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galaxy-dist commit 629e14c5f561: Fix for failing rg Haploview test - finally tracked down trivial pdfjoin error - new pdfjam version does not want quoted filespec
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Ross Lazarus <ross.lazarus(a)gmail.com> # Date 1289235967 18000 # Node ID 629e14c5f561446c963b05560f245e2ed7041ff0 # Parent 7ca26b1cc9b6fd67364a6c6af6005ceecaa3f45b Fix for failing rg Haploview test - finally tracked down trivial pdfjoin error - new pdfjam version does not want quoted filespec --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -100,7 +100,6 @@ class GenomeGraphs( Tabular ): s = ''.join(sl) s = urllib.quote_plus(s) redirect_url = s - log.debug('## rg gg ucsc rdurl=%s; s = %s' % (redirect_url,s)) link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) ret_val.append( (site_name, link) ) return ret_val --- a/tools/rgenetics/rgHaploView.py +++ b/tools/rgenetics/rgHaploView.py @@ -394,7 +394,7 @@ def ld(): p=subprocess.Popen(vcl,shell=True,cwd=outfpath,stderr=lf,stdout=lf) retval = p.wait() lf.write('## executing %s returned %d\n' % (vcl,retval)) - vcl = '%s "*.pdf" --fitpaper true --outfile alljoin.pdf' % pdfjoin + vcl = '%s *.pdf --fitpaper true --outfile alljoin.pdf' % pdfjoin p=subprocess.Popen(vcl,shell=True,cwd=outfpath,stderr=lf,stdout=lf) retval = p.wait() lf.write('## executing %s returned %d\n' % (vcl,retval))

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galaxy-dist commit 3ea6ee14a8b7: Remove debugging statement from previous commit.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289243761 18000 # Node ID 3ea6ee14a8b71cd7ac48da98a6ecdb50b9067040 # Parent c61ec9e333d5a0ade7a23b3f4b55ae3deb3aa0bb Remove debugging statement from previous commit. --- a/lib/galaxy/tools/util/gff_util.py +++ b/lib/galaxy/tools/util/gff_util.py @@ -53,7 +53,6 @@ def parse_gff_attributes( attr_str ): pair = name_value_pair.strip().split(" ") if len( pair ) == 1: pair = name_value_pair.strip().split("=") - print pair if pair == '': continue name = pair[0].strip()

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galaxy-dist commit 74620fac33c7: bug fix caused by the prev commit.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289178573 18000 # Node ID 74620fac33c74b60c0a2faa69364dea0115e8815 # Parent 328b57b1e2e53cbc9ab208379cdd3dc0864f3cc4 bug fix caused by the prev commit. --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -664,6 +664,8 @@ class RequestsAdmin( BaseController, Use if not err_msg: message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to monitor the transfer status." % len( selected_sample_datasets ) status = "done" + else: + status = 'error' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ),

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galaxy-dist commit d46ccc650084: Eliminate check_user flag from tool menu and workflow methods.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289046578 14400 # Node ID d46ccc650084224553b3b48c11df64d43d7673ef # Parent 702f4717a8f3fe38758c54136f81935f7679c937 Eliminate check_user flag from tool menu and workflow methods. --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1206,14 +1206,13 @@ class WorkflowController( BaseController ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) @web.expose - def run( self, trans, id, check_user=True, **kwargs ): + def run( self, trans, id, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) - if check_user: - user = trans.get_user() - if stored.user != user: - if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ - .filter_by( user=user, stored_workflow=stored ).count() == 0: - error( "Workflow is not owned by or shared with current user" ) + user = trans.get_user() + if stored.user != user: + if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ + .filter_by( user=user, stored_workflow=stored ).count() == 0: + error( "Workflow is not owned by or shared with current user" ) # Get the latest revision workflow = stored.latest_workflow # It is possible for a workflow to have 0 steps @@ -1343,14 +1342,13 @@ class WorkflowController( BaseController incoming=kwargs ) @web.expose - def tag_outputs( self, trans, id, check_user=True, **kwargs ): + def tag_outputs( self, trans, id, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) - if check_user: - user = trans.get_user() - if stored.user != user: - if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ - .filter_by( user=user, stored_workflow=stored ).count() == 0: - error( "Workflow is not owned by or shared with current user" ) + user = trans.get_user() + if stored.user != user: + if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ + .filter_by( user=user, stored_workflow=stored ).count() == 0: + error( "Workflow is not owned by or shared with current user" ) # Get the latest revision workflow = stored.latest_workflow # It is possible for a workflow to have 0 steps --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -32,7 +32,7 @@ <div class="toolTitleNoSection"> %endif <% encoded_id = key.lstrip( 'workflow_' ) %> - <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id, check_user=False )}" target="_parent">${_(workflow.name)}</a> + <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id )}" target="_parent">${_(workflow.name)}</a></div></%def>

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galaxy-dist commit dcc68da403f0: Fix for failing rgManQQ functional test - changed R outputs. cut down size of default png - much faster...
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Ross Lazarus <ross.lazarus(a)gmail.com> # Date 1289178885 18000 # Node ID dcc68da403f0e8d3ae0da07529ff96327ca05489 # Parent 74620fac33c74b60c0a2faa69364dea0115e8815 Fix for failing rgManQQ functional test - changed R outputs. cut down size of default png - much faster... Binary file test-data/rgtestouts/rgManQQ/Allelep_manhattan.png has changed --- a/tools/rgenetics/rgManQQ.py +++ b/tools/rgenetics/rgManQQ.py @@ -6,6 +6,7 @@ from rgutils import timenow, RRun, galht progname = os.path.split(sys.argv[0])[1] myversion = 'V000.1 March 2010' verbose = False +debug = False rcode=""" # license not stated so I'm assuming LGPL is ok for my derived work? @@ -156,7 +157,7 @@ if (plen > 0) { mytitle = paste('p=',cname,', ',title,sep='') myfname = chartr(' ','_',cname) myqqplot = qq(rawd[,pvalscolumn],title=mytitle) - ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=11,height=8,dpi=100) + ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=6,height=4,dpi=100) print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { if (doreorder) { @@ -168,7 +169,7 @@ if (plen > 0) { print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) - ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) + ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=6,height=4,dpi=100) } else { print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn, @@ -196,6 +197,8 @@ def doManQQ(input_fname,chrom_col,offset to make them do our bidding - and save the resulting code for posterity this can be called externally, I guess...for QC eg? """ + if debug: + print 'doManQQ',input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir ffd,filtered_fname = tempfile.mkstemp(prefix='rgManQQtemp') f = open(filtered_fname,'w') inf = open(input_fname,'r') @@ -232,6 +235,8 @@ def doManQQ(input_fname,chrom_col,offset pvc = [x+3 for x in range(len(pval_cols))] # 2 for offset and chrom, 1 for r offset start pvc = 'c(%s)' % (','.join(map(str,pvc))) rcmd = '%s%s' % (rcode,rcode2 % (filtered_fname,'1','2',pvc,title,grey)) + if debug: + print 'running\n%s\n' % rcmd rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir) rlog.append('## R script=') rlog.append(rcmd) --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.R +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.R @@ -124,7 +124,7 @@ qq = function(pvector, title=NULL, spart if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) qq } -rgqqMan = function(infile="/tmp/rgManQQtempcWfFkc",chromcolumn=1, offsetcolumn=2, pvalscolumns=c(3), +rgqqMan = function(infile="/tmp/rgManQQtemplYC5wa",chromcolumn=1, offsetcolumn=2, pvalscolumns=c(3), title="rgManQQtest1",grey=0) { rawd = read.table(infile,head=T,sep='\t') dn = names(rawd) @@ -142,7 +142,7 @@ if (plen > 0) { mytitle = paste('p=',cname,', ',title,sep='') myfname = chartr(' ','_',cname) myqqplot = qq(rawd[,pvalscolumn],title=mytitle) - ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=11,height=8,dpi=100) + ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=6,height=4,dpi=100) print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { if (doreorder) { @@ -154,7 +154,7 @@ if (plen > 0) { print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) - ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) + ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=6,height=4,dpi=100) } else { print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn, @@ -171,4 +171,4 @@ if (plen > 0) { rgqqMan() # execute with defaults as substituted -#R script autogenerated by rgenetics/rgutils.py on 18/09/2010 20:46:49 +#R script autogenerated by rgenetics/rgutils.py on 07/11/2010 20:03:37 --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.html +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.html @@ -43,7 +43,7 @@ Loading required package: grid Loading required package: proto -[1] "### 101 values read from /tmp/rgManQQtempcWfFkc read - now running plots" +[1] "### 101 values read from /tmp/rgManQQtemplYC5wa read - now running plots" [1] "## qqplot on Allelep done" @@ -178,7 +178,7 @@ qq = function(pvector, title=NULL, spart if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) qq } -rgqqMan = function(infile="/tmp/rgManQQtempcWfFkc",chromcolumn=1, offsetcolumn=2, pvalscolumns=c(3), +rgqqMan = function(infile="/tmp/rgManQQtemplYC5wa",chromcolumn=1, offsetcolumn=2, pvalscolumns=c(3), title="rgManQQtest1",grey=0) { rawd = read.table(infile,head=T,sep='\t') dn = names(rawd) @@ -196,7 +196,7 @@ if (plen > 0) { mytitle = paste('p=',cname,', ',title,sep='') myfname = chartr(' ','_',cname) myqqplot = qq(rawd[,pvalscolumn],title=mytitle) - ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=11,height=8,dpi=100) + ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=6,height=4,dpi=100) print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { if (doreorder) { @@ -208,7 +208,7 @@ if (plen > 0) { print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) - ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) + ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=6,height=4,dpi=100) } else { print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn, @@ -227,6 +227,6 @@ rgqqMan() </pre> -<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgManQQ.py run at 18/09/2010 20:48:26</h3> +<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgManQQ.py run at 07/11/2010 20:04:20</h3></div></body></html> --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -42,7 +42,7 @@ <param name='chrom_col' value='1' /><param name='offset_col' value='2' /><param name='grey' value='0' /> - <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='40'> + <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='60'><extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" delta = "10000"/><extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" Binary file test-data/rgtestouts/rgManQQ/Allelep_qqplot.png has changed

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galaxy-dist commit 4187ae2fdb9e: Improved error handling in api methods.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289186302 18000 # Node ID 4187ae2fdb9e3f8b7ff5878e7517a24868b8ffca # Parent dcc68da403f0e8d3ae0da07529ff96327ca05489 Improved error handling in api methods. --- a/scripts/api/common.py +++ b/scripts/api/common.py @@ -48,6 +48,13 @@ def put( api_key, url, data ): req.get_method = lambda: 'PUT' return simplejson.loads( urllib2.urlopen( req ).read() ) +def __del( api_key, url, data ): + # Do the actual DELETE + url = make_url( api_key, url ) + req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data )) + req.get_method = lambda: 'DELETE' + return simplejson.loads( urllib2.urlopen( req ).read() ) + def display( api_key, url, return_formatted=True ): # Sends an API GET request and acts as a generic formatter for the JSON response. @@ -89,12 +96,12 @@ def submit( api_key, url, data, return_f try: r = post( api_key, url, data ) except urllib2.HTTPError, e: - print e - print e.read( 1024 ) if return_formatted: + print e + print e.read( 1024 ) sys.exit( 1 ) else: - return 'Error. '+ str( e ) + return 'Error. '+ str( e.read( 1024 ) ) if not return_formatted: return r print 'Response' @@ -123,30 +130,35 @@ def update( api_key, url, data, return_f try: r = put( api_key, url, data ) except urllib2.HTTPError, e: - print e - print e.read( 1024 ) - sys.exit( 1 ) + if return_formatted: + print e + print e.read( 1024 ) + sys.exit( 1 ) + else: + return 'Error. '+ str( e.read( 1024 ) ) if not return_formatted: return r print 'Response' print '--------' - if type( r ) == list: - # Currently the only implemented responses are lists of dicts, because - # submission creates some number of collection elements. - for i in r: - if type( i ) == dict: - if 'url' in i: - print i.pop( 'url' ) - else: - print '----' - if 'name' in i: - print ' name: %s' % i.pop( 'name' ) - for k, v in i.items(): - print ' %s: %s' % ( k, v ) - else: - print i - else: - print r + print r + +def delete( api_key, url, data, return_formatted=True ): + # Sends an API DELETE request and acts as a generic formatter for the JSON response. + # 'data' will become the JSON payload read by Galaxy. + try: + r = __del( api_key, url, data ) + except urllib2.HTTPError, e: + if return_formatted: + print e + print e.read( 1024 ) + sys.exit( 1 ) + else: + return 'Error. '+ str( e.read( 1024 ) ) + if not return_formatted: + return r + print 'Response' + print '--------' + print r # utility method to encode ID's def encode_id( config_id_secret, obj_id ): --- a/scripts/galaxy_messaging/server/amqp_consumer.py +++ b/scripts/galaxy_messaging/server/amqp_consumer.py @@ -95,7 +95,7 @@ def update_request( api_key, request_id try: retval = api.update( api_key, url, data, return_formatted=False ) log.debug( str( retval ) ) - except urllib2.URLError, e: + except Exception, e: log.debug( 'ERROR(update_request (%s)): %s' % ( str((self.api_key, url, data)), str(e) ) ) def recv_callback( message ): --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -662,7 +662,7 @@ class RequestsAdmin( BaseController, Use except Exception, e: err_msg = "Error in sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e) if not err_msg: - message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to monitor the transfer status." % len( selected_sample_datasets ) + err_msg = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to monitor the transfer status." % len( selected_sample_datasets ) status = "done" else: status = 'error' @@ -670,7 +670,7 @@ class RequestsAdmin( BaseController, Use action='manage_datasets', sample_id=trans.security.encode_id( sample.id ), status=status, - message=message ) ) + message=err_msg ) ) @web.expose def update_sample_dataset_status(self, trans, cntrller, sample_dataset_ids, new_status, error_msg=None ): # check if the new status is a valid transfer status

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galaxy-dist commit 328b57b1e2e5: sample tracking data transfer mechanism streamlined.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289177219 18000 # Node ID 328b57b1e2e53cbc9ab208379cdd3dc0864f3cc4 # Parent 4b78bad81e777cf503ac66acb5dbb01da841400f sample tracking data transfer mechanism streamlined. - eliminated the transfer_datasets.ini config file - eliminated the data transfer user - now the admin user initiating the data transfer is used as the data transfer user. - the admin user is provided the add_library_item permission before data transfer if they dont have it - sample update & data transfer amqp messages now includes api_key --- a/scripts/galaxy_messaging/client/galaxy_amq.ini.sample +++ b/scripts/galaxy_messaging/client/galaxy_amq.ini.sample @@ -14,6 +14,7 @@ #queue = galaxy_queue #exchange = galaxy_exchange #routing_key = bar_code_scanner +#api_key = # The following section(s) 'scanner#' is for specifying the state of the # sample this scanner represents. This state name should be one of the --- a/scripts/galaxy_messaging/server/amqp_consumer.py +++ b/scripts/galaxy_messaging/server/amqp_consumer.py @@ -15,6 +15,9 @@ import optparse import xml.dom.minidom import subprocess import urllib2 + +from xml_helper import get_value, get_value_index + from galaxydb_interface import GalaxyDbInterface api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] @@ -44,77 +47,58 @@ log.addHandler(fh) # data transfer script data_transfer_script = os.path.join( os.getcwd(), "scripts/galaxy_messaging/server/data_transfer.py" ) +global config +global config_file_name +global http_server_section -global dbconnstr -global webconfig -global config -def get_value(dom, tag_name): - ''' - This method extracts the tag value from the xml message - ''' - nodelist = dom.getElementsByTagName(tag_name)[0].childNodes - rc = "" - for node in nodelist: - if node.nodeType == node.TEXT_NODE: - rc = rc + node.data - return rc - -def get_value_index(dom, tag_name, index): - ''' - This method extracts the tag value from the xml message - ''' - try: - nodelist = dom.getElementsByTagName(tag_name)[index].childNodes - except: - return None - rc = "" - for node in nodelist: - if node.nodeType == node.TEXT_NODE: - rc = rc + node.data - return rc - -def start_data_transfer(message): +def start_data_transfer( message ): # fork a new process to transfer datasets cmd = '%s "%s" "%s" "%s"' % ( "python", data_transfer_script, message.body, - sys.argv[1] ) # Galaxy config file name + config_file_name ) # Galaxy config file name pid = subprocess.Popen(cmd, shell=True).pid log.debug('Started process (%i): %s' % (pid, str(cmd))) -def update_sample_state(message): +def update_sample_state( message ): dom = xml.dom.minidom.parseString(message.body) barcode = get_value(dom, 'barcode') state = get_value(dom, 'state') + api_key = get_value(dom, 'api_key') log.debug('Barcode: ' + barcode) log.debug('State: ' + state) + log.debug('api_key: ' + api_key) + # validate + if not barcode or not state or not api_key: + log.debug( 'Incomplete sample_state_update message received. Sample barcode, desired state and user API key is required.' ) + return # update the sample state in Galaxy db - galaxydb = GalaxyDbInterface(dbconnstr) - sample_id = galaxydb.get_sample_id(field_name='bar_code', value=barcode) + dbconnstr = config.get("app:main", "database_connection") + galaxydb = GalaxyDbInterface( dbconnstr ) + sample_id = galaxydb.get_sample_id( field_name='bar_code', value=barcode ) if sample_id == -1: - log.debug('Invalid barcode.') + log.debug( 'Invalid barcode.' ) return galaxydb.change_state(sample_id, state) # after updating the sample state, update request status request_id = galaxydb.get_request_id(sample_id) - update_request( request_id ) + update_request( api_key, request_id ) -def update_request( request_id ): - http_server_section = webconfig.get( "universe_wsgi_config", "http_server_section" ) +def update_request( api_key, request_id ): encoded_request_id = api.encode_id( config.get( "app:main", "id_secret" ), request_id ) - api_key = webconfig.get( "data_transfer_user_login_info", "api_key" ) data = dict( update_type=RequestsController.update_types.REQUEST ) url = "http://%s:%s/api/requests/%s" % ( config.get(http_server_section, "host"), config.get(http_server_section, "port"), encoded_request_id ) log.debug( 'Updating request %i' % request_id ) try: - api.update( api_key, url, data, return_formatted=False ) + retval = api.update( api_key, url, data, return_formatted=False ) + log.debug( str( retval ) ) except urllib2.URLError, e: log.debug( 'ERROR(update_request (%s)): %s' % ( str((self.api_key, url, data)), str(e) ) ) -def recv_callback(message): +def recv_callback( message ): # check the meesage type. msg_type = message.properties['application_headers'].get('msg_type') log.debug( 'MESSAGE RECVD: ' + str( msg_type ) ) @@ -126,22 +110,25 @@ def recv_callback(message): update_sample_state( message ) def main(): - if len(sys.argv) < 2: - print 'Usage: python amqp_consumer.py <Galaxy configuration file>' - return + parser = optparse.OptionParser() + parser.add_option('-c', '--config-file', help='Galaxy configuration file', + dest='config_file', action='store') + parser.add_option('-s', '--http-server-section', help='Name of the HTTP server section in the Galaxy configuration file', + dest='http_server_section', action='store') + (opts, args) = parser.parse_args() + log.debug( "GALAXY LISTENER PID: " + str(os.getpid()) + " - " + str( opts ) ) + # read the Galaxy config file + global config_file_name + config_file_name = opts.config_file global config config = ConfigParser.ConfigParser() - config.read( sys.argv[1] ) - global dbconnstr - dbconnstr = config.get("app:main", "database_connection") + config.read( opts.config_file ) + global http_server_section + http_server_section = opts.http_server_section amqp_config = {} for option in config.options("galaxy_amqp"): amqp_config[option] = config.get("galaxy_amqp", option) - log.debug("PID: " + str(os.getpid()) + ", " + str(amqp_config)) - # web server config - global webconfig - webconfig = ConfigParser.ConfigParser() - webconfig.read('transfer_datasets.ini') + log.debug( str( amqp_config ) ) # connect conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], userid=amqp_config['userid'], --- /dev/null +++ b/scripts/galaxy_messaging/server/xml_helper.py @@ -0,0 +1,28 @@ +#======= XML helper methods ==================================================== + +import xml.dom.minidom + +def get_value( dom, tag_name ): + ''' + This method extracts the tag value from the xml message + ''' + nodelist = dom.getElementsByTagName( tag_name )[ 0 ].childNodes + rc = "" + for node in nodelist: + if node.nodeType == node.TEXT_NODE: + rc = rc + node.data + return rc + +def get_value_index( dom, tag_name, dataset_id ): + ''' + This method extracts the tag value from the xml message + ''' + try: + nodelist = dom.getElementsByTagName( tag_name )[ dataset_id ].childNodes + except: + return None + rc = "" + for node in nodelist: + if node.nodeType == node.TEXT_NODE: + rc = rc + node.data + return rc --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -655,8 +655,8 @@ class RequestsCommon( BaseController, Us event = trans.model.RequestEvent( request, request.states.SUBMITTED, message ) trans.sa_session.add( event ) trans.sa_session.flush() - if cntrller == 'api': - return 200, message + if cntrller == 'api': + return 200, message return trans.response.send_redirect( web.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, --- a/scripts/galaxy_messaging/server/data_transfer.py +++ b/scripts/galaxy_messaging/server/data_transfer.py @@ -19,6 +19,8 @@ import urllib,urllib2, cookielib, shutil import logging, time, datetime import xml.dom.minidom +from xml_helper import get_value, get_value_index + log = logging.getLogger( "datatx_" + str( os.getpid() ) ) log.setLevel( logging.DEBUG ) fh = logging.FileHandler( "data_transfer.log" ) @@ -36,35 +38,38 @@ new_path = [ os.path.join( os.getcwd(), new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path +from galaxy import eggs from galaxy.util.json import from_json_string, to_json_string from galaxy.model import SampleDataset from galaxy.web.api.requests import RequestsController -from galaxy import eggs import pkg_resources pkg_resources.require( "pexpect" ) import pexpect - pkg_resources.require( "simplejson" ) import simplejson +log.debug(str(dir(api))) + class DataTransfer( object ): def __init__( self, msg, config_file ): log.info( msg ) self.dom = xml.dom.minidom.parseString( msg ) - self.sequencer_host = self.get_value( self.dom, 'data_host' ) - self.sequencer_username = self.get_value( self.dom, 'data_user' ) - self.sequencer_password = self.get_value( self.dom, 'data_password' ) - self.request_id = self.get_value( self.dom, 'request_id' ) - self.sample_id = self.get_value( self.dom, 'sample_id' ) - self.library_id = self.get_value( self.dom, 'library_id' ) - self.folder_id = self.get_value( self.dom, 'folder_id' ) + self.galaxy_host = get_value( self.dom, 'galaxy_host' ) + self.api_key = get_value( self.dom, 'api_key' ) + self.sequencer_host = get_value( self.dom, 'data_host' ) + self.sequencer_username = get_value( self.dom, 'data_user' ) + self.sequencer_password = get_value( self.dom, 'data_password' ) + self.request_id = get_value( self.dom, 'request_id' ) + self.sample_id = get_value( self.dom, 'sample_id' ) + self.library_id = get_value( self.dom, 'library_id' ) + self.folder_id = get_value( self.dom, 'folder_id' ) self.dataset_files = [] count=0 while True: - dataset_id = self.get_value_index( self.dom, 'dataset_id', count ) - file = self.get_value_index( self.dom, 'file', count ) - name = self.get_value_index( self.dom, 'name', count ) + dataset_id = get_value_index( self.dom, 'dataset_id', count ) + file = get_value_index( self.dom, 'file', count ) + name = get_value_index( self.dom, 'name', count ) if file: self.dataset_files.append( dict( name=name, dataset_id=int( dataset_id ), @@ -72,18 +77,6 @@ class DataTransfer( object ): else: break count=count+1 - try: - # Retrieve the upload user login information from the config file - transfer_datasets_config = ConfigParser.ConfigParser( ) - transfer_datasets_config.read( 'transfer_datasets.ini' ) - self.data_transfer_user_email = transfer_datasets_config.get( "data_transfer_user_login_info", "email" ) - self.data_transfer_user_password = transfer_datasets_config.get( "data_transfer_user_login_info", "password" ) - self.api_key = transfer_datasets_config.get( "data_transfer_user_login_info", "api_key" ) - self.http_server_section = transfer_datasets_config.get( "universe_wsgi_config", "http_server_section" ) - except: - log.error( traceback.format_exc() ) - log.error( 'ERROR reading config values from transfer_datasets.ini.' ) - sys.exit(1) # read config variables config = ConfigParser.ConfigParser() retval = config.read( config_file ) @@ -92,14 +85,6 @@ class DataTransfer( object ): log.error( error_msg ) sys.exit(1) try: - self.server_host = config.get( self.http_server_section, "host" ) - except ConfigParser.NoOptionError,e: - self.server_host = '127.0.0.1' - try: - self.server_port = config.get( self.http_server_section, "port" ) - except ConfigParser.NoOptionError,e: - self.server_port = '8080' - try: self.config_id_secret = config.get( "app:main", "id_secret" ) except ConfigParser.NoOptionError,e: self.config_id_secret = "USING THE DEFAULT IS NOT SECURE!" @@ -198,9 +183,8 @@ class DataTransfer( object ): data[ 'dbkey' ] = '' data[ 'upload_option' ] = 'upload_directory' data[ 'create_type' ] = 'file' - url = "http://%s:%s/api/libraries/%s/contents" % ( self.server_host, - self.server_port, - api.encode_id( self.config_id_secret, self.library_id ) ) + url = "http://%s/api/libraries/%s/contents" % ( self.galaxy_host, + api.encode_id( self.config_id_secret, self.library_id ) ) log.debug( str( ( self.api_key, url, data ) ) ) retval = api.submit( self.api_key, url, data, return_formatted=False ) log.debug( str( retval ) ) @@ -225,9 +209,8 @@ class DataTransfer( object ): data[ 'sample_dataset_ids' ] = sample_dataset_ids data[ 'new_status' ] = status data[ 'error_msg' ] = msg - url = "http://%s:%s/api/requests/%s" % ( self.server_host, - self.server_port, - api.encode_id( self.config_id_secret, self.request_id ) ) + url = "http://%s/api/requests/%s" % ( self.galaxy_host, + api.encode_id( self.config_id_secret, self.request_id ) ) log.debug( str( ( self.api_key, url, data))) retval = api.update( self.api_key, url, data, return_formatted=False ) log.debug( str( retval ) ) @@ -239,31 +222,6 @@ class DataTransfer( object ): log.error( 'FATAL ERROR' ) sys.exit( 1 ) - def get_value( self, dom, tag_name ): - ''' - This method extracts the tag value from the xml message - ''' - nodelist = dom.getElementsByTagName( tag_name )[ 0 ].childNodes - rc = "" - for node in nodelist: - if node.nodeType == node.TEXT_NODE: - rc = rc + node.data - return rc - - def get_value_index( self, dom, tag_name, dataset_id ): - ''' - This method extracts the tag value from the xml message - ''' - try: - nodelist = dom.getElementsByTagName( tag_name )[ dataset_id ].childNodes - except: - return None - rc = "" - for node in nodelist: - if node.nodeType == node.TEXT_NODE: - rc = rc + node.data - return rc - if __name__ == '__main__': log.info( 'STARTING %i %s' % ( os.getpid(), str( sys.argv ) ) ) # --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -109,7 +109,7 @@ class DataTransferGrid( grids.Grid ): default_sort_key = "-create_time" num_rows_per_page = 50 preserve_state = True - use_paging = True + use_paging = False columns = [ NameColumn( "Name", link=( lambda item: dict( operation="view", id=item.id ) ), @@ -299,7 +299,7 @@ class RequestsAdmin( BaseController, Use sample=selected_sample_datasets[0].sample, id_list=id_list ) elif operation == "transfer": - self.__start_datatx( trans, selected_sample_datasets[0].sample, selected_sample_datasets ) + self.initiate_data_transfer( trans, selected_sample_datasets[0].sample, selected_sample_datasets ) # Render the grid view sample_id = params.get( 'sample_id', None ) try: @@ -538,68 +538,36 @@ class RequestsAdmin( BaseController, Use return sample.request.name + '_' + sample.name + '_' + name if opt == options.EXPERIMENT_NAME: return sample.request.name + '_' + name - def __setup_datatx_user( self, trans, sample ): + def __check_library_add_permission( self, trans, target_library, target_folder ): """ - Sets up the datatx user: - - Checks if the user exists, if not creates them. - - Checks if the user had ADD_LIBRARY permission on the target library - and the target folder, if not sets up the permissions. + Checks if the current admin user had ADD_LIBRARY permission on the target library + and the target folder, if not provide the permissions. """ - # Retrieve the upload user login information from the config file - config = ConfigParser.ConfigParser() - ok = True - try: - config.read( 'transfer_datasets.ini' ) - except Exception, e: - message = "Error attempting to read config file named 'transfer_datasets.ini'. Make sure this file is correct." - ok = False - try: - email = config.get( "data_transfer_user_login_info", "email" ) - password = config.get( "data_transfer_user_login_info", "password" ) - except Exception, e: - message = "The 'data_transfer_user_login_info' section is missing from the 'transfer_datasets.ini'. Make sure this file is correct." - ok = False - if not ok: - status = 'error' - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_datasets', - sample_id=trans.security.encode_id( sample.id ), - status=status, - message=message ) ) - # check if the user already exists - datatx_user = trans.sa_session.query( trans.model.User ) \ - .filter( trans.model.User.table.c.email==email ) \ - .first() - if not datatx_user: - # if not create the user - datatx_user = trans.model.User( email=email, password=passsword ) - if trans.app.config.use_remote_user: - datatx_user.external = True - trans.sa_session.add( datatx_user ) - trans.sa_session.flush() - trans.app.security_agent.create_private_user_role( datatx_user ) - trans.app.security_agent.user_set_default_permissions( datatx_user, history=False, dataset=False ) - datatx_user_roles = datatx_user.all_roles() - datatx_user_private_role = trans.app.security_agent.get_private_user_role( datatx_user ) + current_user_roles = trans.user.all_roles() + current_user_private_role = trans.app.security_agent.get_private_user_role( trans.user ) # Make sure this user has LIBRARY_ADD permissions on the target library and folder. # If not, give them permission. - if not trans.app.security_agent.can_add_library_item( datatx_user_roles, sample.library ): + if not trans.app.security_agent.can_add_library_item( current_user_roles, target_library ): lp = trans.model.LibraryPermissions( trans.app.security_agent.permitted_actions.LIBRARY_ADD.action, - sample.library, - datatx_user_private_role ) + target_library, + current_user_private_role ) trans.sa_session.add( lp ) - if not trans.app.security_agent.can_add_library_item( datatx_user_roles, sample.folder ): + if not trans.app.security_agent.can_add_library_item( current_user_roles, target_folder ): lfp = trans.model.LibraryFolderPermissions( trans.app.security_agent.permitted_actions.LIBRARY_ADD.action, - sample.folder, - datatx_user_private_role ) + target_folder, + current_user_private_role ) trans.sa_session.add( lfp ) trans.sa_session.flush() - return datatx_user - def __send_message( self, trans, datatx_info, sample, selected_sample_datasets ): - """Ceates an xml message and sends it to the rabbitmq server""" + def __create_data_transfer_message( self, trans, sample, selected_sample_datasets ): + """ + Creates an xml message to send to the rabbitmq server + """ + datatx_info = sample.request.type.datatx_info # Create the xml message based on the following template xml = \ ''' <data_transfer> + <galaxy_host>%(GALAXY_HOST)s</galaxy_host> + <api_key>%(API_KEY)s</api_key><data_host>%(DATA_HOST)s</data_host><data_user>%(DATA_USER)s</data_user><data_password>%(DATA_PASSWORD)s</data_password> @@ -624,50 +592,77 @@ class RequestsAdmin( BaseController, Use sample_dataset.status = trans.app.model.SampleDataset.transfer_status.IN_QUEUE trans.sa_session.add( sample_dataset ) trans.sa_session.flush() - data = xml % dict( DATA_HOST=datatx_info['host'], - DATA_USER=datatx_info['username'], - DATA_PASSWORD=datatx_info['password'], - REQUEST_ID=str(sample.request.id), - SAMPLE_ID=str(sample.id), - LIBRARY_ID=str(sample.library.id), - FOLDER_ID=str(sample.folder.id), - DATASETS=datasets ) - # Send the message - try: - conn = amqp.Connection( host=trans.app.config.amqp['host'] + ":" + trans.app.config.amqp['port'], - userid=trans.app.config.amqp['userid'], - password=trans.app.config.amqp['password'], - virtual_host=trans.app.config.amqp['virtual_host'], - insist=False ) - chan = conn.channel() - msg = amqp.Message( data.replace( '\n', '' ).replace( '\r', '' ), - content_type='text/plain', - application_headers={'msg_type': 'data_transfer'} ) - msg.properties["delivery_mode"] = 2 - chan.basic_publish( msg, - exchange=trans.app.config.amqp['exchange'], - routing_key=trans.app.config.amqp['routing_key'] ) - chan.close() - conn.close() - except Exception, e: - message = "Error in sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e) - status = "error" - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_datasets', - sample_id=trans.security.encode_id( sample.id ), - status=status, - message=message) ) - - def __start_datatx( self, trans, sample, selected_sample_datasets ): - datatx_user = self.__setup_datatx_user( trans, sample ) - # Validate sequencer information + message = xml % dict( GALAXY_HOST=trans.request.host, + API_KEY=trans.user.api_keys[0].key, + DATA_HOST=datatx_info[ 'host' ], + DATA_USER=datatx_info[ 'username' ], + DATA_PASSWORD=datatx_info[ 'password' ], + REQUEST_ID=str( sample.request.id ), + SAMPLE_ID=str( sample.id ), + LIBRARY_ID=str( sample.library.id ), + FOLDER_ID=str( sample.folder.id ), + DATASETS=datasets ) + return message + def __validate_data_transfer_settings( self, trans, sample ): + err_msg = '' + # check the sequencer login info datatx_info = sample.request.type.datatx_info - if not datatx_info['host'] or not datatx_info['username'] or not datatx_info['password']: - message = "Error in sequencer login information." - status = "error" - else: - self.__send_message( trans, datatx_info, sample, selected_sample_datasets ) - message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to see the latest transfer status." % len( selected_sample_datasets ) + if not datatx_info[ 'host' ] \ + or not datatx_info[ 'username' ] \ + or not datatx_info[ 'password' ]: + err_msg = "Error in sequencer login information." + # check if web API is enabled and API key exists + if not trans.user.api_keys or not trans.app.config.enable_api: + err_msg = "Could not start data transfer as Galaxy Web API is not enabled. Enable Galaxy Web API in the Galaxy config file and create an API key." + # check if library_import_dir is set + if not trans.app.config.library_import_dir: + err_msg = "'library_import_dir' config variable is not set in the Galaxy config file." + # check the RabbitMQ server settings in the config file + for k, v in trans.app.config.amqp.items(): + if not v: + err_msg = 'Set RabbitMQ server settings in the "galaxy_amqp" section of the Galaxy config file. %s is not set.' % k + break + return err_msg + def initiate_data_transfer( self, trans, sample, selected_sample_datasets ): + ''' + This method initiates the transfer of the datasets from the sequencer. It + happens in the following steps: + - The current admin user needs to have ADD_LIBRARY_ITEM permission for the + target library and folder + - Create an XML message encapsulating all the data transfer info and send it + to the message queue (RabbitMQ broker) + ''' + # check data transfer settings + err_msg = self.__validate_data_transfer_settings( trans, sample ) + if not err_msg: + # check if the current user has add_library_item permission to the sample + # target library & folder + self.__check_library_add_permission( trans, sample.library, sample.folder ) + # create the message + message = self.__create_data_transfer_message( trans, + sample, + selected_sample_datasets ) + # Send the message + try: + conn = amqp.Connection( host=trans.app.config.amqp[ 'host' ] + ":" + trans.app.config.amqp[ 'port' ], + userid=trans.app.config.amqp[ 'userid' ], + password=trans.app.config.amqp[ 'password' ], + virtual_host=trans.app.config.amqp[ 'virtual_host' ], + insist=False ) + chan = conn.channel() + msg = amqp.Message( message.replace( '\n', '' ).replace( '\r', '' ), + content_type='text/plain', + application_headers={ 'msg_type': 'data_transfer' } ) + msg.properties[ "delivery_mode" ] = 2 + chan.basic_publish( msg, + exchange=trans.app.config.amqp[ 'exchange' ], + routing_key=trans.app.config.amqp[ 'routing_key' ] ) + chan.close() + conn.close() + except Exception, e: + err_msg = "Error in sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e) + if not err_msg: + message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to monitor the transfer status." % len( selected_sample_datasets ) status = "done" return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', --- a/transfer_datasets.ini.sample +++ /dev/null @@ -1,10 +0,0 @@ -# Galaxy LIMS Transfer Datasets Configuration File - -[data_transfer_user_login_info] -#email = datatx(a)bx.psu.edu -#password = datatx -#api_key = Generate it from the User menu in Galaxy - -[universe_wsgi_config] -# The http server section name in the Galaxy config file (universe_wsgi.ini) -#http_server_section = server:main --- a/lib/galaxy/web/api/requests.py +++ b/lib/galaxy/web/api/requests.py @@ -88,7 +88,7 @@ class RequestsController( BaseController request_id = trans.security.decode_id( id ) except TypeError: trans.response.status = 400 - return "Malformed %s id ( %s ) specified, unable to decode." % ( update_type, str( id ) ) + return "Malformed request id ( %s ) specified, unable to decode." % str( id ) try: request = trans.sa_session.query( trans.app.model.Request ).get( request_id ) except: --- a/run_galaxy_listener.sh +++ b/run_galaxy_listener.sh @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0` -python scripts/galaxy_messaging/server/amqp_consumer.py universe_wsgi.ini 2>&1 +python scripts/galaxy_messaging/server/amqp_consumer.py --config-file=universe_wsgi.ini --http-server-section=server:main 2>&1 --- a/scripts/galaxy_messaging/client/amqp_publisher.py +++ b/scripts/galaxy_messaging/client/amqp_publisher.py @@ -19,13 +19,15 @@ xml = \ ''' <sample><barcode>%(BARCODE)s</barcode><state>%(STATE)s</state> + <api_key>%(API_KEY)s</api_key></sample>''' def handle_scan(states, amqp_config, barcode): if states.get(barcode[:2], None): values = dict( BARCODE=barcode[2:], - STATE=states.get(barcode[:2]) ) + STATE=states.get(barcode[:2]), + API_KEY=amqp_config['api_key'] ) print values data = xml % values print data @@ -68,6 +70,10 @@ def main(): states = {} for option in config.options("galaxy:amqp"): amqp_config[option] = config.get("galaxy:amqp", option) + # abort if api_key is not set in the config file + if not amqp_config['api_key']: + print 'Error: Set the api_key config variable in the config file before starting the amqp_publisher script.' + sys.exit( 1 ) count = 1 while True: section = 'scanner%i' % count

1 0

galaxy-dist commit 4b78bad81e77: Trackster: save current viewport when saving viz
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User James Taylor <james(a)jamestaylor.org> # Date 1289169067 18000 # Node ID 4b78bad81e777cf503ac66acb5dbb01da841400f # Parent fb55bfc792b1d087783055a736d9fb439e5bb41c Trackster: save current viewport when saving viz --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -81,7 +81,7 @@ var Cache = function( num_elements ) { } }); -var View = function( container, title, vis_id, dbkey ) { +var View = function( container, title, vis_id, dbkey, callback ) { this.container = container; this.vis_id = vis_id; this.dbkey = dbkey; @@ -95,11 +95,11 @@ var View = function( container, title, v this.zoom_factor = 3; this.min_separation = 30; this.has_changes = false; - this.init(); + this.init( callback ); this.reset(); }; $.extend( View.prototype, { - init: function() { + init: function( callback ) { // Create DOM elements var parent_element = this.container, view = this; @@ -177,6 +177,9 @@ var View = function( container, title, v view.chrom_select.bind("change", function() { view.change_chrom(view.chrom_select.val()); }); + if ( callback ) { + callback(); + } }, error: function() { alert( "Could not load chroms for this dbkey:", view.dbkey ); @@ -244,8 +247,8 @@ var View = function( container, title, v this.drag_origin_x = e.clientX; this.drag_origin_pos = e.clientX / view.viewport_container.width() * (view.high - view.low) + view.low; this.drag_div = $("<div />").css( { - "height": view.content_div.height()+30, "top": "0px", "position": "absolute", - "background-color": "#cfc", "border": "1px solid #6a6", "opacity": 0.5, "z-index": 1000 + "height": view.content_div.height() + view.top_labeltrack.height() + view.nav_labeltrack.height(), "top": "0px", "position": "absolute", + "background-color": "#ccf", "opacity": 0.5, "z-index": 1000 } ).appendTo( $(this) ); }).bind( "drag", function(e) { var min = Math.min(e.clientX, this.drag_origin_x) - view.container.offset().left, @@ -1216,7 +1219,7 @@ var FeatureTrack = function ( name, view this.show_labels_scale = 0.001; this.showing_details = false; this.vertical_detail_px = 10; - this.vertical_nodetail_px = 2; + this.vertical_nodetail_px = 3; this.summary_draw_height = 30; this.default_font = "9px Monaco, Lucida Console, monospace"; this.inc_slots = {}; --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -1,12 +1,5 @@ """ Support for constructing and viewing custom "track" browsers within Galaxy. - -Track browsers are currently transient -- nothing is stored to the database -when a browser is created. Building a browser consists of selecting a set -of datasets associated with the same dbkey to display. Once selected, jobs -are started to create any necessary indexes in the background, and the user -is redirected to the browser interface, which loads the appropriate datasets. - """ import re, pkg_resources @@ -317,7 +310,7 @@ class TracksController( BaseController, if 'vis_id' in kwargs: vis_id = kwargs['vis_id'].strip('"') dbkey = kwargs['dbkey'] - + # Lookup or create Visualization object if vis_id == "undefined": # new vis vis = model.Visualization() vis.user = trans.user @@ -328,20 +321,30 @@ class TracksController( BaseController, else: decoded_id = trans.security.decode_id( vis_id ) vis = session.query( model.Visualization ).get( decoded_id ) - + # Decode the payload decoded_payload = simplejson.loads( kwargs['payload'] ) + # Create new VisualizationRevision that will be attached to the viz vis_rev = model.VisualizationRevision() vis_rev.visualization = vis vis_rev.title = vis.title vis_rev.dbkey = dbkey + # Tracks from payload tracks = [] - for track in decoded_payload: + for track in decoded_payload['tracks']: tracks.append( { "dataset_id": str(track['dataset_id']), "name": track['name'], "track_type": track['track_type'], "prefs": track['prefs'] } ) - vis_rev.config = { "tracks": tracks } + # Viewport from payload + if 'viewport' in decoded_payload: + chrom = decoded_payload['viewport']['chrom'] + start = decoded_payload['viewport']['start'] + end = decoded_payload['viewport']['end'] + vis_rev.config = { "tracks": tracks, "viewport": { 'chrom': chrom, 'start': start, 'end': end } } + else: + vis_rev.config = { "tracks": tracks } + print vis_rev.config vis.latest_revision = vis_rev session.add( vis_rev ) session.flush() --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -77,7 +77,11 @@ $(function() { %if config: - view = new View( $("#browser-container"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); + var callback; + %if 'viewport' in config: + var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); } + %endif + view = new View( $("#browser-container"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}", callback ); view.editor = true; %for track in config.get('tracks'): view.add_track( @@ -180,21 +184,25 @@ $("#save-button").bind("click", function(e) { var sorted = $(".viewport-container").sortable('toArray'), - payload = []; + tracks = []; + + // Show saving dialog box + show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); for (var i in sorted) { var track_id = parseInt(sorted[i].split("track_")[1]), track = view.tracks[track_id]; - payload.push( { + tracks.push( { "track_type": track.track_type, "name": track.name, "dataset_id": track.dataset_id, "prefs": track.prefs }); } - // Show saving dialog box - show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); + + var payload = { 'tracks': tracks, 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high } } + console.log( payload ); $.ajax({ url: "${h.url_for( action='save' )}", --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -185,6 +185,9 @@ class UsesVisualization( SharableItemSec config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ), "tracks": tracks, "chrom": "", "dbkey": visualization.dbkey } + + if 'viewport' in latest_revision.config: + config['viewport'] = latest_revision.config['viewport'] return config

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galaxy-dist commit fb55bfc792b1: Trackster UI tweaks, mainly moving the navigation to the top, still needs to be compressed and cleaned up. Also, getting borders and spacing a little more even. Some intial keyboard navigation
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User James Taylor <james(a)jamestaylor.org> # Date 1289163413 18000 # Node ID fb55bfc792b1d087783055a736d9fb439e5bb41c # Parent d46ccc650084224553b3b48c11df64d43d7673ef Trackster UI tweaks, mainly moving the navigation to the top, still needs to be compressed and cleaned up. Also, getting borders and spacing a little more even. Some intial keyboard navigation --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -15,8 +15,8 @@ ${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom" )} <style type="text/css"> - #center { - overflow: auto; + #center, #browser-container { + overflow: none; } ul#sortable-ul { list-style: none; @@ -29,10 +29,7 @@ background: #eee; } .nav-container { - position: fixed; width: 100%; - left: 0; - bottom: 0; } # Styles for filters. .filter-name { @@ -57,6 +54,7 @@ <a id="add-track" class="panel-header-button right-float" href="javascript:void(0);">Add Tracks</a></div></div> +<div id="browser-container" class="unified-panel-body"></div></%def> @@ -79,7 +77,7 @@ $(function() { %if config: - view = new View( $("#center"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); + view = new View( $("#browser-container"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); view.editor = true; %for track in config.get('tracks'): view.add_track( @@ -215,6 +213,16 @@ error: function() { alert("Could not save visualization"); } }); }); + + $(document).keydown( function( e ) { + // 37 == left + if ( e.which == 39 ) { + view.move_fraction( -0.25 ); + // 39 == right + } else if ( e.which == 37 ) { + view.move_fraction( 0.25 ); + } + }); }; }); --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -103,15 +103,25 @@ var View = function( container, title, v // Create DOM elements var parent_element = this.container, view = this; - this.top_labeltrack = $("<div/>").addClass("top-labeltrack").appendTo(parent_element); + // Top container for things that are fixed at the top + this.top_container = $("<div/>").addClass("top-container").appendTo(parent_element); + // Content container, primary tracks are contained in here this.content_div = $("<div/>").addClass("content").css("position", "relative").appendTo(parent_element); + // Bottom container for things that are fixed at the bottom + this.bottom_container = $("<div/>").addClass("bottom-container").appendTo(parent_element); + // Label track fixed at top + this.top_labeltrack = $("<div/>").addClass("top-labeltrack").appendTo(this.top_container); + // Viewport for dragging tracks in center this.viewport_container = $("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div); - this.intro_div = $("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide(); // Future overlay - - this.nav_container = $("<div/>").addClass("nav-container").appendTo(parent_element); - this.nav_labeltrack = $("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container); + // Future overlay? + this.intro_div = $("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide(); + // Another label track at bottom + this.nav_labeltrack = $("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container); + // Navigation at top + this.nav_container = $("<div/>").addClass("nav-container").prependTo(this.top_container); this.nav = $("<div/>").addClass("nav").appendTo(this.nav_container); - this.overview = $("<div/>").addClass("overview").appendTo(this.nav); + // Overview (scrollbar and overview plot) at bottom + this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container); this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview); this.overview_close = $("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport); this.overview_highlight = $("<div />").addClass("overview-highlight").hide().appendTo(this.overview_viewport); @@ -327,6 +337,11 @@ var View = function( container, title, v } view.change_chrom(chrom, new_low, new_high); }, + move_fraction : function( fraction ) { + var view = this; + var span = view.high - view.low; + this.move_delta( fraction * span ); + }, move_delta: function(delta_chrom) { var view = this; var current_chrom_span = view.high - view.low; @@ -439,7 +454,7 @@ var View = function( container, title, v this.redraw(); }, resize_window: function() { - this.viewport_container.height( this.container.height() - this.nav_container.height() - 45 ); + this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); this.nav_container.width( this.container.width() ); this.redraw(); }, --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -1,7 +1,7 @@ .viewport-container{overflow-x:hidden;overflow-y:auto;} -.nav{padding:0 0;color:#333;font-weight:bold;} -.content{font:9px verdana;} -.nav-controls{text-align:center;position:relative;background:#cccccc;background-image:url(panel_header_bg.png);background-position:top center;background-repeat:repeat-x;padding:2px 0;} +.nav{padding:0 0;color:#333;font-weight:bold;background:#cccccc;background-image:url(panel_header_bg.png);background-position:bottom center;background-repeat:repeat-x;height:2.5em;border-bottom:solid #333 1px;} +.content{font:10px verdana;} +.nav-controls{text-align:center;position:relative;padding:2px 0;} .nav-controls input{margin:0 5px;} .nav-controls a{padding:0 0.4em;} .nav-input{font-size:12px;width:30em;z-index:1000;} @@ -9,24 +9,23 @@ .draghandle{cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;} .intro{z-index:1000;margin-left:auto;margin-right:auto;color:#555;text-align:center;font-size:16px;} .overview{width:100%;margin:0px;color:white;} -.overview-viewport{position:relative;height:14px;background:white;border-bottom:solid gray 1px;margin:0;} +.overview-viewport{position:relative;height:14px;background:white;margin:0;} .overview-close{font:9px verdana;position:absolute;top:0px;right:0px;padding:5px;z-index:500;background-color:white;} -.overview-highlight{opacity:0.5;top:0px;position:absolute;z-index:100;border-style:solid;border-color:#484848;border-width:0px 1px;} -.overview-boxback{width:100%;bottom:0px;z-index:50;position:absolute;height:14px;background:#eee;} -.overview-box{cursor:pointer;opacity:0.5;bottom:0px;z-index:100;position:absolute;margin-top:0px;height:14px;background:#484848 url(../images/visualization/draggable_horizontal.png) center center no-repeat;border-style:solid;border-color:#484848;border-width:0px 1px;-moz-border-radius:3px;border-radius:3px;} -.overview-box:hover{background-color:#838383;border-color:#838383;} +.overview-highlight{top:0px;position:absolute;z-index:100;border-style:solid;border-color:#666;border-width:0px 1px;} +.overview-boxback{width:100%;bottom:0px;z-index:50;position:absolute;height:14px;background:#eee;border:solid #999 1px;} +.overview-box{cursor:pointer;bottom:0px;z-index:100;position:absolute;margin-top:0px;height:14px;background:#C1C9E5 url(../images/visualization/draggable_horizontal.png) center center no-repeat;border:solid #666 1px;} .viewport-canvas{width:100%;height:100px;} .yaxislabel{color:#777;z-index:100;} .line-track .track-content{border-top:1px solid #ddd;border-bottom:1px solid #ddd;} -.track{background:white;margin-bottom:1px;} +.track{background:white;margin-bottom:1px;padding-bottom:4px;border-bottom:#eee solid 1px;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:3px;} .track-content{overflow:hidden;text-align:center;} -.track.error{background-color:#ECB4AF;} -.track.nodata{background-color:#ddd;} +.track.error .track-content{background-color:#ECB4AF;} +.track.nodata .track-content{background-color:#ddd;} .loading{min-height:100px;} -.label-track{} -.label-track .label{border-left:solid #999 1px;padding:1px;display:inline-block;} +.label-track{font-size:10px;border:none;padding:0;margin:0;height:1.3em;} +.label-track .label{border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block;} .right-float{float:right;margin-left:5px;} .top-labeltrack{position:relative;border-bottom:solid #999 1px;} -.nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #999 1px;} +.nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px;} --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -5,17 +5,19 @@ .nav { padding: 0 0; color:#333;font-weight:bold; + background:#cccccc; + background-image:url(panel_header_bg.png); + background-position: bottom center; + background-repeat:repeat-x; + height: 2.5em; + border-bottom: solid #333 1px; } .content { - font: 9px verdana; + font: 10px verdana; } .nav-controls { text-align: center; position: relative; - background:#cccccc; - background-image:url(panel_header_bg.png); - background-position:top center; - background-repeat:repeat-x; padding: 2px 0; } .nav-controls input { @@ -61,7 +63,6 @@ /* border-top: solid #666 1px;*/ /* border-bottom: solid #aaa 1px;*/ background: white; - border-bottom: solid gray 1px; margin: 0; } .overview-close { @@ -74,12 +75,11 @@ background-color: white; } .overview-highlight { - opacity: 0.5; top: 0px; position: absolute; z-index: 100; border-style: solid; - border-color: #484848; + border-color: #666; border-width: 0px 1px; } .overview-boxback { @@ -89,25 +89,17 @@ position: absolute; height: 14px; background: #eee; + border: solid #999 1px; } .overview-box { cursor: pointer; - opacity: 0.5; bottom: 0px; z-index: 100; position: absolute; margin-top: 0px; height: 14px; - background: #484848 url(../images/visualization/draggable_horizontal.png) center center no-repeat; - border-style: solid; - border-color: #484848; - border-width: 0px 1px; - -moz-border-radius: 3px; - border-radius: 3px; -} -.overview-box:hover { - background-color: #838383; - border-color: #838383; + background: #C1C9E5 url(../images/visualization/draggable_horizontal.png) center center no-repeat; + border: solid #666 1px; } .viewport-canvas { width: 100%; @@ -129,6 +121,8 @@ /* border-bottom: solid #DDDDDD 1px; */ background: white; margin-bottom: 1px; + padding-bottom: 4px; + border-bottom: #eee solid 1px; } .track-header { @@ -146,10 +140,10 @@ text-align: center; } -.track.error { +.track.error .track-content { background-color: #ECB4AF; } -.track.nodata { +.track.nodata .track-content { background-color: #ddd; } @@ -159,11 +153,16 @@ .label-track { /* font-weight: bold; */ - /* font-size: 10px; */ + font-size: 10px; + border: none; + padding: 0; + margin: 0; + height: 1.3em; } .label-track .label { border-left: solid #999 1px; padding: 1px; + padding-bottom: 2px; display: inline-block; } .right-float { @@ -178,5 +177,5 @@ .nav-labeltrack { border-top: solid #999 1px; - border-bottom: solid #999 1px; + border-bottom: solid #333 1px; }

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galaxy-dist commit 11abfc8eed60: Update cufflinks and cuffdiff wrappers to indicate that, as of version 0.9, setting parameters for paired-end reads is not recommended.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288979059 14400 # Node ID 11abfc8eed60c0bdd231d06992f72001a2c785fa # Parent 9545e8675a5d43408d75c66fcf3115cbdaf4af8a Update cufflinks and cuffdiff wrappers to indicate that, as of version 0.9, setting parameters for paired-end reads is not recommended. --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -25,6 +25,11 @@ --inputA=$gtf_input --input1=$aligned_reads1 --input2=$aligned_reads2 + + #if $singlePaired.sPaired == "Yes": + -m $singlePaired.mean_inner_distance + -s $singlePaired.inner_distance_std_dev + #end if </command><inputs><param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/> @@ -34,12 +39,12 @@ <param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/><param name="min_alignment_count" type="integer" value="0" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/><conditional name="singlePaired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> + <param name="sPaired" type="select" label="Set Parameters for Paired-end Reads? (not recommended)"> + <option value="No">No</option> + <option value="Yes">Yes</option></param> - <when value="single"></when> - <when value="paired"> + <when value="No"></when> + <when value="Yes"><param name="mean_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs"/><param name="inner_distance_std_dev" type="integer" value="20" label="Standard Deviation for Inner Distance between Mate Pairs"/></when> --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -17,7 +17,7 @@ #if $reference_annotation.use_ref == "Yes": -G $reference_annotation.reference_annotation_file #end if - #if $singlePaired.sPaired == "paired": + #if $singlePaired.sPaired == "Yes": -m $singlePaired.mean_inner_distance -s $singlePaired.inner_distance_std_dev #end if @@ -39,12 +39,12 @@ </when></conditional><conditional name="singlePaired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> + <param name="sPaired" type="select" label="Set Parameters for Paired-end Reads? (not recommended)"> + <option value="No">No</option> + <option value="Yes">Yes</option></param> - <when value="single"></when> - <when value="paired"> + <when value="No"></when> + <when value="Yes"><param name="mean_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs"/><param name="inner_distance_std_dev" type="integer" value="20" label="Standard Deviation for Inner Distance between Mate Pairs"/></when>

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