def html_summary_xtriage(self):
"""
Create HTML/php files for xtriage output results.
"""
if self.verbose:
self.logger.debug("AutoStats::html_summary_xtriage")
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.html_summary_xtriage**")
def html_summary_molrep(self):
"""
Create HTML/php files for Molrep output results.
"""
if self.verbose:
self.logger.debug("AutoStats::html_summary_molrep")
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.html_summary_molrep**")
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.preprocess_labelit()
self.process_labelit()
#Sorts labelit results by highest symmetry.
self.labelit_sort()
if self.labelit_failed == False:
#Run labelit_precession_photo for the 3 planes
self.process_labelit_precession()
self.run_queue()
else:
Utils.failedHTML(self, "jon_summary_pp")
# Finish everything up
self.postprocess()
def plot_xtriage(self):
"""
generate plots html/php file
"""
if self.verbose:
self.logger.debug("AutoStats::plot_xtriage")
try:
anom = self.xtriage_results.get("Xtriage results").get("Xtriage anom plot")
intensity = self.xtriage_results.get("Xtriage results").get("Xtriage int 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")
if self.ncs_results:
cid0 = self.ncs_results.get("PhaserNCS results").get("CID").get("before", False)
cid1 = self.ncs_results.get("PhaserNCS results").get("CID").get("after", False)
#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")]
]
e = len(l) - 2
if self.ncs_results:
#If job is killed early, it will only have the before CID.
if cid0:
e += 1
if cid1:
e += 1
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 = $.plot($("
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 += "%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.plot_xtriage**")
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.plot_xtriage()
if self.xtriage_results:
Summary.summaryXtriage(self)
self.html_summary_xtriage()
if self.molrep_results:
Summary.summaryMolrep(self)
self.html_summary_molrep()
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.command_input.insert(0, "STATS")
self.command_input.append(results)
if self.gui:
rapd_send(self.controller_address, self.command_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)
rapd_send(self.controller_address, 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*'-'
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)
rapd_send(self.controller_address, 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 * '-'
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', False)
cid1 = self.NCS_results.get('PhaserNCS results').get(
'CID').get('after', False)
#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')
]
]
e = len(l) - 2
if self.NCS_results:
#If job is killed early, it will only have the before CID.
if cid0:
e += 1
if cid1:
e += 1
"""
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:
rapd_send(self.controller_address, 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 htmlSummaryXOalign(self):
"""
Create the html/php results file for XOalign.
"""
if self.verbose:
self.logger.debug('RunStac::htmlSummaryXOalign')
try:
if self.xoalign_failed == False:
if self.gui:
jon_summary = open('jon_summary_xoalign.php','w')
else:
jon_summary = open('jon_summary_xoalign.html','w')
jon_summary.write(Utils.getHTMLHeader(self,'strat'))
jon_summary.write("%6s$(document).ready(function() {\n%8s$('#accordion2').accordion({\n"%('',''))
jon_summary.write('%11scollapsible: true,\n%11sactive: false });\n'%('',''))
if self.auto1_summary:
jon_summary.write("%8s$('#xoalign-auto').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bAutoWidth": false });\n'%(4*('',)))
if self.xoalign_summary:
jon_summary.write("%8sXOalignTable = $('#xoalign').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bAutoWidth": false });\n'%(4*('',)))
jon_summary.write('%8s//Tooltips\n'%'')
jon_summary.write("%8s$('#xoalign thead th').each(function(){\n"%'')
jon_summary.write("%11sif ($(this).text() == 'V1') {\n"%'')
jon_summary.write("%16sthis.setAttribute('title','The crystal vector to be aligned parallel to the spindle axis');\n%11s}\n"%('',''))
jon_summary.write("%11selse if ($(this).text() == 'V2') {\n"%'')
jon_summary.write("%16sthis.setAttribute('title','The crystal vector describing the plane including the spindle and beam axes');\n%11s}\n%8s});\n"%(3*('',)))
jon_summary.write("%8s// Handler for click events on the XOalign table\n"%'')
jon_summary.write('%8s$("#xoalign tbody tr").click(function(event) {\n'%'')
jon_summary.write("%11s//take highlight from other rows\n"%'')
jon_summary.write("%11s$(XOalignTable.fnSettings().aoData).each(function (){\n"%'')
jon_summary.write("%14s$(this.nTr).removeClass('row_selected');\n%11s});\n"%('',''))
jon_summary.write("%11s//highlight the clicked row\n"%'')
jon_summary.write("%11s$(event.target.parentNode).addClass('row_selected');\n%8s});\n"%('',''))
jon_summary.write('%8s$("#xoalign tbody tr").dblclick(function(event) {\n'%'')
jon_summary.write("%11s//Get the current data of the clicked-upon row\n"%'')
jon_summary.write("%11saData = XOalignTable.fnGetData(this);\n"%'')
jon_summary.write("%11s//Use the values from the line to fill the form\n"%'')
jon_summary.write('%11svar omega = aData[3];\n%11svar kappa = aData[4];\n%11svar phi = aData[5];\n'%(3*('',)))
jon_summary.write('%11s$.ajax({\n%16stype: "POST",\n%16surl: "d_add_minikappa.php",\n'%(3*('',)))
jon_summary.write('%16sdata: { omega:omega,\n%23skappa:kappa,\n%23sphi:phi,\n'%(3*('',)))
jon_summary.write('%23sip_address:my_ip,\n%23sbeamline:my_beamline }\n%11s});\n'%(3*('',)))
jon_summary.write("%11s//Popup the success dialog\n"%'')
jon_summary.write('%11sPopupSuccessDialog("Minikappa settings sent to beamline");\n%8s});\n'%('',''))
jon_summary.write('%6s});\n%4s</script>\n\n%2s</head>\n'%(3*('',)))
jon_summary.write('%2s<body id="dt_example">\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">Cell and SG summary for:</h1>\n'%'')
jon_summary.write("%7s<h2 class='results'>Image: %s</h2>\n"%('',self.header.get('fullname')))
if self.header2:
jon_summary.write("%7s<h2 class='results'>Image: %s</h2>\n"%('',self.header2.get('fullname')))
if self.auto1_summary:
jon_summary.writelines(self.auto1_summary)
jon_summary.write('%4s<div id="container">\n%5s<div class="full_width big">\n%6s<div id="demo">\n'%(3*('',)))
if self.xoalign_summary:
jon_summary.writelines(self.xoalign_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'>XOalign Logfile</h1>\n"%'')
jon_summary.write('%6s</div>\n%5s</div>\n%5s<div id="accordion2">\n'%(3*('',)))
jon_summary.write('%6s<h3><a href="#">Click to view log</a></h3>\n%6s<div>\n%7s<pre>\n'%(3*('',)))
jon_summary.write('\n---------------XOALIGN RESULTS---------------\n\n')
if self.xoalign_log:
for line in self.xoalign_log:
jon_summary.write(line)
else:
jon_summary.write('---------------XOALIGN 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_stac','You MUST select a successful solution and NOT another XOalign alignment'))
except:
self.logger.exception('**Error in stac.htmlSummaryXOalign**')
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',False)
cid1 = self.NCS_results.get('PhaserNCS results').get('CID').get('after',False)
#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')]
]
e = len(l) - 2
if self.NCS_results:
#If job is killed early, it will only have the before CID.
if cid0:
e += 1
if cid1:
e += 1
"""
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:
rapd_send(self.controller_address, 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 '-------------------------------------'
