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[hg] galaxy 2926: Fix a bug whereby PYTHONPATH would grow endles...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ea0342f2df03 changeset: 2926:ea0342f2df03 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Oct 27 15:11:41 2009 -0400 description: Fix a bug whereby PYTHONPATH would grow endlessly in the local runner 1 file(s) affected in this change: lib/galaxy/jobs/runners/local.py diffs (47 lines): diff -r c2bed70a9b58 -r ea0342f2df03 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py Tue Oct 27 14:31:59 2009 -0400 +++ b/lib/galaxy/jobs/runners/local.py Tue Oct 27 15:11:41 2009 -0400 @@ -20,6 +20,12 @@ """Start the job runner with 'nworkers' worker threads""" self.app = app self.sa_session = app.model.context + # put lib into the PYTHONPATH for subprocesses + if 'PYTHONPATH' in os.environ: + os.environ['PYTHONPATH'] = '%s:%s' % ( os.environ['PYTHONPATH'], os.path.abspath( 'lib' ) ) + else: + os.environ['PYTHONPATH'] = os.path.abspath( 'lib' ) + # start workers self.queue = Queue() self.threads = [] nworkers = app.config.local_job_queue_workers @@ -54,12 +60,6 @@ return # If we were able to get a command line, run the job if command_line: - env = os.environ - if job_wrapper.galaxy_lib_dir is not None: - if 'PYTHONPATH' in os.environ: - env['PYTHONPATH'] = "%s:%s" % ( os.environ['PYTHONPATH'], job_wrapper.galaxy_lib_dir ) - else: - env['PYTHONPATH'] = job_wrapper.galaxy_lib_dir try: log.debug( 'executing: %s' % command_line ) proc = subprocess.Popen( args = command_line, @@ -67,7 +67,7 @@ cwd = job_wrapper.working_directory, stdout = subprocess.PIPE, stderr = subprocess.PIPE, - env = env, + env = os.environ, preexec_fn = os.setpgrp ) job_wrapper.set_runner( 'local:///', proc.pid ) job_wrapper.change_state( model.Job.states.RUNNING ) @@ -110,7 +110,7 @@ log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) external_metadata_proc = subprocess.Popen( args = external_metadata_script, shell = True, - env = env, + env = os.environ, preexec_fn = os.setpgrp ) job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) external_metadata_proc.wait()

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[hg] galaxy 2921: trackster: fix layout issue
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9d0d6a33a435 changeset: 2921:9d0d6a33a435 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Oct 26 19:47:27 2009 -0400 description: trackster: fix layout issue 2 file(s) affected in this change: static/trackster.css templates/tracks/browser.mako diffs (115 lines): diff -r fa0483a31237 -r 9d0d6a33a435 static/trackster.css --- a/static/trackster.css Mon Oct 26 15:05:20 2009 -0400 +++ b/static/trackster.css Mon Oct 26 19:47:27 2009 -0400 @@ -15,14 +15,10 @@ overflow: auto; } -#nav { +#nav-container { position: fixed; bottom: 0; width: 100%; - background: #333; - color: white; - font-weight: bold; - text-align: center; } input { @@ -36,14 +32,14 @@ background-position:top center; background-repeat:repeat-x;border-top:solid #999 1px; color:#333;font-weight:bold; - } +} -/* + #nav-controls { - padding: 15px 0; + text-align: center; } -*/ + #nav-controls a { color: white; padding: 0.1em 0.4em; @@ -77,14 +73,13 @@ /* border-top: solid #666 1px;*/ /* border-bottom: solid #aaa 1px;*/ background: white; - border: solid grey 1px; + border: solid gray 1px; margin: 5px; } #overview-box { position: absolute; margin-top: 0px; height: 14px; - background: grey; background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat; /*border-style: outset;*/ } @@ -143,5 +138,4 @@ #nav-labeltrack { border-top: solid #999 1px; - border-bottom: solid #999 1px; } diff -r fa0483a31237 -r 9d0d6a33a435 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Mon Oct 26 15:05:20 2009 -0400 +++ b/templates/tracks/browser.mako Mon Oct 26 19:47:27 2009 -0400 @@ -54,6 +54,7 @@ view.redraw(); }); + // To adjust the size of the viewport to fit the fixed-height footer $(window).resize( function( e ) { $("#viewport").height( $(window).height() - 120 ); view.redraw(); @@ -105,24 +106,26 @@ <div id="content"> <div id="top-labeltrack"></div> <div id="viewport"></div> +</div> +<div id="nav-container"> <div id="nav-labeltrack"></div> -</div> -<div id="nav"> - <div id="nav-controls"> - <form name="chr" id="chr" method="get"> - <select id="chrom" name="chrom" style="width: 15em;"> - <option value="">Loading</option> - </select> - <input id="low" size="12"></input>:<input id="high" size="12"></input> - ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> - <input type="hidden" name="id" value="${id}" /> - <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> - <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> - </form> - </div> - <div id="overview"> - <div id="overview-viewport"> - <div id="overview-box"></div> + <div id="nav"> + <div id="overview"> + <div id="overview-viewport"> + <div id="overview-box"></div> + </div> + </div> + <div id="nav-controls"> + <form name="chr" id="chr" method="get"> + <select id="chrom" name="chrom" style="width: 15em;"> + <option value="">Loading</option> + </select> + <input id="low" size="12" />:<input id="high" size="12" /> + ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> + <input type="hidden" name="id" value="${id}" /> + <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> + <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> + </form> </div> </div> </div>

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[hg] galaxy 2924: Require login to perform visualization (otherw...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a471575d1e4a changeset: 2924:a471575d1e4a user: James Taylor <james(a)jamestaylor.org> date: Tue Oct 27 13:39:48 2009 -0400 description: Require login to perform visualization (otherwise we have no way to store them) 2 file(s) affected in this change: lib/galaxy/web/controllers/tracks.py lib/galaxy/web/controllers/visualization.py diffs (28 lines): diff -r 734722f10df8 -r a471575d1e4a lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue Oct 27 13:28:25 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Tue Oct 27 13:39:48 2009 -0400 @@ -63,6 +63,7 @@ return trans.fill_template( "tracks/index.mako" ) @web.expose + @web.require_login() def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None, title=None ): """ Build a new browser from datasets in the current history. Redirects diff -r 734722f10df8 -r a471575d1e4a lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py Tue Oct 27 13:28:25 2009 -0400 +++ b/lib/galaxy/web/controllers/visualization.py Tue Oct 27 13:39:48 2009 -0400 @@ -28,11 +28,13 @@ class VisualizationController( BaseController ): @web.expose + @web.require_login() def index( self, trans ): return trans.fill_template( "panels.mako", active_view='visualization', main_url=url_for( action='list' ) ) list_grid = VisualizationListGrid() @web.expose + @web.require_login() def list( self, trans, *args, **kwargs ): return self.list_grid( trans, *args, **kwargs )

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[hg] galaxy 2922: A get_platform() monkeypatch for fat versions ...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d8ce43b63ebb changeset: 2922:d8ce43b63ebb user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Oct 27 11:36:57 2009 -0400 description: A get_platform() monkeypatch for fat versions of python on Mac. Also do more explicit version checking ( >= 2.4, <= 2.5 ) and provide helpful messages if the version is not supported. 6 file(s) affected in this change: lib/galaxy/__init__.py lib/galaxy/eggs/__init__.py scripts/check_python.py scripts/get_python.sh scripts/paster.py setup.sh diffs (189 lines): diff -r 9d0d6a33a435 -r d8ce43b63ebb lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py Mon Oct 26 19:47:27 2009 -0400 +++ b/lib/galaxy/__init__.py Tue Oct 27 11:36:57 2009 -0400 @@ -2,4 +2,29 @@ Galaxy root package -- this is a namespace package. """ -__import__( "pkg_resources" ).declare_namespace( __name__ ) \ No newline at end of file +# Starting somewhere in 2.5.x, Python on Mac became broken - despite being fat, +# the machine portion of the platform is not set to 'fat'. +# +# For more, see: +# +# http://bugs.python.org/setuptools/issue19 +# +import os, sys +from distutils.sysconfig import get_config_vars + +if ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and sys.prefix.startswith( '/System' ) ) or \ + ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ): + # Has to be before anything imports pkg_resources + def _get_platform_monkeypatch(): + plat = distutils.util._get_platform() + if plat.startswith( 'macosx-' ): + plat = 'macosx-10.3-fat' + return plat + import distutils.util + try: + assert distutils.util._get_platform + except: + distutils.util._get_platform = distutils.util.get_platform + distutils.util.get_platform = _get_platform_monkeypatch + +__import__( "pkg_resources" ).declare_namespace( __name__ ) diff -r 9d0d6a33a435 -r d8ce43b63ebb lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Mon Oct 26 19:47:27 2009 -0400 +++ b/lib/galaxy/eggs/__init__.py Tue Oct 27 11:36:57 2009 -0400 @@ -533,9 +533,9 @@ egg = c.get_for_require( name ) try: if egg is None: - pkg_resources.working_set.require( pkg ) + return pkg_resources.working_set.require( pkg ) else: - pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) ) + return pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) ) except pkg_resources.VersionConflict, e: # there's a conflicting egg on the pythonpath, remove it dist = e.args[0] @@ -551,9 +551,10 @@ del working_set.by_key[dist.key] working_set.entry_keys[entry] = [] sys.path.remove(entry) - require( pkg ) + r = require( pkg ) if location is not None and not location.endswith( '.egg' ): working_set.entries.append( location ) # re-add to the set if it's a dir. + return r except pkg_resources.DistributionNotFound, e: # the initial require itself is the first dep, but it can have # multiple deps, which will be fetched by the require below. @@ -566,7 +567,7 @@ if not egg.have: if not egg.fetch(): raise EggNotFetchable( egg.name ) - require( pkg ) + return require( pkg ) # convenience stuff def get_ucs(): diff -r 9d0d6a33a435 -r d8ce43b63ebb scripts/check_python.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/check_python.py Tue Oct 27 11:36:57 2009 -0400 @@ -0,0 +1,22 @@ +import os, sys + +def check_python(): + try: + assert sys.version_info[:2] >= ( 2, 4 ) and sys.version_info[:2] <= ( 2, 5 ) + except AssertionError: + print >>sys.stderr, "ERROR: Your Python version is:", sys.version.split( ' ', 1 )[0] + print >>sys.stderr, "Galaxy is currently only supported on Python 2.4 and Python 2.5." + if sys.version_info[:2] < ( 2, 4 ): + print >>sys.stderr, "To run Galaxy, please download and install Python 2.5 from http://python.org" + else: + print >>sys.stderr, "To track the progress of Python 2.6 support, please see:" + print >>sys.stderr, " http://bitbucket.org/galaxy/galaxy-central/issue/76/support-python-26" + print >>sys.stderr, "For hints on how to direct Galaxy to use a different python installation, see:" + print >>sys.stderr, " http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy" + raise + +if __name__ == '__main__': + try: + check_python() + except: + sys.exit( 1 ) diff -r 9d0d6a33a435 -r d8ce43b63ebb scripts/get_python.sh --- a/scripts/get_python.sh Mon Oct 26 19:47:27 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -#!/bin/sh -# -# Try to find a usable python -# - -if [ "$GALAXY_PYTHON" != "" ]; then - PYTHONS="$GALAXY_PYTHON" -else - PYTHONS="python python2.4 python2.5" -fi - -found="" -for python in $PYTHONS; do - version=`$python -c 'import sys; print sys.version[:3]' 2>/dev/null` - if [ $? -eq 0 ]; then - case $version in - 2.4|2.5) - found="$python" - break - ;; - esac - fi -done - -if [ "$found" != "" ]; then - GALAXY_PYTHON="$found" -else - - # user manually defined $GALAXY_PYTHON - if [ "$GALAXY_PYTHON" != "" ]; then - - /bin/cat <<EOF -ERROR: \$GALAXY_PYTHON is set, but what it points to is not a suitable -Python interpreter. This version of Galaxy requires either Python 2.4 -or 2.5. Possible solutions: - * Unset \$GALAXY_PYTHON to let Galaxy attempt to find a suitable - Python itself - * Set \$GALAXY_PYTHON to a suitable Python interpreter. -\$GALAXY_PYTHON is currently set to: $GALAXY_PYTHON -EOF - - # couldn't find one in $PATH - else - - /bin/cat <<EOF -ERROR: Unable to find a suitable Python interpreter. This version of -Galaxy requires either Python 2.4 or 2.5. Possible solutions: - * If you have a suitable Python installed outside your \$PATH, modify - your \$PATH to include it. - * If you have a suitable Python installed outside your \$PATH and - don't want to change your \$PATH, set the \$GALAXY_PYTHON environment - variable to the path of your python executable. - * If you don't have a suitable Python installed anywhere, install one. -EOF - - fi - - exit 1 - -fi diff -r 9d0d6a33a435 -r d8ce43b63ebb scripts/paster.py --- a/scripts/paster.py Mon Oct 26 19:47:27 2009 -0400 +++ b/scripts/paster.py Tue Oct 27 11:36:57 2009 -0400 @@ -7,7 +7,12 @@ import os, sys -assert sys.version_info[:2] >= ( 2, 4 ) +# ensure supported version +from check_python import check_python +try: + check_python() +except: + sys.exit( 1 ) new_path = [ os.path.join( os.getcwd(), "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path diff -r 9d0d6a33a435 -r d8ce43b63ebb setup.sh --- a/setup.sh Mon Oct 26 19:47:27 2009 -0400 +++ b/setup.sh Tue Oct 27 11:36:57 2009 -0400 @@ -1,4 +1,7 @@ #!/bin/sh + +python ./scripts/check_python.py +[ $? -ne 0 ] && exit 1 SAMPLES=" datatypes_conf.xml.sample

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[hg] galaxy 2923: Fix display of stranded features without block...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/734722f10df8 changeset: 2923:734722f10df8 user: James Taylor <james(a)jamestaylor.org> date: Tue Oct 27 13:28:25 2009 -0400 description: Fix display of stranded features without blocks in trackster. Hacky. 4 file(s) affected in this change: lib/galaxy/visualization/tracks/data/interval_index.py static/images/visualization/strand_left_inv.png static/images/visualization/strand_right_inv.png static/scripts/trackster.js diffs (114 lines): diff -r d8ce43b63ebb -r 734722f10df8 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Tue Oct 27 11:36:57 2009 -0400 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Tue Oct 27 13:28:25 2009 -0400 @@ -21,7 +21,11 @@ for start, end, offset in index.find(chrom, start, end): source.seek(offset) feature = source.readline().split() - payload = { 'start': start, 'end': end, 'name': feature[3], 'strand': feature[5] } + payload = { 'start': start, 'end': end, 'name': feature[3] } + try: + payload['strand'] = feature[5] + except IndexError: + pass try: block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] diff -r d8ce43b63ebb -r 734722f10df8 static/images/visualization/strand_left_inv.png Binary file static/images/visualization/strand_left_inv.png has changed diff -r d8ce43b63ebb -r 734722f10df8 static/images/visualization/strand_right_inv.png Binary file static/images/visualization/strand_right_inv.png has changed diff -r d8ce43b63ebb -r 734722f10df8 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Oct 27 11:36:57 2009 -0400 +++ b/static/scripts/trackster.js Tue Oct 27 13:28:25 2009 -0400 @@ -19,6 +19,17 @@ left_img.src = "../images/visualization/strand_left.png"; left_img.onload = function() { LEFT_STRAND = CONTEXT.createPattern(left_img, "repeat"); +} + +var right_img_inv = new Image(); +right_img_inv.src = "../images/visualization/strand_right_inv.png"; +right_img_inv.onload = function() { + RIGHT_STRAND_INV = CONTEXT.createPattern(right_img_inv, "repeat"); +} +var left_img_inv = new Image(); +left_img_inv.src = "../images/visualization/strand_left_inv.png"; +left_img_inv.onload = function() { + LEFT_STRAND_INV = CONTEXT.createPattern(left_img_inv, "repeat"); } function commatize( number ) { @@ -402,7 +413,7 @@ y_center = this.slots[feature.name] * this.vertical_gap; if (feature.strand && this.showing_labels) { - if (feature.strand == "+") { + if (feature.strand == "+") { ctx.fillStyle = RIGHT_STRAND; } else if (feature.strand == "-") { ctx.fillStyle = LEFT_STRAND; @@ -415,26 +426,53 @@ } if (this.showing_labels && ctx.fillText) { - ctx.fillText(feature.name, f_start, y_center + 8); + ctx.fillText(feature.name, f_start - 1, y_center + 8); } + // If there is no thickStart/thickEnd, draw the whole thing + // as thick. var exon_start, exon_end; if (feature.exon_start && feature.exon_end) { exon_start = Math.floor( Math.max(0, (feature.exon_start - tile_low) * w_scale) ); exon_end = Math.ceil( Math.min(width, (feature.exon_end - tile_low) * w_scale) ); - } + } else { + exon_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ); + exon_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ); + } - if (feature.blocks && this.showing_labels) { - for (var k = 0, k_len = feature.blocks.length; k < k_len; k++) { - var block = feature.blocks[k], + if (this.showing_labels) { + // If there are no blocks, we treat the feature as one + // big exon + var blocks = feature.blocks; + var arrows_in_blocks = false; + if ( ! blocks ) { + blocks = [[feature.start,feature.end]]; + arrows_in_blocks = true + } + for (var k = 0, k_len = blocks.length; k < k_len; k++) { + var block = blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); - var thickness = 5, y_start = 3; + var thickness, y_start; if (exon_start && block_start >= exon_start && block_end <= exon_end) { - thickness = 7; - y_start = 2; - } - ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); + thickness = 9; + y_start = 1; + ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); + if ( feature.strand && arrows_in_blocks ) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND_INV; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND_INV; + } + ctx.fillRect(block_start, y_center, block_end - block_start, 10); + ctx.fillStyle = "#000"; + } + } else { + thickness = 5; + y_start = 3; + ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); + } + // console.log(block_start, block_end); } }

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[hg] galaxy 2918: Tweaking trackster UI to fit Galaxy interface ...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b53985e5548c changeset: 2918:b53985e5548c user: James Taylor <james(a)jamestaylor.org> date: Fri Oct 23 18:49:18 2009 -0400 description: Tweaking trackster UI to fit Galaxy interface a little better (broke something with spacing though) 3 file(s) affected in this change: static/scripts/trackster.js static/trackster.css templates/tracks/browser.mako diffs (224 lines): diff -r 8f57bd9b180c -r b53985e5548c static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Oct 23 14:57:08 2009 -0400 +++ b/static/scripts/trackster.js Fri Oct 23 18:49:18 2009 -0400 @@ -68,8 +68,8 @@ // Minimum width for usability width: Math.max( 12, ( ( this.high - this.low ) / this.span ) * $("#overview-viewport").width() ) }).show(); - $("#low").text( commatize(this.low) ); - $("#high").text( commatize(this.high) ); + $("#low").val( commatize(this.low) ); + $("#high").val( commatize(this.high) ); for ( var i = 0, len = this.tracks.length; i < len; i++ ) { this.tracks[i].draw(); } @@ -204,9 +204,11 @@ chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (!data || data == "error") { - track.content_div.addClass("error").text(DATA_ERROR); + track.container_div.addClass("error"); + track.content_div.text(DATA_ERROR); } else if (data == "no data") { - track.content_div.addClass("nodata").text(DATA_NONE); + track.container_div.addClass("nodata"); + track.content_div.text(DATA_NONE); } else { track.content_div.css( "height", track.height_px + "px" ); track.min_value = data.min; @@ -298,9 +300,11 @@ high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { if (data == "error") { - track.content_div.addClass("error").text(DATA_ERROR); + track.container_div.addClass("error"); + track.content_div.text(DATA_ERROR); } else if (data.length === 0 || data == "no data") { - track.content_div.addClass("nodata").text(DATA_NONE); + track.container_div.addClass("nodata"); + track.content_div.text(DATA_NONE); } else { track.content_div.css( "height", track.height_px + "px" ); track.values = data; diff -r 8f57bd9b180c -r b53985e5548c static/trackster.css --- a/static/trackster.css Fri Oct 23 14:57:08 2009 -0400 +++ b/static/trackster.css Fri Oct 23 18:49:18 2009 -0400 @@ -25,9 +25,25 @@ text-align: center; } +input { + font-size: 100%; +} + +#nav { + padding: 0.5em 0; + background:#cccccc; + background-image:url(style/panel_header_bg.png); + background-position:top center; + background-repeat:repeat-x;border-top:solid #999 1px; + color:#333;font-weight:bold; + } + + +/* #nav-controls { padding: 15px 0; } +*/ #nav-controls a { color: white; padding: 0.1em 0.4em; @@ -37,6 +53,8 @@ -webkit-border-radius: 1em; -moz-border-radius: 1em; } + +/* #low { margin-left: 0.1em; float: left; @@ -45,27 +63,30 @@ margin-right: 0.1em; float: right; } +*/ #overview { width: 100%; margin: 0px; - background: #333; color: white; } #overview-viewport { - height: 20px; + position: relative; + height: 14px; /* border-top: solid #666 1px;*/ /* border-bottom: solid #aaa 1px;*/ - background: #888; + background: white; + border: solid grey 1px; + margin: 5px; } #overview-box { position: absolute; - margin-top: 1px; - height: 16px; + margin-top: 0px; + height: 14px; + background: grey; background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat; - border-style: outset; - border-width: 1px; + /*border-style: outset;*/ } #viewport { @@ -80,29 +101,25 @@ height: 100px; } .track { -/* border-top: solid gray 1px;*/ - border-bottom: solid gray 1px; +/* border-top: solid gray 1px; */ +/* border-bottom: solid gray 1px; */ } .track-header { text-align: center; + padding: 2px 0; } .track-content { overflow: hidden; + text-align: center; } -.track-content.error { - text-align: center; - padding-top: 10px; +.track.error { background-color: #ECB4AF; - height: 30px; } -.track-content.nodata { - text-align: center; - padding-top: 10px; +.track.nodata { background-color: #ddd; - height: 30px; } .loading { @@ -110,12 +127,21 @@ } .label-track { - font-weight: bold; - font-size: 10px; - background-color: #333; - color: white; + /* font-weight: bold; */ + /* font-size: 10px; */ + } .label-track .label { - border-left: solid gray 1px; - padding-left: 2px; + border-left: solid #999 1px; + padding: 1px; + display: inline-block; } + +#top-labeltrack { + border-bottom: solid #999 1px; +} + +#nav-labeltrack { + border-top: solid #999 1px; + border-bottom: solid #999 1px; +} diff -r 8f57bd9b180c -r b53985e5548c templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri Oct 23 14:57:08 2009 -0400 +++ b/templates/tracks/browser.mako Fri Oct 23 18:49:18 2009 -0400 @@ -105,25 +105,24 @@ <div id="content"> <div id="top-labeltrack"></div> <div id="viewport"></div> + <div id="nav-labeltrack"></div> </div> <div id="nav"> - <div id="nav-labeltrack"></div> + <div id="nav-controls"> + <form name="chr" id="chr" method="get"> + <select id="chrom" name="chrom" style="width: 15em;"> + <option value="">Loading</option> + </select> + <input id="low" size="12"></input>:<input id="high" size="12"></input> + ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> + <input type="hidden" name="id" value="${id}" /> + <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> + <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> + </form> + </div> <div id="overview"> <div id="overview-viewport"> <div id="overview-box"></div> </div> </div> - <span id="low"></span> - <span id="high"></span> - <div id="nav-controls"> - <form name="chr" id="chr" method="get"> - <select id="chrom" name="chrom"> - <option value="">Loading</option> - </select> - ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> - <input type="hidden" name="id" value="${id}" /> - <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> - <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> - </form> - </div> </div>

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[hg] galaxy 2917: trackster: fix blocks display, navigation issu...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8f57bd9b180c changeset: 2917:8f57bd9b180c user: Kanwei Li <kanwei(a)gmail.com> date: Fri Oct 23 14:57:08 2009 -0400 description: trackster: fix blocks display, navigation issues, now displays strand direction arrows 7 file(s) affected in this change: lib/galaxy/visualization/tracks/data/interval_index.py static/images/visualization/draggable_horizontal.png static/images/visualization/strand_left.png static/images/visualization/strand_right.png static/scripts/trackster.js static/trackster.css templates/tracks/browser.mako diffs (218 lines): diff -r 02127dd91492 -r 8f57bd9b180c lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Fri Oct 23 14:51:22 2009 -0400 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Fri Oct 23 14:57:08 2009 -0400 @@ -21,19 +21,19 @@ for start, end, offset in index.find(chrom, start, end): source.seek(offset) feature = source.readline().split() - payload = { 'start': start, 'end': end, 'name': feature[3] } + payload = { 'start': start, 'end': end, 'name': feature[3], 'strand': feature[5] } try: block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] blocks = zip(block_sizes, block_starts) - payload['block_start_end'] = [ (chrom_start + block[1], chrom_start + block[1] + block[0]) for block in blocks] - except: + payload['blocks'] = [ (start + block[1], start + block[1] + block[0]) for block in blocks] + except IndexError: pass try: payload['exon_start'] = int(feature[6]) payload['exon_end'] = int(feature[7]) - except: + except IndexError: pass results.append(payload) diff -r 02127dd91492 -r 8f57bd9b180c static/images/visualization/draggable_horizontal.png Binary file static/images/visualization/draggable_horizontal.png has changed diff -r 02127dd91492 -r 8f57bd9b180c static/images/visualization/strand_left.png Binary file static/images/visualization/strand_left.png has changed diff -r 02127dd91492 -r 8f57bd9b180c static/images/visualization/strand_right.png Binary file static/images/visualization/strand_right.png has changed diff -r 02127dd91492 -r 8f57bd9b180c static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Oct 23 14:51:22 2009 -0400 +++ b/static/scripts/trackster.js Fri Oct 23 14:57:08 2009 -0400 @@ -6,7 +6,20 @@ DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", CACHED_TILES = 50, - CACHED_DATA = 20; + CACHED_DATA = 20, + CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), + RIGHT_STRAND, LEFT_STRAND; + +var right_img = new Image(); +right_img.src = "../images/visualization/strand_right.png"; +right_img.onload = function() { + RIGHT_STRAND = CONTEXT.createPattern(right_img, "repeat"); +} +var left_img = new Image(); +left_img.src = "../images/visualization/strand_left.png"; +left_img.onload = function() { + LEFT_STRAND = CONTEXT.createPattern(left_img, "repeat"); +} function commatize( number ) { number += ''; // Convert to string @@ -101,6 +114,7 @@ var TiledTrack = function() { this.tile_cache = new Cache(CACHED_TILES); + // this.tile_cache = {}; }; $.extend( TiledTrack.prototype, Track.prototype, { draw: function() { @@ -126,20 +140,20 @@ while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache var key = this.view.zoom_level + "_" + tile_index; - if ( this.tile_cache[key] ) { + var cached = this.tile_cache.getItem(key); + if ( cached ) { // console.log("cached tile"); - tile_element = this.tile_cache[key]; var tile_low = tile_index * DENSITY * resolution; - tile_element.css( { + cached.css( { left: ( tile_low - this.view.low ) * w_scale }); // Our responsibility to move the element to the new parent - parent_element.append( tile_element ); + parent_element.append( cached ); } else { tile_element = this.draw_tile( resolution, tile_index, parent_element, w_scale, h ); } if ( tile_element ) { - this.tile_cache[key] = tile_element; + this.tile_cache.setItem(key, tile_element); } tile_index += 1; } @@ -340,6 +354,7 @@ if (!this.values) { // Still loading return null; } + // console.log("drawing"); // Once we zoom in enough, show name labels if (w_scale > this.show_labels_scale && !this.showing_labels) { this.showing_labels = true; @@ -373,7 +388,7 @@ ctx.fillStyle = "#000"; ctx.font = "10px monospace"; ctx.textAlign = "right"; - + var j = 0; for (var i = 0, len = this.values.length; i < len; i++) { var feature = this.values[i]; @@ -381,9 +396,19 @@ var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), y_center = this.slots[feature.name] * this.vertical_gap; - - // console.log(feature.start, feature.end, f_start, f_end, j); - ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); + + if (feature.strand && this.showing_labels) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND; + } + ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillStyle = "#000"; + } else { + ctx.fillStyle = "#000"; + ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); + } if (this.showing_labels && ctx.fillText) { ctx.fillText(feature.name, f_start, y_center + 8); @@ -393,18 +418,17 @@ if (feature.exon_start && feature.exon_end) { exon_start = Math.floor( Math.max(0, (feature.exon_start - tile_low) * w_scale) ); exon_end = Math.ceil( Math.min(width, (feature.exon_end - tile_low) * w_scale) ); - ctx.fillRect(exon_start, y_center + 4, exon_end - exon_start, 3); } - if (feature.blocks) { + if (feature.blocks && this.showing_labels) { for (var k = 0, k_len = feature.blocks.length; k < k_len; k++) { var block = feature.blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); - var thickness = 3, y_start = 4; + var thickness = 5, y_start = 3; if (exon_start && block_start >= exon_start && block_end <= exon_end) { - thickness = 5; - y_start = 3; + thickness = 7; + y_start = 2; } ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); // console.log(block_start, block_end); diff -r 02127dd91492 -r 8f57bd9b180c static/trackster.css --- a/static/trackster.css Fri Oct 23 14:51:22 2009 -0400 +++ b/static/trackster.css Fri Oct 23 14:57:08 2009 -0400 @@ -63,7 +63,7 @@ position: absolute; margin-top: 1px; height: 16px; - background: #ddd url(images/draggable_horizontal.png) center center no-repeat; + background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat; border-style: outset; border-width: 1px; } @@ -79,7 +79,6 @@ width: 100%; height: 100px; } - .track { /* border-top: solid gray 1px;*/ border-bottom: solid gray 1px; diff -r 02127dd91492 -r 8f57bd9b180c templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri Oct 23 14:51:22 2009 -0400 +++ b/templates/tracks/browser.mako Fri Oct 23 14:57:08 2009 -0400 @@ -16,7 +16,7 @@ $(function() { - view.add_track( new LabelTrack( $("#viewport" ) ) ); + view.add_track( new LabelTrack( $("#top-labeltrack" ) ) ); view.add_track( new LabelTrack( $("#nav-labeltrack" ) ) ); %for track in tracks: @@ -51,11 +51,6 @@ var delta_chrom = Math.round(delta / $(document).width() * view.span); view.center += delta_chrom; - if (view.center < 0) { - view.center = 0; - } else if (view.center > view.max_high) { - view.center = view.max_high; - } view.redraw(); }); @@ -79,8 +74,8 @@ this.current_height = e.clientY; this.current_x = e.offsetX; - var delta_chrom = Math.round(delta / $(document).width() * (view.max_high - view.max_low)); - view.center += delta_chrom; + var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low)); + view.center -= delta_chrom; view.redraw(); }); (function () { @@ -108,6 +103,7 @@ </%def> <div id="content"> + <div id="top-labeltrack"></div> <div id="viewport"></div> </div> <div id="nav">

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[hg] galaxy 2920: Samples go to to next state when bar codes are...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fa0483a31237 changeset: 2920:fa0483a31237 user: rc date: Mon Oct 26 15:05:20 2009 -0400 description: Samples go to to next state when bar codes are assigned to them 3 file(s) affected in this change: lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py templates/admin/requests/show_request.mako diffs (58 lines): diff -r ef5215401458 -r fa0483a31237 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Mon Oct 26 14:01:46 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Mon Oct 26 15:05:20 2009 -0400 @@ -460,7 +460,7 @@ select_request_type = self.__select_request_type(trans, request_type.id) # list of widgets to be rendered on the request form widgets = [] - widgets.append(dict(label='Name', + widgets.append(dict(label='Name of the Experiment', widget=TextField('name', 40, util.restore_text( params.get( 'name', '' ) )), helptext='(Required)')) diff -r ef5215401458 -r fa0483a31237 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Oct 26 14:01:46 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Oct 26 15:05:20 2009 -0400 @@ -358,7 +358,7 @@ widgets.append(dict(label='Select user', widget=self.__select_user(trans, user_id), helptext='The request would be submitted on behalf of this user (Required)')) - widgets.append(dict(label='Name', + widgets.append(dict(label='Name of the Experiment', widget=TextField('name', 40, util.restore_text( params.get( 'name', '' ) )), helptext='(Required)')) @@ -391,7 +391,7 @@ def __get_email(user): return user.email user_list = trans.sa_session.query( trans.app.model.User ) - user_list.sort(key=__get_email) + #user_list.sort(key=__get_email) for user in user_list: if not user.deleted: if userid == str(user.id): @@ -1038,6 +1038,12 @@ bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, '')) sample.bar_code = bar_code sample.flush() + # change the state of all the samples to the next state + # get the new state + new_state = request.type.states[1] + for s in request.samples: + event = trans.app.model.SampleEvent(s, new_state, 'Bar code added to this sample') + event.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', action='bar_codes', request_id=request.id, diff -r ef5215401458 -r fa0483a31237 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Mon Oct 26 14:01:46 2009 -0400 +++ b/templates/admin/requests/show_request.mako Mon Oct 26 15:05:20 2009 -0400 @@ -180,7 +180,7 @@ ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)} %endif <td> - %if request.unsubmitted() and grid_index == 0: + %if grid_index == 0: <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> <img src="${h.url_for('/static/images/delete_icon.png')}" /> <span></span></a>

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[hg] galaxy 2919: Fixed a bug in viewing request type
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ef5215401458 changeset: 2919:ef5215401458 user: rc date: Mon Oct 26 14:01:46 2009 -0400 description: Fixed a bug in viewing request type 1 file(s) affected in this change: templates/admin/requests/view_request_type.mako diffs (21 lines): diff -r b53985e5548c -r ef5215401458 templates/admin/requests/view_request_type.mako --- a/templates/admin/requests/view_request_type.mako Fri Oct 23 18:49:18 2009 -0400 +++ b/templates/admin/requests/view_request_type.mako Mon Oct 26 14:01:46 2009 -0400 @@ -5,8 +5,6 @@ %if msg: ${render_msg( msg, messagetype )} %endif - -<% num_states=len(states_list) %> <div class="toolForm"> <div class="toolFormTitle">View request type details</div> @@ -38,7 +36,7 @@ <label> Possible states </label> - %for element_count, state in enumerate(states_list): + %for element_count, state in enumerate(states_list.all()): <div class="form-row"> <label>${1+element_count}. ${state.name}</label> ${state.desc}

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[hg] galaxy 2916: Migration script for viz
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/02127dd91492 changeset: 2916:02127dd91492 user: James Taylor <james(a)jamestaylor.org> date: Fri Oct 23 14:51:22 2009 -0400 description: Migration script for viz 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0022_visualization_tables.py diffs (59 lines): diff -r 1ce07e82a4c1 -r 02127dd91492 lib/galaxy/model/migrate/versions/0022_visualization_tables.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0022_visualization_tables.py Fri Oct 23 14:51:22 2009 -0400 @@ -0,0 +1,55 @@ +""" +Migration script to add support for storing visualizations. + 1) Creates Visualization and VisualizationRevision tables +""" + +from sqlalchemy import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +Visualization_table = Table( "visualization", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), + Column( "latest_revision_id", Integer, + ForeignKey( "visualization_revision.id", use_alter=True, name='visualization_latest_revision_id_fk' ), index=True ), + Column( "title", TEXT ), + Column( "type", TEXT ) + ) + +VisualizationRevision_table = Table( "visualization_revision", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True, nullable=False ), + Column( "title", TEXT ), + Column( "config", TEXT ) + ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + Visualization_table.create() + except: + log.debug( "Could not create page table" ) + try: + VisualizationRevision_table.create() + except: + log.debug( "Could not create page_revision table" ) + + +def downgrade(): + metadata.reflect() + Visualization_table.drop() + VisualizationRevision_table.drop() +

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