def rvapi_shutdown(self, amopt):
"""Return any results to jscofe
Parameters
----------
amopt : dict
AMPLE results dictionary with all information
"""
rvdoc = amopt['rvapi_document']
if not rvdoc: return
work_dir = amopt['work_dir']
# Create dictionary we're going to return
meta = {'first_tab_id': self.summary_tab_id, 'results': []}
nresults = 0
if 'mrbump_results' in amopt and amopt['mrbump_results']:
mrb_results = amopt['mrbump_results']
nresults = min(3, len(mrb_results))
if nresults > 0:
root = os.path.join(work_dir, "..")
for fdata in mrbump_util.ResultsSummary(
mrb_results[:nresults]).topFiles(nresults):
# Mangle paths
fdata['pdb'] = os.path.relpath(root, fdata['pdb'])
fdata['mtz'] = os.path.relpath(root, fdata['mtz'])
meta['results'].append(fdata)
# Commit to file
logger.debug("Exporting pyrvapi metadata:\n{0}".format(meta))
pyrvapi.rvapi_put_meta(json.dumps(meta))
pyrvapi.rvapi_store_document2(rvdoc)
return
def rvapi_shutdown(self, amopt):
"""Return any results to jscofe
Parameters
----------
amopt : dict
AMPLE results dictionary with all information
"""
rvdoc = amopt['rvapi_document']
if not rvdoc:
return
# Create dictionary we're going to return
meta = {'results': []}
nresults = 0
if bool(amopt.get('mrbump_results')):
mrb_results = amopt['mrbump_results']
nresults = min(3, len(mrb_results))
if nresults > 0:
for fdata in mrbump_util.ResultsSummary(
mrb_results[:nresults]).topFiles(nresults):
# Mangle paths. relpath assumes args are directories so need to add ..
fdata['pdb'] = self.fix_path(fdata['pdb'])
fdata['mtz'] = self.fix_path(fdata['mtz'])
meta['results'].append(fdata)
# Commit to file
logger.debug("Exporting pyrvapi metadata:\n{0}".format(meta))
pyrvapi.rvapi_put_meta(json.dumps(meta))
pyrvapi.rvapi_store_document2(rvdoc)
return
def create_results_tab(self, ample_dict):
if self.ccp4i2 or not self.summary_tab_id or not self._got_mrbump_results(
ample_dict):
return
mrb_results = ample_dict.get('mrbump_results')
if mrb_results == self.old_mrbump_results:
return
self.old_mrbump_results = mrb_results
if not self.results_tab_id:
self.results_tab_id = "results_tab"
pyrvapi.rvapi_insert_tab(self.results_tab_id, "Results",
self.summary_tab_id, False)
# Delete old sections:
pyrvapi.rvapi_flush()
for section_id in self.results_tab_sections:
pyrvapi.rvapi_remove_widget(section_id)
pyrvapi.rvapi_flush()
self.results_tab_sections = []
ensemble_results = ample_dict[
'ensembles_data'] if 'ensembles_data' in ample_dict[
'ensembles_data'] else None
mrbsum = mrbump_util.ResultsSummary(
results=mrb_results[0:min(len(mrb_results), mrbump_util.TOP_KEEP)])
mrbsum.sortResults(prioritise="SHELXE_CC")
self.results_section(
self.results_tab_id, mrbsum.results, ensemble_results,
"Top {0} SHELXE Results".format(mrbump_util.TOP_KEEP))
mrbsum.sortResults(prioritise="PHASER_TFZ")
# Add seperator between results - doesn't work as not deleted on refresh
# pyrvapi.rvapi_add_text("<br/><hr/><br/>", self.results_tab_id, 0, 0, 1, 1)
self.results_section(
self.results_tab_id, mrbsum.results, ensemble_results,
"Top {0} PHASER Results".format(mrbump_util.TOP_KEEP))
return self.results_tab_id
def create_summary_tab(self, ample_dict):
self._create_summary_tab()
if self.do_create_ensembles_section(ample_dict):
self.create_ensembles_section(ample_dict)
if not self._got_mrbump_results(ample_dict):
return self.summary_tab_id
if not self.summary_tab_results_sec_id:
self.rm_pending_section()
# Only create the table once
self.summary_tab_results_sec_id = "mrbump"
pyrvapi.rvapi_add_section(self.summary_tab_results_sec_id,
"MRBUMP", self.summary_tab_id, 0, 0, 1, 1, True)
self.summary_tab_results_sec_table_id = "mrbump_table"
pyrvapi.rvapi_add_table1(self.summary_tab_results_sec_id + "/" + self.summary_tab_results_sec_table_id,
"MRBUMP Results", 1, 0, 1, 1, True)
mrb_results = ample_dict.get('mrbump_results')
if not mrb_results == self.old_mrbump_results:
# We set old_mrbump_results when we create the results_tab
self.fill_table(self.summary_tab_results_sec_table_id,
mrbump_util.ResultsSummary().results_table(mrb_results),
tooltips=self._mrbump_tooltips)
if not self.summary_tab_survey_sec_id and not self.ccp4i2:
# Only create the table once
self.summary_tab_survey_sec_id = "survey"
pyrvapi.rvapi_add_section(self.summary_tab_survey_sec_id, "Feedback", self.summary_tab_id, 0, 0, 1, 1, True)
rstr = "<h2>How did we do?</h2><h3>Please follow this link and leave some feedback:</h3><a href='{0}' style='color: blue'>{0}</a>".format(reference_manager.survey_url)
pyrvapi.rvapi_add_text(rstr, self.summary_tab_survey_sec_id, 0, 0, 1, 1)
return self.summary_tab_id
def processOutputFiles(self):
'''
Associate the tasks output coordinate file with the output coordinate object XYZOUT:
'''
#debug_console()
# Split an MTZ file into minimtz data objects
'''
outputFilesToMake = ['FPHIOUT','DIFFPHIOUT']
columnsToTake = ['FWT,PHWT','DELFWT,PHDELWT']
infile = os.path.join(self.workDirectory,'final.mtz')
error = self.splitHklout(outputFilesToMake, columnsToTake, infile=infile)
import CCP4ErrorHandling
if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING:
return CPluginScript.FAILED
'''
#Create (dummy) PROGRAMXML, which basically contains only the log text of the job
#without this, a report will not be generated
# logfilePath = os.path.join(self.getWorkDirectory(),LOGFILE_NAME)
# with open(self.makeFileName("PROGRAMXML"),"w") as programXMLFile:
# xmlStructure = etree.Element(AMPLE_ROOT_NODE)
# logText = etree.SubElement(xmlStructure,AMPLE_LOG_NODE)
# with open(logfilePath,"r") as logFile:
# logText.text = etree.CDATA(logFile.read())
# programXMLFile.write(etree.tostring(xmlStructure))
# programXML file is generated by pyrvapi so we only handle the results specific for I2 here.
# results_summary.sortResults(mrb_results, prioritise="SHELXE_CC")[0:min(len(mrb_results),mrbump_util.TOP_KEEP)],
top_files = mrbump_util.ResultsSummary(results_pkl=os.path.join(
self.getWorkDirectory(), I2DIR, AMPLE_PKL)).topFiles()
if top_files:
for i, d in enumerate(top_files):
# Need to copy the files into the actual project directory - cannot be a sub-directory. Not entirely sure why but...
xyz = os.path.join(self.getWorkDirectory(),
os.path.basename(d['pdb']))
mtz = os.path.join(self.getWorkDirectory(),
os.path.basename(d['mtz']))
# REMOVE CHECK AS FILES SHOULD EXIST
if os.path.isfile(d['pdb']): shutil.copy2(d['pdb'], xyz)
if os.path.isfile(d['mtz']): shutil.copy2(d['mtz'], mtz)
self.container.outputData.XYZOUT.append(xyz)
self.container.outputData.XYZOUT[
-1].annotation = 'PDB file of {0} #{1}'.format(
d['source'], i + 1)
self.container.outputData.HKLOUT.append(mtz)
self.container.outputData.HKLOUT[
-1].annotation = 'MTZ file of {0} #{1}'.format(
d['source'], i + 1)
# logPath = os.path.join(self.getWorkDirectory(),LOGFILE_NAME)
# if os.path.isfile(logPath):
# with open(logPath, 'r') as logFile:
# element = etree.SubElement(self.xmlroot,AMPLE_LOG_NODE)
# element.text = etree.CDATA(logFile.read())
# self.flushXML()
return self.SUCCEEDED
def create_results_tab(self, ample_dict):
if self.ccp4i2 or not self.summary_tab_id: return
if not self._got_mrbump_results(ample_dict): return
mrb_results = ample_dict['mrbump_results']
if mrb_results == self.old_mrbump_results: return
self.old_mrbump_results = mrb_results
if not self.results_tab_id:
self.results_tab_id = "results_tab"
# Insert results tab before summary tab
pyrvapi.rvapi_insert_tab(
self.results_tab_id, "Results", self.summary_tab_id,
False) # Last arg is "open" - i.e. show or hide
# Delete old sections:
pyrvapi.rvapi_flush()
for section_id in self.results_tab_sections:
pyrvapi.rvapi_remove_widget(section_id)
pyrvapi.rvapi_flush()
self.results_tab_sections = []
ensemble_results = ample_dict[
'ensembles_data'] if 'ensembles_data' in ample_dict[
'ensembles_data'] else None
mrbsum = mrbump_util.ResultsSummary(
results=mrb_results[0:min(len(mrb_results), mrbump_util.TOP_KEEP)])
mrbsum.sortResults(prioritise="SHELXE_CC")
self.results_section(
self.results_tab_id, mrbsum.results, ensemble_results,
"Top {0} SHELXE Results".format(mrbump_util.TOP_KEEP))
mrbsum.sortResults(prioritise="PHASER_TFZ")
self.results_section(
self.results_tab_id, mrbsum.results, ensemble_results,
"Top {0} PHASER Results".format(mrbump_util.TOP_KEEP))
return self.results_tab_id
def monitor():
r = mrbump_util.ResultsSummary()
r.extractResults(optd['mrbump_dir'], purge=bool(optd['purge']))
optd['mrbump_results'] = r.results
return self.ample_output.display_results(optd)
def molecular_replacement(self, optd):
if not optd['mrbump_scripts']:
# MRBUMP analysis of the ensembles
logger.info('----- Running MRBUMP on ensembles--------\n\n')
if len(optd['ensembles']) < 1:
msg = "ERROR! Cannot run MRBUMP as there are no ensembles!"
exit_util.exit_error(msg)
if optd['mrbump_dir'] is None:
bump_dir = os.path.join(optd['work_dir'], 'MRBUMP')
optd['mrbump_dir'] = bump_dir
else:
bump_dir = optd['mrbump_dir']
if not os.path.exists(bump_dir):
os.mkdir(bump_dir)
optd['mrbump_results'] = []
logger.info("Running MRBUMP jobs in directory: %s", bump_dir)
# Set an ensemble-specific phaser_rms if required
if optd['phaser_rms'] == 'auto':
ensembler.set_phaser_rms_from_subcluster_score(optd)
# Sort the ensembles in a favourable way
logger.info("Sorting ensembles")
sort_keys = [
'cluster_num', 'truncation_level',
'subcluster_radius_threshold', 'side_chain_treatment'
]
ensemble_pdbs_sorted = ensembler.sort_ensembles(
optd['ensembles'],
optd['ensembles_data'],
keys=sort_keys,
prioritise=True)
# Create job scripts
logger.info("Generating MRBUMP runscripts")
optd['mrbump_scripts'] = mrbump_util.write_mrbump_files(
ensemble_pdbs_sorted,
optd,
job_time=mrbump_util.MRBUMP_RUNTIME,
ensemble_options=optd['ensemble_options'],
directory=bump_dir)
# Create function for monitoring jobs - static function decorator?
if self.ample_output:
def monitor():
r = mrbump_util.ResultsSummary()
r.extractResults(optd['mrbump_dir'], purge=bool(optd['purge']))
optd['mrbump_results'] = r.results
return self.ample_output.display_results(optd)
else:
monitor = None
# Save results here so that we have the list of scripts and mrbump directory set
ample_util.save_amoptd(optd)
# Change to mrbump directory before running
os.chdir(optd['mrbump_dir'])
ok = workers_util.run_scripts(
job_scripts=optd['mrbump_scripts'],
monitor=monitor,
check_success=mrbump_util.checkSuccess,
early_terminate=optd['early_terminate'],
nproc=optd['nproc'],
job_time=mrbump_util.MRBUMP_RUNTIME,
job_name='mrbump',
submit_cluster=optd['submit_cluster'],
submit_qtype=optd['submit_qtype'],
submit_queue=optd['submit_queue'],
submit_pe_lsf=optd['submit_pe_lsf'],
submit_pe_sge=optd['submit_pe_sge'],
submit_array=optd['submit_array'],
submit_max_array=optd['submit_max_array'])
if not ok:
msg = "An error code was returned after running MRBUMP on the ensembles!\n" + \
"For further information check the logs in directory: {0}".format(optd['mrbump_dir'])
logger.critical(msg)
# Collect the MRBUMP results
results_summary = mrbump_util.ResultsSummary()
optd['mrbump_results'] = results_summary.extractResults(
optd['mrbump_dir'], purge=bool(optd['purge']))
optd['success'] = results_summary.success
ample_util.save_amoptd(optd)
summary = mrbump_util.finalSummary(optd)
logger.info(summary)
def test_topfiles(self):
topf = mrbump_util.ResultsSummary(results_pkl=os.path.join(
self.testfiles_dir, AMPLE_PKL)).topFiles()
self.assertEqual(len(topf), 3)
self.assertIn('info', topf[2])
def results_section(self, results_tab_id, mrb_results, ensemble_results,
section_title):
#
# Results Tab
#
if not mrb_results: return
# Create unique identifier for this section by using the id
# All ids will have this appended to avoid clashes
uid = str(uuid.uuid4())
section_id = section_title.replace(" ", "_") + uid
self.results_tab_sections.append(
section_id) # Add to list so we can remove if we update
pyrvapi.rvapi_add_panel(section_id, results_tab_id, 0, 0, 1, 1)
pyrvapi.rvapi_add_text("<h3>{0}</h3>".format(section_title),
section_id, 0, 0, 1, 1)
results_tree = "results_tree" + section_id
pyrvapi.rvapi_add_tree_widget(results_tree, section_title, section_id,
0, 0, 1, 1)
for r in mrb_results:
name = r['ensemble_name']
# container_id="sec_{0}".format(name)
# pyrvapi.rvapi_add_section(container_id,"Results for: {0}".format(name),results_tree,0,0,1,1,True)
container_id = "sec_{0}".format(name) + uid
pyrvapi.rvapi_add_panel(container_id, results_tree, 0, 0, 1, 1)
header = "<h3>Results for ensemble: {0}</h3>".format(name)
pyrvapi.rvapi_add_text(header, container_id, 0, 0, 1, 1)
sec_table = "sec_table_{0}".format(name) + uid
title = "Results table: {0}".format(name)
title = "Summary"
pyrvapi.rvapi_add_section(sec_table, title, container_id, 0, 0, 1,
1, True)
table_id = "table_{0}".format(name) + uid
pyrvapi.rvapi_add_table(table_id, "", sec_table, 1, 0, 1, 1, False)
tdata = mrbump_util.ResultsSummary().results_table([r])
self.fill_table(table_id, tdata, tooltips=self._mrbump_tooltips)
# Ensemble
if ensemble_results:
epdb = self.ensemble_pdb(r, ensemble_results)
if epdb:
sec_ensemble = "sec_ensemble_{0}".format(name) + uid
pyrvapi.rvapi_add_section(sec_ensemble,
"Ensemble Search Model",
container_id, 0, 0, 1, 1, False)
data_ensemble = "data_ensemble_{0}".format(name) + uid
pyrvapi.rvapi_add_data(data_ensemble, "Ensemble PDB",
self.fix_path(epdb), "XYZOUT",
sec_ensemble, 2, 0, 1, 1, True)
# PHASER
if os.path.isfile(str(r['PHASER_logfile'])) or (
os.path.isfile(str(r['PHASER_pdbout']))
and os.path.isfile(str(r['PHASER_mtzout']))):
sec_phaser = "sec_phaser_{0}".format(name) + uid
pyrvapi.rvapi_add_section(sec_phaser, "PHASER Outputs",
container_id, 0, 0, 1, 1, False)
if os.path.isfile(str(r['PHASER_pdbout'])) and os.path.isfile(
str(r['PHASER_mtzout'])):
data_phaser = "data_phaser_out_{0}".format(name) + uid
pyrvapi.rvapi_add_data(
data_phaser, "PHASER PDB",
os.path.splitext(self.fix_path(r['PHASER_pdbout']))[0],
"xyz:map", sec_phaser, 2, 0, 1, 1, True)
pyrvapi.rvapi_append_to_data(
data_phaser, self.fix_path(r['PHASER_mtzout']),
"xyz:map")
if os.path.isfile(str(r['PHASER_logfile'])):
pyrvapi.rvapi_add_data(
"data_phaser_logfile_{0}".format(name),
"PHASER Logfile", self.fix_path(r['PHASER_logfile']),
"text", sec_phaser, 2, 0, 1, 1, True)
# REFMAC
if os.path.isfile(str(r['REFMAC_logfile'])) or (
os.path.isfile(str(r['REFMAC_pdbout']))
and os.path.isfile(str(r['REFMAC_mtzout']))):
sec_refmac = "sec_refmac_{0}".format(name) + uid
pyrvapi.rvapi_add_section(sec_refmac, "REFMAC Outputs",
container_id, 0, 0, 1, 1, False)
if os.path.isfile(str(r['REFMAC_pdbout'])) and os.path.isfile(
str(r['REFMAC_mtzout'])):
data_refmac = "data_refmac_out_{0}".format(name) + uid
pyrvapi.rvapi_add_data(
data_refmac, "REFMAC PDB",
os.path.splitext(self.fix_path(r['REFMAC_pdbout']))[0],
"xyz:map", sec_refmac, 2, 0, 1, 1, True)
pyrvapi.rvapi_append_to_data(
data_refmac, self.fix_path(r['REFMAC_mtzout']),
"xyz:map")
if os.path.isfile(str(r['REFMAC_logfile'])):
pyrvapi.rvapi_add_data(
"data_refmac_logfile_{0}".format(name),
"REFMAC Logfile", self.fix_path(r['REFMAC_logfile']),
"text", sec_refmac, 2, 0, 1, 1, True)
# Buccaner
if os.path.isfile(str(r['BUCC_logfile'])) or (
os.path.isfile(str(r['BUCC_pdbout']))
and os.path.isfile(str(r['BUCC_mtzout']))):
sec_bucc = "sec_bucc_{0}".format(name) + uid
pyrvapi.rvapi_add_section(sec_bucc, "BUCCANEER Outputs",
container_id, 0, 0, 1, 1, False)
if os.path.isfile(str(r['BUCC_pdbout'])) and os.path.isfile(
str(r['BUCC_mtzout'])):
data_bucc = "data_bucc_out_{0}".format(name) + uid
pyrvapi.rvapi_add_data(
data_bucc, "BUCC PDB",
os.path.splitext(self.fix_path(r['BUCC_pdbout']))[0],
"xyz:map", sec_bucc, 2, 0, 1, 1, True)
pyrvapi.rvapi_append_to_data(
data_bucc, self.fix_path(r['BUCC_mtzout']), "xyz:map")
if os.path.isfile(str(r['BUCC_logfile'])):
pyrvapi.rvapi_add_data(
"data_bucc_logfile_{0}".format(name), "BUCC Logfile",
self.fix_path(r['BUCC_logfile']), "text", sec_bucc, 2,
0, 1, 1, True)
# Arpwarp
if os.path.isfile(str(r['ARP_logfile'])) or (
os.path.isfile(str(r['ARP_pdbout']))
and os.path.isfile(str(r['ARP_mtzout']))):
sec_arp = "sec_arp_{0}".format(name) + uid
pyrvapi.rvapi_add_section(sec_arp, "ARPWARP Outputs",
container_id, 0, 0, 1, 1, False)
if os.path.isfile(str(r['ARP_pdbout'])) and os.path.isfile(
str(r['ARP_mtzout'])):
data_arp = "data_arp_out_{0}".format(name) + uid
pyrvapi.rvapi_add_data(
data_arp, "ARP PDB",
os.path.splitext(self.fix_path(r['ARP_pdbout']))[0],
"xyz:map", sec_arp, 2, 0, 1, 1, True)
pyrvapi.rvapi_append_to_data(
data_arp, self.fix_path(r['ARP_mtzout']), "xyz:map")
if os.path.isfile(str(r['ARP_logfile'])):
pyrvapi.rvapi_add_data("data_arp_logfile_{0}".format(name),
"ARP Logfile",
self.fix_path(r['ARP_logfile']),
"text", sec_arp, 2, 0, 1, 1, True)
# SHELXE
if os.path.isfile(str(r['SHELXE_logfile'])) or (
os.path.isfile(str(r['SHELXE_pdbout']))
and os.path.isfile(str(r['SHELXE_mtzout']))):
sec_shelxe = "sec_shelxe_{0}".format(name) + uid
pyrvapi.rvapi_add_section(sec_shelxe, "SHELXE Outputs",
container_id, 0, 0, 1, 1, False)
if os.path.isfile(str(r['SHELXE_pdbout'])) and os.path.isfile(
str(r['SHELXE_mtzout'])):
data_shelxe = "data_shelxe_out_{0}".format(name) + uid
pyrvapi.rvapi_add_data(
data_shelxe, "SHELXE PDB",
os.path.splitext(self.fix_path(r['SHELXE_pdbout']))[0],
"xyz:map", sec_shelxe, 2, 0, 1, 1, True)
pyrvapi.rvapi_append_to_data(
data_shelxe, self.fix_path(r['SHELXE_mtzout']),
"xyz:map")
if os.path.isfile(str(r['SHELXE_logfile'])):
pyrvapi.rvapi_add_data(
"data_shelxe_logfile_{0}".format(name),
"SHELXE Logfile", self.fix_path(r['SHELXE_logfile']),
"text", sec_shelxe, 2, 0, 1, 1, True)
# Buccaner Rebuild
if os.path.isfile(str(r['SXRBUCC_logfile'])) or (
os.path.isfile(str(r['SXRBUCC_pdbout']))
and os.path.isfile(str(r['SXRBUCC_mtzout']))):
sec_sxrbucc = "sec_sxrbucc_{0}".format(name) + uid
pyrvapi.rvapi_add_section(
sec_sxrbucc, "BUCCANEER SHELXE Trace Rebuild Outputs",
container_id, 0, 0, 1, 1, False)
if os.path.isfile(str(r['SXRBUCC_pdbout'])) and os.path.isfile(
str(r['SXRBUCC_mtzout'])):
data_sxrbucc = "data_sxrbucc_out_{0}".format(name) + uid
pyrvapi.rvapi_add_data(
data_sxrbucc, "SXRBUCC PDB",
os.path.splitext(self.fix_path(
r['SXRBUCC_pdbout']))[0], "xyz:map", sec_sxrbucc,
2, 0, 1, 1, True)
pyrvapi.rvapi_append_to_data(
data_sxrbucc, self.fix_path(r['SXRBUCC_mtzout']),
"xyz:map")
if os.path.isfile(str(r['SXRBUCC_logfile'])):
pyrvapi.rvapi_add_data(
"data_sxrbucc_logfile_{0}".format(name),
"SXRBUCC Logfile", self.fix_path(r['SXRBUCC_logfile']),
"text", sec_sxrbucc, 2, 0, 1, 1, True)
# Arpwarp Rebuild
if os.path.isfile(str(r['SXRARP_logfile'])) or (
os.path.isfile(str(r['SXRARP_pdbout']))
and os.path.isfile(str(r['SXRARP_mtzout']))):
sec_sxrarp = "sec_sxrarp_{0}".format(name) + uid
pyrvapi.rvapi_add_section(
sec_sxrarp, "ARPWARP SHELXE Trace Redbuild Outputs",
container_id, 0, 0, 1, 1, False)
if os.path.isfile(str(r['SXRARP_pdbout'])) and os.path.isfile(
str(r['SXRARP_mtzout'])):
data_sxrarp = "data_sxrarp_out_{0}".format(name) + uid
pyrvapi.rvapi_add_data(
data_sxrarp, "SXRARP PDB",
os.path.splitext(self.fix_path(r['SXRARP_pdbout']))[0],
"xyz:map", sec_sxrarp, 2, 0, 1, 1, True)
pyrvapi.rvapi_append_to_data(
data_sxrarp, self.fix_path(r['SXRARP_mtzout']),
"xyz:map")
if os.path.isfile(str(r['SXRARP_logfile'])):
pyrvapi.rvapi_add_data(
"data_sxrarp_logfile_{0}".format(name),
"SXRARP Logfile", self.fix_path(r['SXRARP_logfile']),
"text", sec_sxrarp, 2, 0, 1, 1, True)
pyrvapi.rvapi_set_tree_node(results_tree, container_id,
"{0}".format(name), "auto", "")
return
def create_summary_tab(self, ample_dict):
#
# Summary Tab
#
self._create_summary_tab()
if not (ample_dict['single_model_mode'] or ample_dict['homologs'] or ample_dict['ideal_helices']) and \
bool(ample_dict['ensembles_data']) and not self.summary_tab_ensemble_sec_id:
self.rm_pending_section()
ensembles_data = ample_dict['ensembles_data']
self.summary_tab_ensemble_sec_id = "ensembles"
pyrvapi.rvapi_add_section(self.summary_tab_ensemble_sec_id,
"Ensembles", self.summary_tab_id, 0, 0,
1, 1, True)
# Get the ensembling data
d = ensembler.collate_cluster_data(ensembles_data)
clusters = d['clusters']
rstr = ""
rstr += "Ensemble Results<br/>"
rstr += "----------------<br/><br/>"
rstr += "Cluster method: {0}<br/>".format(d['cluster_method'])
rstr += "Cluster score type: {0}<br/>".format(
d['cluster_score_type'])
rstr += "Truncation method: {0}<br/>".format(
d['truncation_method'])
rstr += "Percent truncation: {0}<br/>".format(
d['percent_truncation'])
rstr += "Side-chain treatments: {0}<br/>".format(
d['side_chain_treatments'])
rstr += "Number of clusters: {0}<br/><br/>".format(
len(clusters.keys()))
rstr += "Generated {0} ensembles<br/><br/>".format(
len(ensembles_data))
pyrvapi.rvapi_add_text(rstr, self.summary_tab_ensemble_sec_id, 0,
0, 1, 1)
ensemble_table = "ensemble_table"
pyrvapi.rvapi_add_table1(
self.summary_tab_ensemble_sec_id + "/" + ensemble_table,
"Ensembling Results", 1, 0, 1, 1, True)
# for cluster_num in sorted(clusters.keys()):
# rstr += "\n"
# rstr += "Cluster {0}\n".format(cluster_num)
# rstr += "Number of models: {0}\n".format(clusters[cluster_num]['cluster_num_models'])
# rstr += "Cluster centroid: {0}\n".format(clusters[cluster_num]['cluster_centroid'])
# rstr += "\n"
# tdata = cluster_table_data(clusters, cluster_num)
# rstr += tableFormat.pprint_table(tdata)
#
cluster_num = 1
tdata = ensembler.cluster_table_data(clusters, cluster_num,
d['side_chain_treatments'])
self.fill_table(ensemble_table,
tdata,
tooltips=self._ensemble_tooltips)
#
# MRBUMP Results
#
if not self._got_mrbump_results(ample_dict): return self.summary_tab_id
if not self.summary_tab_results_sec_id:
self.rm_pending_section()
# Only create the table once
self.summary_tab_results_sec_id = "mrbump"
pyrvapi.rvapi_add_section(self.summary_tab_results_sec_id,
"MRBUMP", self.summary_tab_id, 0, 0, 1,
1, True)
self.summary_tab_results_sec_table_id = "mrbump_table"
pyrvapi.rvapi_add_table1(
self.summary_tab_results_sec_id + "/" +
self.summary_tab_results_sec_table_id, "MRBUMP Results", 1, 0,
1, 1, True)
mrb_results = ample_dict['mrbump_results']
if not mrb_results == self.old_mrbump_results:
# We set old_mrbump_results when we create the results_tab
self.fill_table(
self.summary_tab_results_sec_table_id,
mrbump_util.ResultsSummary().results_table(mrb_results),
tooltips=self._mrbump_tooltips)
#
# Survey section
#
if not self.summary_tab_survey_sec_id and not self.ccp4i2:
# Only create the table once
self.summary_tab_survey_sec_id = "survey"
pyrvapi.rvapi_add_section(self.summary_tab_survey_sec_id,
"Feedback", self.summary_tab_id, 0, 0, 1,
1, True)
rstr = "<h2>How did we do?</h2><h3>Please follow this link and leave some feedback:</h3><a href='{0}' style='color: blue'>{0}</a>".format(
ample_util.survey_url)
pyrvapi.rvapi_add_text(rstr, self.summary_tab_survey_sec_id, 0, 0,
1, 1)
return self.summary_tab_id
def results_section(self, results_tab_id, mrb_results, ensemble_results,
section_title):
"""Results Tab"""
if not mrb_results:
return
# Create unique identifier for this section by using the id
# All ids will have this appended to avoid clashes
uid = str(uuid.uuid4())
section_id = section_title.replace(" ", "_") + uid
self.results_tab_sections.append(
section_id) # Add to list so we can remove if we update
pyrvapi.rvapi_add_panel(section_id, results_tab_id, 0, 0, 1, 1)
pyrvapi.rvapi_add_text("<h3>{0}</h3>".format(section_title),
section_id, 0, 0, 1, 1)
results_tree = "results_tree" + section_id
pyrvapi.rvapi_add_tree_widget(results_tree, section_title, section_id,
0, 0, 1, 1)
for r in mrb_results:
ensemble_name = r['ensemble_name']
container_id = "sec_{0}".format(ensemble_name) + uid
pyrvapi.rvapi_add_panel(container_id, results_tree, 0, 0, 1, 1)
header = "<h3>Results for ensemble: {0}</h3>".format(ensemble_name)
pyrvapi.rvapi_add_text(header, container_id, 0, 0, 1, 1)
sec_table = "sec_table_{0}".format(ensemble_name) + uid
title = "Results table: {0}".format(ensemble_name)
title = "Summary"
pyrvapi.rvapi_add_section(sec_table, title, container_id, 0, 0, 1,
1, True)
table_id = "table_{0}".format(ensemble_name) + uid
pyrvapi.rvapi_add_table(table_id, "", sec_table, 1, 0, 1, 1, False)
tdata = mrbump_util.ResultsSummary().results_table([r])
self.fill_table(table_id, tdata, tooltips=self._mrbump_tooltips)
# Ensemble
if ensemble_results:
epdb = self.ensemble_pdb(r, ensemble_results)
if epdb:
sec_ensemble = "sec_ensemble_{0}".format(
ensemble_name) + uid
pyrvapi.rvapi_add_section(sec_ensemble,
"Ensemble Search Model",
container_id, 0, 0, 1, 1, False)
data_ensemble = "data_ensemble_{0}".format(
ensemble_name) + uid
pyrvapi.rvapi_add_data(data_ensemble, "Ensemble PDB",
self.fix_path(epdb), "XYZOUT",
sec_ensemble, 2, 0, 1, 1, True)
# PHASER
self.add_results_section(
result_dict=r,
ensemble_name=ensemble_name,
program_name='PHASER',
logfile_key='PHASER_logfile',
pdb_key='PHASER_pdbout',
mtz_key='PHASER_mtzout',
uid=uid,
container_id=container_id,
)
# REFMAC
self.add_results_section(
result_dict=r,
ensemble_name=ensemble_name,
program_name='Refmac',
logfile_key='REFMAC_logfile',
pdb_key='REFMAC_pdbout',
mtz_key='REFMAC_mtzout',
uid=uid,
container_id=container_id,
)
# Buccaner
self.add_results_section(
result_dict=r,
ensemble_name=ensemble_name,
program_name='BUCCANEER',
logfile_key='BUCC_logfile',
pdb_key='BUCC_pdbout',
mtz_key='BUCC_mtzout',
uid=uid,
container_id=container_id,
)
# Arpwarp
self.add_results_section(
result_dict=r,
ensemble_name=ensemble_name,
program_name='ArpWarp',
logfile_key='ARP_logfile',
pdb_key='ARP_pdbout',
mtz_key='ARP_mtzout',
uid=uid,
container_id=container_id,
)
# SHELXE
self.add_results_section(
result_dict=r,
ensemble_name=ensemble_name,
program_name='SHELXE',
logfile_key='SHELXE_logfile',
pdb_key='SHELXE_pdbout',
mtz_key='SHELXE_mtzout',
uid=uid,
container_id=container_id,
)
# Buccaner Rebuild
self.add_results_section(
result_dict=r,
ensemble_name=ensemble_name,
program_name='BUCCANEER SHELXE Trace Rebuild',
logfile_key='SXRBUCC_logfile',
pdb_key='SXRBUCC_pdbout',
mtz_key='SXRBUCC_mtzout',
uid=uid,
container_id=container_id,
)
# Arpwarp Rebuild
self.add_results_section(
result_dict=r,
ensemble_name=ensemble_name,
program_name='ARPWARP SHELXE Trace Rebuild',
logfile_key='SXRARP_logfile',
pdb_key='SXRARP_pdbout',
mtz_key='SXRARP_mtzout',
uid=uid,
container_id=container_id,
)
pyrvapi.rvapi_set_tree_node(results_tree, container_id,
"{0}".format(ensemble_name), "auto",
"")
return
def test_topfiles(self):
topf = mrbump_util.ResultsSummary(results_pkl=os.path.join(
self.testfiles_dir, AMPLE_PKL)).topFiles()
self.assertEqual(len(topf), 3)
self.assertEqual(topf[2]['info'], 'SHELXE trace of MR result')
