def htmlSummaryXtriage(self):
"""
Create HTML/php files for xtriage output results.
"""
if self.verbose:
self.logger.debug('AutoStats::htmlSummaryXtriage')
try:
if self.xtriage_summary:
if self.gui:
sl = 'jon_summary_xtriage.php'
else:
sl = 'jon_summary_xtriage.html'
jon_summary = open(sl,'w')
jon_summary.write(Utils.getHTMLHeader(self,'xtriage'))
jon_summary.write('%6s$(document).ready(function() {\n'%'')
jon_summary.write("%8s$('#accordion-xtriage').accordion({\n%11scollapsible: true,\n%11sactive: false });\n"%(3*('',)))
jon_summary.write("%8s$('#xtriage-auto2').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false });\n'%(5*('',)))
jon_summary.write("%8s$('#xtriage_pat').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false });\n'%(5*('',)))
if self.pts:
jon_summary.write("%8s$('#xtriage_pts').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false });\n'%(5*('',)))
if self.twin:
jon_summary.write("%8s$('#xtriage_twin').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false });\n'%(5*('',)))
jon_summary.write('%6s});\n%4s</script>\n%2s</head>\n%2s<body id="dt_example">\n'%(4*('',)))
jon_summary.writelines(self.xtriage_summary)
jon_summary.write('%4s<div id="container">\n%5s<div class="full_width big">\n%6s<div id="demo">\n'%(3*('',)))
jon_summary.write("%7s<h1 class='Results'>Xtriage Output</h1>\n%6s</div>\n%5s</div>\n"%(3*('',)))
jon_summary.write('%5s<div id="accordion-xtriage">\n'%'')
jon_summary.write('%6s<h3><a href="#">Click to view Xtriage log</a></h3>\n%6s<div>\n%7s<pre>\n'%(3*('',)))
if self.xtriage_log:
for line in self.xtriage_log:
jon_summary.write(line)
else:
jon_summary.write('---------------Xtriage FAILED---------------\n')
jon_summary.write('%7s</pre>\n%6s</div>\n%5s</div>\n%4s</div>\n%2s</body>\n</html>\n'%(5*('',)))
jon_summary.close()
else:
Utils.failedHTML(self,('jon_summary_xtriage','Input data could not be analysed, probably because resolution was too low.'))
except:
self.logger.exception('**ERROR in AutoStats.htmlSummaryXtriage**')
def htmlSummaryMolrep(self):
"""
Create HTML/php files for Molrep output results.
"""
if self.verbose:
self.logger.debug('AutoStats::htmlSummaryMolrep')
try:
if self.molrep_summary:
molrep_log = self.molrep_results.get('Molrep results').get('Molrep log')
if self.gui:
sl = 'jon_summary_molrep.php'
else:
sl = 'jon_summary_molrep.html'
jon_summary = open(sl,'w')
jon_summary.write(Utils.getHTMLHeader(self))
jon_summary.write('%6s$(document).ready(function() {\n'%'')
jon_summary.write("%8s$('#accordion-molrep').accordion({\n"%'')
jon_summary.write('%11scollapsible: true,\n%11sactive: false });\n'%('',''))
if self.molrep_summary:
jon_summary.write("%8s$('#molrep').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false});\n'%(5*('',)))
jon_summary.write('%6s});\n%4s</script>\n%2s</head>\n%2s<body id="dt_example">\n'%(4*('',)))
if self.molrep_summary:
jon_summary.writelines(self.molrep_summary)
else:
jon_summary.write("%7s<h2 class='Results'>Error in molrep analysis</h1>\n"%'')
jon_summary.write('%4s<div id="container">\n%5s<div class="full_width big">\n%6s<div id="demo">\n'%(3*('',)))
jon_summary.write("%7s<h1 class='Results'>Molrep Output</h1>\n%6s</div>\n%5s</div>\n"%(3*('',)))
jon_summary.write('%5s<div id="accordion-molrep">\n'%'')
jon_summary.write('%6s<h3><a href="#">Click to view Molrep log</a></h3>\n%6s<div>\n%7s<pre>\n\n'%(3*('',)))
if molrep_log:
for line in open(molrep_log,'r').readlines():
jon_summary.write(line)
else:
jon_summary.write('---------------Molrep FAILED---------------\n')
jon_summary.write('%7s</pre>\n%6s</div>\n%5s</div>\n%4s</div>\n%2s</body>\n</html>\n'%(5*('',)))
jon_summary.close()
else:
Utils.failedHTML(self,'jon_summary_molrep')
except:
self.logger.exception('**ERROR in AutoStats.htmlSummaryMolrep**')
def run(self):
"""
Convoluted path of modules to run.
"""
if self.verbose:
self.logger.debug('LabelitPP::run')
self.preprocess()
if self.failed == False:
#Run Labelit
self.preprocessLabelit()
self.processLabelit()
#Sorts labelit results by highest symmetry.
self.labelitSort()
if self.labelit_failed == False:
#Run labelit_precession_photo for the 3 planes
self.processLabelitPP()
self.Queue()
else:
Utils.failedHTML(self, 'jon_summary_pp')
#Finish everything up
self.postprocess()
def run(self):
"""
Convoluted path of modules to run.
"""
if self.verbose:
self.logger.debug('LabelitPP::run')
self.preprocess()
if self.failed == False:
#Run Labelit
self.preprocessLabelit()
self.processLabelit()
#Sorts labelit results by highest symmetry.
self.labelitSort()
if self.labelit_failed == False:
#Run labelit_precession_photo for the 3 planes
self.processLabelitPP()
self.Queue()
else:
Utils.failedHTML(self,'jon_summary_pp')
#Finish everything up
self.postprocess()
def plotXtriage(self):
"""
generate plots html/php file
"""
if self.verbose:
self.logger.debug('AutoStats::plotXtriage')
try:
cid0 = False
cid1 = False
anom = self.xtriage_results.get('Xtriage results').get('Xtriage anom plot')
intensity = self.xtriage_results.get('Xtriage results').get('Xtriage int plot')
#xtriage_i = self.xtriage_results.get('Xtriage results').get('Xtriage i plot')
nz = self.xtriage_results.get('Xtriage results').get('Xtriage nz plot')
l_test = self.xtriage_results.get('Xtriage results').get('Xtriage l-test plot')
#xtriage_z = self.xtriage_results.get('Xtriage results').get('Xtriage z plot')
if self.NCS_results:
cid0 = self.NCS_results.get('PhaserNCS results').get('CID').get('before')
cid1 = self.NCS_results.get('PhaserNCS results').get('CID').get('after')
#List of params for parsing later.
l = [['Intensity','Mean I vs. Resolution','Resolution(A)','M e a n   I',intensity,
("< I > smooth","< I > binning","< I > expected")],
#['Z scores','Data Sanity and Completeness check','Resolution(A)','Z   S c o r e','z',
#('Z_score','Completeness')],
['Anom_Signal','Anomalous Measurability','Resolution(A)','',anom,
('Obs_anom_meas','Smoothed')],
#['I/sigI','Signal to Noise vs. Resolution','Resolution(A)','I / S i g I','i',
#('Signal_to_Noise',)],
['NZ_Test','NZ Test','z','',nz,('Acen_obs','Acen_untwinned','Cen_obs','Cen_untwinned')],
['L_Test','L-Test','|I|','',l_test,('Obs','Acen_th_untwinned','Acen_th_perfect_twin')],
['CID0','CID before Anisotropic and tNCS correction','Z','',cid0,
('Acen_theo','Acen_twin','Acen_obs','Cen_theo','Cen_obs')],
['CID1','CID after Anisotropic and tNCS correction','Z','',cid1,
('Acen_theo','Acen_twin','Acen_obs','Cen_theo','Cen_obs')]
]
if self.NCS_results:
e = len(l)
else:
e = len(l) - 2
if nz != 'None':
xtriage_plot = ''
xtriage_plot += Utils.getHTMLHeader(self,'plots')
xtriage_plot +="%4s$(function() {\n%6s$('.tabs').tabs();\n%4s});\n"%(3*('',))
xtriage_plot +="%4s</script>\n%2s</head>\n%2s<body>\n%4s<table>\n%6s<tr>\n"%(5*('',))
xtriage_plot +='%8s<td width="100%%">\n%10s<div class="tabs">\n%12s<ul>\n'%(3*('',))
for i in range(e):
xtriage_plot += '%14s<li><a href="#tabs-44%s">%s</a></li>\n'%('',i,l[i][0])
xtriage_plot += "%12s</ul>\n"%''
for i in range(e):
xtriage_plot += '%12s<div id="tabs-44%s">\n%14s<div class=title><b>%s</b></div>\n'%('',i,'',l[i][1])
xtriage_plot += '%14s<div id="chart%s_div3" style="width:750px;height:550px;margin-left:20;"></div>\n'%('',i)
xtriage_plot += '%14s<div class=x-label>%s</div>\n%14s<span class=y-label>%s</span>\n%12s</div>\n'%('',l[i][2],'',l[i][3],'')
xtriage_plot +="%10s</div>\n%8s</td>\n%6s</tr>\n%4s</table>\n"%(4*('',))
xtriage_plot += '%4s<script id="source" language="javascript" type="text/javascript">\n'%''
xtriage_plot += "%6s$(function () {\n"%''
s = '\n%8svar '%''
for i in range(e):
l1 = []
l2 = []
label = ['%10s[\n'%'']
s1 = s
for x in range(len(l[i][4][0])-1):
var = '%s%s'%(l[i][0].upper(),x)
s1 += '%s=[],'%var
label.append('%12s{ data: %s, label:"%s" },\n'%('',var,l[i][5][x]))
for y in range(len(l[i][4])):
if l[i][0] == 'Anom_Signal':
l2.append(float(l[i][4][y][0]))
if l[i][0] in ('Intensity','Anom_Signal'):
l1.append("%8s%s.push([-%s,%s]);\n"%('',var,l[i][4][y][0],l[i][4][y][x+1]))
else:
l1.append("%8s%s.push([%s,%s]);\n"%('',var,l[i][4][y][0],l[i][4][y][x+1]))
if l[i][0] == 'Anom_Signal':
xtriage_plot += '%s,mark=[];\n'%s1[:-1]
label.append('%12s{ data: mark, label:"min level for anom signal" },\n'%'')
else:
xtriage_plot += '%s;\n'%s1[:-1]
label.append('%10s],\n'%'')
l[i].append(label)
for line in l1:
xtriage_plot += line
if l[i][0] == 'Anom_Signal':
xtriage_plot += "%8sfor (var i = -%s; i < -%s; i +=0.25)\n%8smark.push([i,0.05]);\n"%('',max(l2),min(l2),'')
for i in range(e):
xtriage_plot += '%8svar plot%s = $.plot($("#chart%s_div3"),\n'%('',i,i)
for line in l[i][-1]:
xtriage_plot += line
xtriage_plot += "%10s{ lines: { show: true},\n%12spoints: { show: true },\n"%('','')
xtriage_plot += "%12sselection: { mode: 'xy' },\n%12sgrid: { hoverable: false, clickable: false },\n"%('','')
if l[i][0] in ('Intensity','Anom_Signal'):
xtriage_plot += "%12sxaxis: { transform: function (v) { return Math.log(-v); },\n"%''
xtriage_plot += "%21sinverseTransform: function (v) { return Math.exp(-v); },\n"%''
xtriage_plot += "%21stickFormatter: ( function negformat(val,axis){return -val.toFixed(axis.tickDecimals);} ) },\n"%''
else:
xtriage_plot += "%12sxaxis: {min:0},\n"%''
xtriage_plot += "%12syaxis: {min:0},\n%10s});\n\n"%('','')
"""
xtriage_plot += "%8sfunction showTooltip(x, y, contents) {\n"%''
xtriage_plot += "%10s$('<div id=\"tooltip\">' + contents + '</div>').css( {\n"%''
xtriage_plot += "%12sposition: 'absolute',\n%12sdisplay: 'none',\n"%('','')
xtriage_plot += "%12stop: y + 5,\n%12sleft: x + 5,\n%12sborder: '1px solid #fdd',\n"%(3*('',))
xtriage_plot += "%12spadding: '2px',\n%12s'background-color': '#fee',\n"%('','')
xtriage_plot += '%12sopacity: 0.80\n%10s}).appendTo("body").fadeIn(200);\n'%('','')
xtriage_plot += "%8s}\n%6s});\n%4s</script>\n%2s</body>\n</html>\n"%(4*('',))
"""
xtriage_plot += "%6s});\n%4s</script>\n%2s</body>\n</html>\n"%(3*('',))
if xtriage_plot:
if self.gui:
sp = 'plots_xtriage.php'
else:
sp = 'plots_xtriage.html'
xtriage_plot_file = open(sp,'w')
xtriage_plot_file.writelines(xtriage_plot)
xtriage_plot_file.close()
else:
Utils.failedHTML(self,'plots_xtriage')
except:
self.logger.exception('**ERROR in AutoStats.plotXtriage**')
Utils.failedHTML(self,'plots_xtriage')
def postprocess(self):
"""
Run summaries, make php/html files, send data back, and clean up.
"""
if self.verbose:
self.logger.debug('AutoStats::postprocess')
output = {}
status = {}
results = {}
failed = False
cell_results = False
cell_out = False
pp_results = False
pp_out = False
#Make the output html files
self.plotXtriage()
if self.xtriage_results:
Summary.summaryXtriage(self)
self.htmlSummaryXtriage()
if self.molrep_results:
Summary.summaryMolrep(self)
self.htmlSummaryMolrep()
if self.gui:
e = '.php'
else:
e = '.html'
l = [('jon_summary_xtriage%s'%e,'Xtriage summary html'),
('plots_xtriage%s'%e,'Xtriage plots html'),
('jon_summary_molrep%s'%e,'Molrep summary html')]
for i in range(len(l)):
try:
path = os.path.join(self.working_dir,l[i][0])
if os.path.exists(path):
output[l[i][1]] = path
else:
output[l[i][1]] = 'None'
except:
self.logger.exception('**Could not update paths of %s file.**'%l[i][0])
output[l[i][1]] = 'FAILED'
failed = True
#Get rapd_agent_cell results back
try:
cell_results = self.cell_output.get()
if cell_results.has_key('status'):
if cell_results['status'] == 'FAILED':
failed = True
del cell_results['status']
if cell_results.has_key('Output files'):
cell_out = cell_results['Output files']
del cell_results['Output files']
except:
self.logger.exception('**Error importing rapd_agent_cell results**')
#Get rapd_agent_pp results back
try:
if self.pp:
pp_results = self.pp_output.get()
if pp_results.has_key('status'):
if pp_results['status'] == 'FAILED':
failed = True
del pp_results['status']
if pp_results.has_key('Output files'):
pp_out = pp_results['Output files']
del pp_results['Output files']
else:
#Put together the dict from LabelitPP and create an html summary.
pp_results = {'LabelitPP results': {'HK0 jpg':None,'H0L jpg':None,'0KL jpg':None}}
Utils.failedHTML(self,('jon_summary_pp','Cannot create precession photos from merged datasets.'))
if os.path.exists(os.path.join(self.working_dir,'jon_summary_pp%s'%e)):
pp_out = {'LabelitPP summary html':os.path.join(self.working_dir,'jon_summary_pp%s'%e)}
else:
pp_out = {'LabelitPP summary html':'None'}
except:
self.logger.exception('**Error importing rapd_agent_cell results**')
#Get proper status.
if failed:
status['status'] = 'FAILED'
else:
status['status'] = 'SUCCESS'
#Put all the result dicts from all the programs run into one resultant dict and pass it along the pipe.
try:
results.update(status)
if self.xtriage_results:
results.update(self.xtriage_results)
if self.molrep_results:
results.update(self.molrep_results)
if cell_results:
results.update(cell_results)
if pp_results:
results.update(pp_results)
if output:
if cell_out:
output.update(cell_out)
if pp_out:
output.update(pp_out)
results.update(output)
self.input.insert(0,'STATS')
self.input.append(results)
if self.gui:
self.sendBack2(self.input)
except:
self.logger.exception('**Could not send results to pipe.**')
try:
#Cleanup my mess.
if self.clean:
if failed == False:
if self.verbose:
self.logger.debug('Cleaning up files')
os.system('rm -rf *.ps *.btc *.tab *.xml *.com molrep.doc molrep.log logfile.log xtriage.log phaser2.log PHASER.mtz')
except:
self.logger.exception('**Could not cleanup**')
#Say job is complete.
t = round(time.time()-self.st)
self.logger.debug('-------------------------------------')
self.logger.debug('RAPD AutoStat complete.')
self.logger.debug('Total elapsed time: %s seconds'%t)
self.logger.debug('-------------------------------------')
print '\n-------------------------------------'
print 'RAPD AutoStat complete.'
print 'Total elapsed time: %s seconds'%t
print '-------------------------------------'
def postprocess(self,final=True):
"""
Things to do after the main process runs
1. Return the data through the pipe
"""
if self.verbose:
self.logger.debug('AutoMolRep::postprocess')
#Run summary files for each program to print to screen
output = {}
results = {}
output_files = False
status = False
cell_results = False
failed = False
#Setup output file name
if self.phaser_results:
Summary.summaryCell(self,'phaser')
if self.input_pdb:
self.htmlSummaryPhaser()
else:
Utils.failedHTML(self,('jon_summary_cell','Input PDB file does not exist.'))
try:
if self.gui:
sl = 'jon_summary_cell.php'
else:
sl = 'jon_summary_cell.html'
if os.path.exists(os.path.join(self.working_dir,sl)):
output['Cell summary html'] = os.path.join(self.working_dir,sl)
else:
output['Cell summary html'] = 'None'
except:
self.logger.exception('**Could not update path of cell summary html file in AutoMolRep.postprocess.**')
output['Cell summary html'] = 'FAILED'
try:
#Only tar up files at end to see if they show up in the user dir.
#if final:
if self.input_pdb:
#pdb = os.path.basename(self.input_pdb)
for sg in self.phaser_results.keys():
dir1 = self.phaser_results[sg].get('AutoMR results').get('AutoMR dir')
l = ['pdb','mtz','adf','peak']
if dir1 not in ('No solution','Timed out','NA','DL Failed','Still running'):
#pack all the output files in a tar and save the path in results.
os.chdir(dir1)
#tar = '%s_%s.tar'%(pdb[:-4],sg)
tar = '%s_%s.tar'%(sg.split('_')[0],sg.split('_')[1])
if os.path.exists('%s.bz2'%tar) == False:
for p in l:
f = self.phaser_results[sg].get('AutoMR results').get('AutoMR %s'%p)
if os.path.exists(f):
os.system('tar -rf %s %s'%(tar,f))
if os.path.exists(tar):
os.system('bzip2 -qf %s'%tar)
#Remove old tar's in working dir, if they exist and copy new one over.
if os.path.exists(os.path.join(self.working_dir,'%s.bz2'%tar)):
os.system('rm -rf %s'%os.path.join(self.working_dir,'%s.bz2'%tar))
shutil.copy('%s.bz2'%tar,self.working_dir)
self.phaser_results[sg].get('AutoMR results').update({'AutoMR tar': os.path.join(self.working_dir,'%s.bz2'%tar)})
else:
self.phaser_results[sg].get('AutoMR results').update({'AutoMR tar': 'None'})
cell_results = { 'Cell analysis results': self.phaser_results }
except:
self.logger.exception('**Could not AutoMR results in AutoMolRep.postprocess.**')
cell_results = { 'Cell analysis results': 'FAILED'}
self.clean = False
failed = True
try:
output_files = {'Output files' : output}
except:
self.logger.exception('**Could not update the output dict in AutoMolRep.postprocess.**')
#Get proper status.
if final:
if failed:
status = {'status': 'FAILED'}
else:
status = {'status': 'SUCCESS'}
else:
status = {'status': 'WORKING'}
#Put all the result dicts from all the programs run into one resultant dict and pass it back.
try:
if self.gui == False:
if self.input[0] == "SAD":
self.input.remove("SAD")
self.input.insert(0,'MR')
if status:
results.update(status)
if cell_results:
results.update(cell_results)
#Utils.pp(self,cell_results)
if output_files:
results.update(output_files)
#Utils.pp(results)
if self.gui:
if results:
if len(self.input) == 6:
#Delete the previous Phaser results sent back.
del self.input[5]
self.input.append(results)
self.sendBack2(self.input)
except:
self.logger.exception('**Could not send results to pipe in AutoMolRep.postprocess.**')
if final:
try:
#Cleanup my mess.
if self.clean:
os.chdir(self.working_dir)
if self.verbose:
self.logger.debug('Cleaning up Phaser files and folders')
os.system('rm -rf Phaser_* *.com *.pdb *.mtz *.sum')
except:
self.logger.exception('**Could not cleanup in AutoMolRep.postprocess**')
#Say job is complete.
t = round(time.time()-self.st)
self.logger.debug(50*'-')
self.logger.debug('RAPD AutoMolRep complete.')
self.logger.debug('Total elapsed time: %s seconds'%t)
self.logger.debug(50*'-')
print 50*'-'
print 'RAPD AutoMolRep complete.'
print 'Total elapsed time: %s seconds'%t
print 50*'-'
