" \ - % ( self.url, library_id, item_id, item_type ) ) + self.visit_url( "%s/library_common/undelete_library_item?cntrller=%s&library_id=%s&item_id=%s&item_type=%s" \ + % ( self.url, cntrller, library_id, item_id, item_type ) ) if item_type == 'library_dataset': item_desc = 'Dataset' else: diff -r 1486617bfae8 -r 6e0fc1622959 test/functional/test_library_features.py --- a/test/functional/test_library_features.py Wed Apr 14 14:09:01 2010 -0400 +++ b/test/functional/test_library_features.py Wed Apr 14 15:16:03 2010 -0400 @@ -476,7 +476,8 @@ def test_080_mark_dataset_deleted( self ): """Testing marking a library dataset as deleted""" # Logged in as admin_user - self.delete_library_item( self.security.encode_id( library_one.id ), + self.delete_library_item( 'library_admin', + self.security.encode_id( library_one.id ), self.security.encode_id( ldda_two.library_dataset.id ), ldda_two.name, item_type='library_dataset' ) @@ -496,7 +497,8 @@ def test_090_mark_folder_deleted( self ): """Testing marking a library folder as deleted""" # Logged in as admin_user - self.delete_library_item( self.security.encode_id( library_one.id ), + self.delete_library_item( 'library_admin', + self.security.encode_id( library_one.id ), self.security.encode_id( folder_two.id ), folder_two.name, item_type='folder' ) @@ -506,7 +508,8 @@ def test_095_mark_folder_undeleted( self ): """Testing marking a library folder as undeleted""" # Logged in as admin_user - self.undelete_library_item( self.security.encode_id( library_one.id ), + self.undelete_library_item( 'library_admin', + self.security.encode_id( library_one.id ), self.security.encode_id( folder_two.id ), folder_two.name, item_type='folder' ) @@ -520,11 +523,13 @@ """Testing marking a library as deleted""" # Logged in as admin_user # First mark folder_two as deleted to further test state saving when we undelete the library - self.delete_library_item( self.security.encode_id( library_one.id ), + self.delete_library_item( 'library_admin', + self.security.encode_id( library_one.id ), self.security.encode_id( folder_two.id ), folder_two.name, item_type='folder' ) - self.delete_library_item( self.security.encode_id( library_one.id ), + self.delete_library_item( 'library_admin', + self.security.encode_id( library_one.id ), self.security.encode_id( library_one.id ), library_one.name, item_type='library' ) @@ -533,7 +538,8 @@ def test_105_mark_library_undeleted( self ): """Testing marking a library as undeleted""" # Logged in as admin_user - self.undelete_library_item( self.security.encode_id( library_one.id ), + self.undelete_library_item( 'library_admin', + self.security.encode_id( library_one.id ), self.security.encode_id( library_one.id ), library_one.name, item_type='library' ) @@ -545,7 +551,8 @@ def test_110_purge_library( self ): """Testing purging a library""" # Logged in as admin_user - self.delete_library_item( self.security.encode_id( library_one.id ), + self.delete_library_item( 'library_admin', + self.security.encode_id( library_one.id ), self.security.encode_id( library_one.id ), library_one.name, item_type='library' ) @@ -612,7 +619,8 @@ # TODO: add a functional test to cover adding a library dataset via url_paste here... # TODO: Add a functional test to cover checking the space_to_tab checkbox here... # Delete and purge the library - self.delete_library_item( self.security.encode_id( library_two.id ), + self.delete_library_item( 'library_admin', + self.security.encode_id( library_two.id ), self.security.encode_id( library_two.id ), library_two.name, item_type='library' ) @@ -625,7 +633,8 @@ # Purge all libraries ################## for library in [ library_one, library_two ]: - self.delete_library_item( self.security.encode_id( library.id ), + self.delete_library_item( 'library_admin', + self.security.encode_id( library.id ), self.security.encode_id( library.id ), library.name, item_type='library' ) diff -r 1486617bfae8 -r 6e0fc1622959 test/functional/test_library_security.py --- a/test/functional/test_library_security.py Wed Apr 14 14:09:01 2010 -0400 +++ b/test/functional/test_library_security.py Wed Apr 14 15:16:03 2010 -0400 @@ -569,7 +569,8 @@ # Purge all libraries ################## for library in [ library_one, library_two ]: - self.delete_library_item( self.security.encode_id( library.id ), + self.delete_library_item( 'library_admin', + self.security.encode_id( library.id ), self.security.encode_id( library.id ), library.name, item_type='library' )

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