def rm_pending_section(self):
if self.summary_tab_pending_sec_id:
pyrvapi.rvapi_flush()
pyrvapi.rvapi_remove_widget(self.summary_tab_pending_sec_id)
pyrvapi.rvapi_flush()
self.summary_tab_pending_sec_id = None
return
def display_results(self, summarize, results_to_display):
if self.display_gui or self.ccp4i2:
if not self.lattice_search_results_displayed:
lattice_results = os.path.join(self.work_dir, 'latt', 'lattice_search.csv')
lattice_mr_results = os.path.join(self.work_dir, 'latt', 'lattice_mr.csv')
if os.path.isfile(lattice_results) or os.path.isfile(lattice_mr_results):
self.create_lattice_results_tab(lattice_results, lattice_mr_results, results_to_display)
self.lattice_search_results_displayed = True
if not self.contaminant_results_displayed:
contaminant_results = os.path.join(self.work_dir, 'cont', 'rot_search.csv')
contaminant_mr_results = os.path.join(self.work_dir, 'cont', 'cont_mr.csv')
if os.path.isfile(contaminant_results) or os.path.isfile(contaminant_mr_results):
self.create_contaminant_results_tab(contaminant_results, contaminant_mr_results, results_to_display)
self.contaminant_results_displayed = True
if not self.morda_results_displayed:
morda_db_results = os.path.join(self.work_dir, 'morda', 'rot_search.csv')
morda_db_mr_results = os.path.join(self.work_dir, 'morda', 'morda_mr.csv')
if os.path.isfile(morda_db_results) or os.path.isfile(morda_db_mr_results):
self.create_morda_db_results_tab(morda_db_results, morda_db_mr_results, results_to_display)
self.morda_results_displayed = True
if summarize:
self.display_summary_tab()
pyrvapi.rvapi_flush()
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 rm_pending_section(self):
if self.summary_tab_pending_sec_id:
pyrvapi.rvapi_flush()
pyrvapi.rvapi_remove_widget(self.summary_tab_pending_sec_id)
pyrvapi.rvapi_flush()
self.summary_tab_pending_sec_id = None
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")
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 display_results(self, summarize, results_to_display):
if self.display_gui or self.ccp4i2:
if not self.lattice_search_results_displayed:
lattice_results = os.path.join(self.work_dir, 'latt', 'lattice_search.csv')
lattice_mr_results = os.path.join(self.work_dir, 'latt', 'lattice_mr.csv')
if os.path.isfile(lattice_results) or os.path.isfile(lattice_mr_results):
self.create_lattice_results_tab(lattice_results, lattice_mr_results, results_to_display)
self.lattice_search_results_displayed = True
if not self.contaminant_results_displayed:
contaminant_results = os.path.join(self.work_dir, 'cont', 'rot_search.csv')
contaminant_mr_results = os.path.join(self.work_dir, 'cont', 'cont_mr.csv')
if os.path.isfile(contaminant_results) or os.path.isfile(contaminant_mr_results):
self.create_contaminant_results_tab(contaminant_results, contaminant_mr_results, results_to_display)
self.contaminant_results_displayed = True
if not self.morda_results_displayed:
morda_db_results = os.path.join(self.work_dir, 'morda', 'rot_search.csv')
morda_db_mr_results = os.path.join(self.work_dir, 'morda', 'morda_mr.csv')
if os.path.isfile(morda_db_results) or os.path.isfile(morda_db_mr_results):
self.create_morda_db_results_tab(morda_db_results, morda_db_mr_results, results_to_display)
self.morda_results_displayed = True
if summarize:
self.display_summary_tab()
self.display_citation_tab()
pyrvapi.rvapi_flush()
def exit_error(msg, ample_tb=None):
"""Exit on error collecting as much information as we can.
args:
ample_tb - this can be got from sys.exc_info()[2]
"""
# Get the root logger
logger = logging.getLogger()
# An error may have occured before we started logging so we need to create one here
if not logger.handlers:
logging.basicConfig(format='%(message)s\n', level=logging.DEBUG)
logger = logging.getLogger()
#header="**** AMPLE ERROR ****\n\n"
header = "*" * 70 + "\n"
header += "*" * 20 + " " * 10 + "AMPLE ERROR" + " " * 10 + "*" * 19 + "\n"
header += "*" * 70 + "\n\n"
# Create the Footer
footer = "\n\n" + "*" * 70 + "\n\n"
# Get the name of the debug log file
debug_log = _debug_logfile(logger)
if debug_log:
footer += "More information may be found in the debug log file: {0}\n".format(
debug_log)
footer += "\nIf you believe that this is an error with AMPLE, please email: [email protected]\n"
footer += "providing as much information as you can about how you ran the program.\n"
if debug_log:
footer += "\nPlease include the debug logfile with your email: {0}\n".format(
debug_log)
# String it all together
msg = header + msg + footer
# Print out main message
logger.critical(msg)
# Get traceback of where we failed for the log file
if not ample_tb:
ample_tb = traceback.extract_stack()
else:
ample_tb = traceback.extract_tb(ample_tb)
msg = "AMPLE EXITING AT..." + os.linesep + "".join(
traceback.format_list(ample_tb))
if debug_log:
logger.debug(msg)
else:
# If we don't have a debug file we want to output the traceback to the console
logger.info(msg)
# Make sure the error widget is updated
if pyrvapi: pyrvapi.rvapi_flush()
sys.exit(1)
def makeUnmergedTable(body, tableId, holderId, data, row):
pyrvapi.rvapi_add_table(tableId, "<h2>Summary</h2>", holderId, row, 0, 1,
1, 0)
pyrvapi.rvapi_set_table_style(tableId, "table-blue", "text-align:left;")
r = body.putTableLine(tableId, "File name", "Imported file name",
data.files[0], 0)
r = body.putTableLine(tableId, "Assigned name", "Assigned data name",
data.dname, r)
r = body.putTableLine(tableId, "Dataset name", "Original data name",
data.dataset.name, r)
r = body.putTableLine(tableId, "Resolution (Å)",
"Dataset resolution in angstroms", data.dataset.reso,
r)
r = body.putTableLine(tableId, "Wavelength (Å)",
"Beam wavelength in angstroms", data.dataset.wlen, r)
if data.HM:
r = body.putTableLine(tableId, "Space group", "Space group", data.HM,
r)
else:
r = body.putTableLine(tableId, "Space group", "Space group",
"unspecified", r)
cell_spec = "not specified"
"""
if data.CELL:
cell_spec = str(data.CELL[0]) + " " + \
str(data.CELL[1]) + " " + \
str(data.CELL[2]) + " " + \
" " + \
str(data.CELL[3]) + " " + \
str(data.CELL[4]) + " " + \
str(data.CELL[5])
"""
cell_spec = data.dataset.cell[0] + " " + \
data.dataset.cell[1] + " " + \
data.dataset.cell[2] + " " + \
data.dataset.cell[3] + " " + \
data.dataset.cell[4] + " " + \
data.dataset.cell[5]
r = body.putTableLine(tableId, "Cell", "Cell parameters", cell_spec, r)
"""
range = "not found"
if data.BRNG:
range = str(data.BRNG)
r = body.putTableLine ( tableId,"Batches","Batch range(s)",range,r );
"""
range = []
for run in data.dataset.runs:
range += [(int(run[1]), int(run[2]))]
r = body.putTableLine(tableId, "Ranges", "Image range(s)", str(range), r)
pyrvapi.rvapi_flush()
return
def display_results(self, ample_dict):
if not (pyrvapi or ('no_gui' in ample_dict and ample_dict['no_gui'])):
return
if not self.header:
pyrvapi.rvapi_add_header("AMPLE Results")
self.header = True
if not self.ccp4i2: self.create_log_tab(ample_dict)
self.create_summary_tab(ample_dict)
self.create_results_tab(ample_dict)
pyrvapi.rvapi_flush()
return True
def setGenericLogParser(self, split_sections_bool, graphTables=False):
self.log_parser_cnt += 1
panel_id = "genlogparser_" + str(self.log_parser_cnt)
self.putPanel(panel_id)
self.generic_parser_summary = {}
self.log_parser = pyrvapi_ext.parsers.generic_parser(
panel_id,
split_sections_bool,
summary=self.generic_parser_summary,
graph_tables=graphTables)
pyrvapi.rvapi_flush()
return panel_id
def run(body): # body is reference to the main Import class
files_map = []
for f in body.files_all:
fl = f.lower();
if fl.endswith(('.map', '.mrc')):
files_map.append ( f )
if len(files_map) <= 0:
return
body.file_stdout.write ( "\n" + "%"*80 + "\n" )
body.file_stdout.write ( "%%%%% Map volume data\n" )
body.file_stdout.write ( "%"*80 + "\n" )
mapSecId = "map_sec_" + str(body.widget_no)
body.widget_no += 1
pyrvapi.rvapi_add_section ( mapSecId, "Map", body.report_page_id(),
body.rvrow, 0, 1, 1, False )
k = 0
for f in files_map:
body.files_all.remove ( f )
pyrvapi.rvapi_put_table_string ( body.import_summary_id(), f, body.summary_row, 0 )
fpath = os.path.join ( body.importDir(), f );
with mrcfile.mmap(fpath) as mrc:
msg = "MAP {0} x {1} x {2}".format(mrc.header.nx, mrc.header.ny, mrc.header.nz)
pyrvapi.rvapi_put_table_string ( body.import_summary_id(), msg, body.summary_row, 1 )
map_ = dtype_map.DType ( body.job_id )
map_.subtype = ['final_map']
map_.setFile ( f )
body.dataSerialNo += 1
map_.makeDName ( body.dataSerialNo )
body.outputDataBox.add_data ( map_ )
# Essential to rename uploaded file to put it in output directory
# Might be better to use the standard register() method instead if possible?
# Currently the file ends up remaining in the upload directory on the front end,
# even though it's removed on the number cruncher...
os.rename ( fpath, os.path.join(body.outputDir(), f) )
body.file_stdout.write ( "... processed: " + f + "\n" )
k += 1
body.rvrow += 1
pyrvapi.rvapi_flush()
return
def display_results(self, ample_dict):
"""Display the results of an AMPLE run using pyrvapi
Parameters
----------
ample_dict : dict
An AMPLE job dictionary
"""
if not (pyrvapi or self.generate_output):
return
try:
if not self.header:
pyrvapi.rvapi_add_header("AMPLE Results")
self.header = True
self.create_log_tab(ample_dict)
self.create_citation_tab(ample_dict)
self.create_summary_tab(ample_dict)
self.create_results_tab(ample_dict)
pyrvapi.rvapi_flush()
except Exception as e:
logger.critical("Error displaying results!\n%s", traceback.format_exc())
return True
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 exit_error(exc_type, exc_value, exc_traceback):
"""Exit on error collecting as much information as we can.
Parameters
----------
exc_type : str
The exception type
exc_value : str
The exception value
exc_traceback
The exception traceback
Warnings
--------
This function terminates the program after printing appropriate
error messages.
"""
# Get the root logger
logger = logging.getLogger(__name__)
# Traceback info
traceback_value_msg = exc_value
traceback_full_msg = traceback.format_exception(exc_type, exc_value, exc_traceback)
# Find debug log file
debug_log = _debug_logfile(logger)
# Construct the message
main_msg = "%(sep)s%(hashish)s%(sep)s"\
+ "%(short_hash)s%(msg)s%(short_hash)s%(sep)s"\
+ "%(hashish)s%(sep)s%(sep)s"\
+ "SIMBAD exited with message: %(tb_value)s"\
+ "%(sep)s%(sep)s%(hashish)s%(sep)s%(sep)s"
if debug_log:
main_msg += "More information may be found in the debug log file: %(logfile)s%(sep)s"
main_msg += "%(sep)sIf you believe that this is an error with SIMBAD, please email: %(email)s%(sep)s"
main_msg += "providing as much information as you can about how you ran the program.%(sep)s"
if debug_log:
main_msg += "%(sep)sPlease static the debug logfile with your email: %(logfile)s%(sep)s"
nhashes = 70
main_msg_kwargs = {
'sep': os.linesep,
'hashish': '*' * nhashes,
'short_hash': '*' * 19,
'msg': "SIMBAD_ERROR".center(32, " "),
'tb_value': traceback_value_msg,
'logfile': debug_log,
'email': '*****@*****.**'
}
# String it all together
logger.critical(main_msg, main_msg_kwargs)
logger.critical("SIMBAD EXITING AT...")
logger.critical("".join(traceback_full_msg))
# Make sure the error widget is updated
if pyrvapi:
pyrvapi.rvapi_flush()
sys.exit(1)
def run(body): # body is reference to the main Import class
files_xyz = []
for f in body.files_all:
fl = f.lower()
if fl.endswith(('.pdb', '.cif', '.mmcif', '.ent')):
files_xyz.append(f)
if len(files_xyz) <= 0:
return
body.file_stdout.write("\n" + "%" * 80 + "\n")
body.file_stdout.write("%%%%% IMPORT OF XYZ COORDINATES\n")
body.file_stdout.write("%" * 80 + "\n")
xyzSecId = "xyz_sec_" + str(body.widget_no)
body.widget_no += 1
pyrvapi.rvapi_add_section(xyzSecId, "XYZ Coordinates",
body.report_page_id(), body.rvrow, 0, 1, 1,
False)
k = 0
for f in files_xyz:
body.files_all.remove(f)
fpath = os.path.join(body.importDir(), f)
#coor.stripLigWat ( fpath,fpath ) # strip ligands and waters
# split input file to chains
scr_file = open("pdbcur.script", "w")
scr_file.write("SPLITTOCHAINS\nEND\n")
scr_file.close()
# Start pdbcur
rc = command.call("pdbcur", ['XYZIN', fpath], "./", "pdbcur.script",
body.file_stdout, body.file_stderr)
# read pdbcur's json
fnamesplit = os.path.splitext(f)
fpathsplit = os.path.join(body.importDir(), fnamesplit[0]) + ".json"
if not os.path.isfile(fpathsplit):
body.putSummaryLine_red(f, "UNKNOWN",
"Failed to recognise, ignored")
else:
with open(fpathsplit, 'r') as json_file:
json_str = json_file.read()
json_file.close()
#xyzmeta = eval(json_str)
xyzMeta = xyzmeta.XYZMeta(json_str)
if len(xyzMeta["xyz"]) <= 0:
body.putSummaryLine_red(f, "XYZ", "Empty file -- ignored")
else:
subSecId = xyzSecId
if len(files_xyz) > 1:
subSecId = xyzSecId + str(k)
pyrvapi.rvapi_add_section(subSecId, "Import " + f,
xyzSecId, k, 0, 1, 1, False)
xyz = dtype_xyz.DType(body.job_id)
xyz.setFile(f)
dtype_xyz.setXYZMeta(xyz, xyzMeta)
body.dataSerialNo += 1
xyz.makeDName(body.dataSerialNo)
os.rename(fpath, os.path.join(body.outputDir(), f))
xyz.makeUniqueFNames(body.outputDir())
body.outputDataBox.add_data(xyz)
xyzTableId = "xyz_" + str(k) + "_table"
body.putTable(xyzTableId, "", subSecId, 0)
jrow = 0
if len(files_xyz) <= 1:
body.putTableLine(xyzTableId, "File name",
"Imported file name", f, jrow)
jrow += 1
body.putTableLine(xyzTableId, "Assigned name",
"Assigned data name", xyz.dname, jrow)
crystData = getCrystData(xyzMeta)
body.putTableLine(xyzTableId, "Space group", "Space group",
crystData[0], jrow + 1)
body.putTableLine(
xyzTableId, "Cell parameters",
"Cell parameters (a,b,c, α,β,γ)",
crystData[1], jrow + 2)
contents = ""
nChains = 0
for model in xyzMeta["xyz"]:
for chain in model["chains"]:
if chain["type"] != "UNK":
nChains += 1
if len(contents) > 0:
contents += "<br>"
contents += "Model " + str(model['model']) + ", chain " + \
chain['id'] + ": " + str(chain['size']) + \
" residues, type: " + chain['type']
if len(xyzMeta["ligands"]) > 0:
if len(contents) > 0:
contents += "<br>"
contents += "Ligands:"
for name in xyzMeta["ligands"]:
contents += " " + name
body.putTableLine(xyzTableId, "Contents", "File contents",
contents, jrow + 3)
pyrvapi.rvapi_add_data(
xyzTableId + "_structure_btn",
xyz.dname + " ",
# always relative to job_dir from job_dir/html
os.path.join("..", body.outputDir(), xyz.files[0]),
"xyz",
subSecId,
1,
0,
1,
1,
-1)
body.putSummaryLine(f, "XYZ", xyz.dname)
"""
if nChains>1:
irow = 2
for model in xyzMeta["xyz"]:
for chain in model['chains']:
if chain["type"] != "UNK":
fname = fnamesplit[0] + "_" + str(model['model']) + "_" + \
chain['id'] + fnamesplit[1]
xyz = dtype_xyz.DType ( body.job_id )
xyz.setFile ( fname )
mdl = {}
mdl['model'] = model['model']
mdl['chains'] = [chain]
xyz_meta = {}
xyz_meta["cryst"] = xyzMeta["cryst"]
xyz_meta["xyz"] = [mdl]
xyz_meta["ligands"] = chain["ligands"]
dtype_xyz.setXYZMeta ( xyz,xyz_meta )
body.dataSerialNo += 1
xyz.makeDName ( body.dataSerialNo )
os.rename ( os.path.join(body.importDir(),fname),
os.path.join(body.outputDir(),fname) )
xyz.makeUniqueFNames ( body.outputDir() )
body.outputDataBox.add_data ( xyz )
xyzTableId = "xyz_" + str(k) + "_" + str(model['model']) + \
"_" + chain['id'] + "_table"
body.putMessage1 ( subSecId ," ",irow )
body.putTable ( xyzTableId,"",subSecId,irow+1 )
body.putTableLine ( xyzTableId,"Assigned name",
"Assigned data name",xyz.dname,0 )
crystData = getCrystData ( xyz_meta )
body.putTableLine ( xyzTableId,"Space group",
"Space group",crystData[0],1 )
body.putTableLine ( xyzTableId,"Cell parameters",
"Cell parameters (a,b,c, α,β,γ)",
crystData[1],2 )
contents = "Model " + str(model['model']) + ", chain " + \
chain['id'] + ": " + str(chain['size'])
contents += " residues, type: " + chain['type']
if len(xyz.xyzmeta["ligands"])>0:
contents += "<br>Ligands:"
for name in xyz.xyzmeta["ligands"]:
contents += " " + name
body.putTableLine ( xyzTableId,"Contents",
"File contents",contents,3 )
pyrvapi.rvapi_add_data ( xyzTableId+"_structure_btn",xyz.dname,
# always relative to job_dir from job_dir/html
os.path.join("..",body.outputDir(),xyz.files[0]),
"xyz",subSecId,irow+2,0,1,1,-1 )
#fdebug = open ( "_debug.txt",'a' )
#fdebug.write ( fname + "\n")
#fdebug.close()
body.addSummaryLine ( "XYZ",xyz.dname )
irow += 3
"""
body.file_stdout.write("... processed: " + f + "\n")
k += 1
body.rvrow += 1
pyrvapi.rvapi_flush()
return
def putSRFDiagram(
body, # reference on Basic class
hkl, # hkl data object
dirPath, # directory with hkl object files (outputDir)
reportDir, # directory with html report (reportDir)
holderId, # rvapi holder of SRF widget
row,
col, # rvapi coordinates for SRF widget
rowSpan,
colSpan, # coordinate spans for STF widget
file_stdout, # standard output stream
file_stderr, # standard error stream
log_parser=None # log file parser
):
fpath = hkl.getFilePath(dirPath, 0)
Fmean = hkl.getMeta("Fmean.value", "")
sigF = hkl.getMeta("Fmean.sigma", "")
if Fmean == "" or sigF == "":
file_stderr.write ( "Fmean and sigFmean columns not found in " +\
hkl.files[0] + " -- SRF not calculated\n" )
return [-1, "Fmean and sigFmean columns not found"]
scr_file = open("molrep_srf.script", "w")
scr_file.write ( "file_f " + fpath +\
"\nlabin F=" + Fmean + " SIGF=" + sigF + "\n" )
scr_file.close()
"""
cols = hkl.getMeanColumns()
if cols[2]!="F":
file_stderr.write ( "Fmean and sigFmean columns not found in " +\
hkl.files[0] + " -- SRF not calculated\n" )
return [-1,"Fmean and sigFmean columns not found"]
scr_file = open ( "molrep_srf.script","w" )
scr_file.write ( "file_f " + fpath +\
"\nlabin F=" + cols[0] + " SIGF=" + cols[1] + "\n" )
scr_file.close ()
"""
# Start molrep
rc = command.call("molrep", ["-i"], "./", "molrep_srf.script", file_stdout,
file_stderr, log_parser)
if not os.path.isfile("molrep_rf.ps"):
file_stderr.write ( "\nSRF postscript was not generated for " +\
hkl.files[0] + "\n" )
return [-2, rc.msg]
rc = command.call("ps2pdf", ["molrep_rf.ps"], "./", None, file_stdout,
file_stderr, log_parser)
if not os.path.isfile("molrep_rf.pdf"):
file_stderr.write ( "\nSRF pdf was not generated for " +\
hkl.files[0] + "\n" )
return [-3, rc.msg]
pdfpath = os.path.splitext(hkl.files[0])[0] + ".pdf"
os.rename("molrep_rf.pdf", os.path.join(reportDir, pdfpath))
subsecId = body.getWidgetId(holderId) + "_srf"
pyrvapi.rvapi_add_section(subsecId, "Self-Rotation Function", holderId,
row, col, rowSpan, colSpan, False)
pyrvapi.rvapi_set_text ( "<object data=\"" + pdfpath +\
"\" type=\"application/pdf\" " +\
"style=\"border:none;width:100%;height:1000px;\"></object>",
subsecId,0,0,1,1 )
pyrvapi.rvapi_flush()
return [0, "Ok"]
def exit_error(*args, **kwargs):
"""Exit on error collecting as much information as we can.
Parameters
----------
message : str, optional
A error message to print
Notes
-----
This previously accepted two arguments of a string to print as an error message and
an exception traceback.
We now just use sys.exch_info() so the messsage argument is no longer required but optional.
While we refactor the code, we'll use *args to get any argument parameters passed in
as the first argument.
"""
# Get the root logger
logger = logging.getLogger()
# An error may have occured before we started logging so we need to create one here
if not logger.handlers:
logging.basicConfig(format='%(message)s\n', level=logging.DEBUG)
logger = logging.getLogger()
exc_type, exc_value, exc_traceback = sys.exc_info()
msg = kwargs.get('message')
if msg is None:
if len(args) >= 1: # Fix for old cases
msg = args[0]
else:
msg = "{0}: {1}".format(exc_type.__name__, exc_value.message)
#header="**** AMPLE ERROR ****\n\n"
header="*"*70 + "\n"
header+="*"*20 + " "*10 + "AMPLE ERROR" + " "*10 +"*"*19 + "\n"
header+="*"*70 + "\n\n"
# Create the Footer
footer="\n\n" + "*"*70+"\n\n"
# Get the name of the debug log file
debug_log = _debug_logfile(logger)
if debug_log: footer += "More information may be found in the debug log file: {0}\n".format(debug_log)
footer += "\nIf you believe that this is an error with AMPLE, please email: [email protected]\n"
footer += "providing as much information as you can about how you ran the program.\n"
if debug_log: footer += "\nPlease include the debug logfile with your email: {0}\n".format(debug_log)
# String it all together
msg = header + msg + footer
# Print out main message
logger.critical(msg)
# If we were called without an exception being raised, we just print the current stack
if exc_traceback is None:
traceback_str = "".join(traceback.format_stack())
else:
traceback_str = "".join(traceback.format_exception(exc_type, exc_value, exc_traceback))
msg = "AMPLE EXITING AT2..." + os.linesep + traceback_str
if debug_log:
logger.debug(msg)
else:
# If we don't have a debug file we want to output the traceback to the console
logger.info(msg)
# Make sure the error widget is updated
if pyrvapi: pyrvapi.rvapi_flush()
sys.exit(1)
def makeHKLTable(body, tableId, holderId, original_data, new_data, truncation,
trunc_msg, row):
pyrvapi.rvapi_add_table(tableId, "<h2>Summary</h2>", holderId, row, 0, 1,
1, 0)
pyrvapi.rvapi_set_table_style(tableId, "table-blue", "text-align:left;")
r = body.putTableLine(tableId, "File name", "Imported file name",
new_data.files[0], 0)
r = body.putTableLine(tableId, "Dataset name", "Original dataset name",
new_data.getDataSetName(), r)
r = body.putTableLine(tableId, "Assigned name", "Assigned dataset name",
new_data.dname, r)
r = body.putTableLine(tableId, "Wavelength", "Wavelength",
str(new_data.getMeta("DWAVEL", "unspecified")), r)
r = body.putTableLine(tableId, "Space group", "Space group",
new_data.getMeta("HM", "unspecified"), r)
dcell = new_data.getMeta("DCELL", "*")
if dcell == "*":
cell_spec = "not specified"
else:
cell_spec = str(dcell[0]) + " " + \
str(dcell[1]) + " " + \
str(dcell[2]) + " " + \
" " + \
str(dcell[3]) + " " + \
str(dcell[4]) + " " + \
str(dcell[5])
r = body.putTableLine(tableId, "Cell", "Cell parameters", cell_spec, r)
r = body.putTableLine(tableId, "Resolution low", "Low resolution limit",
new_data.getLowResolution(), r)
r = body.putTableLine(tableId, "Resolution high", "High resolution limit",
new_data.getHighResolution(), r)
if dtype_hkl.subtypeAnomalous() in new_data.subtype:
anom = "Present"
else:
anom = "Not present"
r = body.putTableLine(tableId, "Anomalous scattering",
"Presence of anomalous data", anom, r)
# print new_data.getColumnNames()
if trunc_msg:
r = body.putTableLine(tableId, "Original columns",
"Original data columns",
original_data.getColumnNames(), r)
r = body.putTableLine ( tableId,"Truncation",
"Truncation result","Failed: " + trunc_msg + \
"<br>The dataset cannot be used",r )
elif truncation == 0:
r = body.putTableLine(tableId, "Original columns",
"Original data columns",
original_data.getColumnNames(), r)
r = body.putTableLine ( tableId,"Truncation",
"Truncation result",
"Was not performed due to the absence of " + \
"intensity data.<br>" + \
"The dataset will be used untruncated",r )
else:
r = body.putTableLine(tableId, "Original columns",
"Original data columns",
original_data.getColumnNames(), r)
r = body.putTableLine ( tableId,"Truncation",
"Truncation result",
"Truncated dataset will be used instead of " + \
"the original one.",r )
r = body.putTableLine(tableId, "Columns to be used",
"Data columns which will be used further on",
new_data.getColumnNames(), r)
pyrvapi.rvapi_flush()
return
def exit_error(exc_type, exc_value, exc_traceback):
"""Exit on error collecting as much information as we can.
Parameters
----------
exc_type : str
The exception type
exc_value : str
The exception value
exc_traceback
The exception traceback
Warnings
--------
This function terminates the program after printing appropriate
error messages.
"""
# Get the root logger
logger = logging.getLogger(__name__)
# Traceback info
traceback_value_msg = exc_value
traceback_full_msg = traceback.format_exception(exc_type, exc_value,
exc_traceback)
# Find debug log file
debug_log = _debug_logfile(logger)
# Construct the message
main_msg = "%(sep)s%(hashish)s%(sep)s"\
+ "%(short_hash)s%(msg)s%(short_hash)s%(sep)s"\
+ "%(hashish)s%(sep)s%(sep)s"\
+ "SIMBAD exited with message: %(tb_value)s"\
+ "%(sep)s%(sep)s%(hashish)s%(sep)s%(sep)s"
if debug_log:
main_msg += "More information may be found in the debug log file: %(logfile)s%(sep)s"
main_msg += "%(sep)sIf you believe that this is an error with SIMBAD, please email: %(email)s%(sep)s"
main_msg += "providing as much information as you can about how you ran the program.%(sep)s"
if debug_log:
main_msg += "%(sep)sPlease static the debug logfile with your email: %(logfile)s%(sep)s"
nhashes = 70
main_msg_kwargs = {
'sep': os.linesep,
'hashish': '*' * nhashes,
'short_hash': '*' * 19,
'msg': "SIMBAD_ERROR".center(32, " "),
'tb_value': traceback_value_msg,
'logfile': debug_log,
'email': '*****@*****.**'
}
# String it all together
logger.critical(main_msg, main_msg_kwargs)
logger.critical("SIMBAD EXITING AT...")
logger.critical("".join(traceback_full_msg))
# Make sure the error widget is updated
if pyrvapi:
pyrvapi.rvapi_flush()
sys.exit(1)
def run(
body, # body is reference to the main Import class
sectionTitle="Reflection datasets created",
sectionOpen=False, # to keep result section closed if several datasets
freeRflag=True # will be run if necessary
):
files_mtz = []
for f_orig in body.files_all:
f_base, f_ext = os.path.splitext(f_orig)
if f_ext.lower() in ('.hkl', '.mtz'):
p_orig = os.path.join(body.importDir(), f_orig)
f_fmt = mtz.hkl_format(p_orig, body.file_stdout)
if f_fmt in ('xds_merged', 'mtz_merged'):
files_mtz.append((f_orig, f_fmt))
if not files_mtz:
return
mtzSecId = body.getWidgetId("mtz_sec") + "_"
k = 0
for f_orig, f_fmt in files_mtz:
body.files_all.remove(f_orig)
p_orig = os.path.join(body.importDir(), f_orig)
p_mtzin = p_orig
if not f_fmt.startswith('mtz_'):
p_mtzin = os.path.splitext(f_orig)[0] + '.mtz'
sp = subprocess.Popen('pointless',
stdin=subprocess.PIPE,
stdout=body.file_stdout,
stderr=body.file_stderr)
sp.stdin.write('XDSIN ' + p_orig + '\nHKLOUT ' + p_mtzin +
'\nCOPY\n')
sp.stdin.close()
if sp.wait():
p_mtzin = None
if p_mtzin:
p_mtzout = p_mtzin
rc = command.comrc()
if freeRflag:
p_mtzout = os.path.join(body.outputDir(),
os.path.basename(f_orig))
if k == 0:
scr_file = open(freerflag_script(), "w")
scr_file.write("UNIQUE\n")
scr_file.close()
# run freerflag: generate FreeRFlag if it is absent, and expand
# all reflections
rc = command.call("freerflag",
["HKLIN", p_mtzin, "HKLOUT", p_mtzout],
"./",
freerflag_script(),
body.file_stdout,
body.file_stderr,
log_parser=None)
if rc.msg:
msg = "\n\n Freerflag failed with message:\n\n" + \
rc.msg + \
"\n\n File " + f_orig + \
" cannot be processed.\n\n"
body.file_stdout.write(msg)
body.file_stderr.write(msg)
body.putSummaryLine_red(f_orig, "MTZ",
"Failed to process/import, ignored")
else:
mf = mtz.mtz_file(p_mtzout)
body.summary_row_0 = -1 # to signal the beginning of summary row
for ds in mf:
if k == 0:
body.file_stdout.write("\n" + "%" * 80 + "\n")
body.file_stdout.write(
"%%%%% IMPORT REFLECTION DATA\n")
body.file_stdout.write("%" * 80 + "\n")
# make HKL dataset annotation
hkl = dtype_hkl.DType(body.job_id)
hkl.importMTZDataset(ds)
body.dataSerialNo += 1
hkl.makeDName(body.dataSerialNo)
datasetName = ""
if k == 0:
if sectionTitle:
pyrvapi.rvapi_add_section(mtzSecId, sectionTitle,
body.report_page_id(),
body.rvrow, 0, 1, 1,
sectionOpen)
else:
pyrvapi.rvapi_add_section(
mtzSecId,
"Reflection dataset created: " + hkl.dname,
body.report_page_id(), body.rvrow, 0, 1, 1,
sectionOpen)
subSecId = mtzSecId
if len(files_mtz) > 1 or len(mf) > 1:
subSecId = mtzSecId + str(k)
pyrvapi.rvapi_add_section(subSecId, hkl.dname,
mtzSecId, k, 0, 1, 1, False)
#pyrvapi.rvapi_add_section ( subSecId,
# f_orig + " / " + hkl.getDataSetName(),
# mtzSecId,k,0,1,1,False )
# run crtruncate
outFileName = os.path.join(body.outputDir(),
hkl.dataId + ".mtz")
outXmlName = os.path.join("ctruncate" + hkl.dataId +
".xml")
cmd = ["-hklin", p_mtzout, "-hklout", outFileName]
amplitudes = ""
meanCols = hkl.getMeanColumns()
if meanCols[2] != "X":
cols = "/*/*/["
if meanCols[1] != None:
cols = cols + meanCols[0] + "," + meanCols[1]
else:
cols = cols + meanCols[0]
if meanCols[2] == "F":
amplitudes = "-amplitudes"
cmd += ["-colin", cols + "]"]
anomCols = hkl.getAnomalousColumns()
anomalous = False
if anomCols[4] != "X":
anomalous = True
cols = "/*/*/["
for i in range(0, 4):
if anomCols[i] != None:
if i > 0:
cols = cols + ","
cols = cols + anomCols[i]
if anomCols[4] == "F":
amplitudes = "-amplitudes"
cmd += ["-colano", cols + "]"]
if amplitudes:
cmd += [amplitudes]
cmd += ["-xmlout", outXmlName]
cmd += ["-freein"]
pyrvapi.rvapi_add_text(
" <p><h2>Data analysis (CTruncate)</h2>",
subSecId, 1, 0, 1, 1)
pyrvapi.rvapi_add_panel(mtzSecId + str(k), subSecId, 2, 0,
1, 1)
"""
log_parser = pyrvapi_ext.parsers.generic_parser ( mtzSecId+str(k),
False,body.generic_parser_summary,False )
rc = command.call ( "ctruncate",cmd,"./",None,
body.file_stdout,body.file_stderr,log_parser )
"""
body.file_stdin = None # not clear why this is not None at
# this point and needs to be forced,
# or else runApp looks for input script
body.setGenericLogParser(mtzSecId + str(k), False)
body.runApp("ctruncate", cmd)
body.file_stdout.flush()
mtzTableId = body.getWidgetId("mtz") + "_" + str(
k) + "_table"
if rc.msg:
msg = "\n\n CTruncate failed with message:\n\n" + \
rc.msg + \
"\n\n Dataset " + hkl.dname + \
" cannot be used.\n\n"
body.file_stdout.write(msg)
body.file_stderr.write(msg)
makeHKLTable(body, mtzTableId, subSecId, hkl, hkl, -1,
msg, 0)
datasetName = hkl.dname
elif not os.path.exists(outFileName):
body.file_stdout.write ( "\n\n +++ Dataset " + hkl.dname + \
"\n was not truncated and will be used as is\n\n" )
hkl.makeUniqueFNames(body.outputDir())
body.outputDataBox.add_data(hkl)
makeHKLTable(body, mtzTableId, subSecId, hkl, hkl, 0,
"", 0)
datasetName = hkl.dname
srf.putSRFDiagram(body, hkl, body.outputDir(),
body.reportDir(), subSecId, 3, 0, 1,
1, body.file_stdout,
body.file_stderr, None)
pyrvapi.rvapi_set_text (
" <br><hr/><h3>Created Reflection Data Set (merged)</h3>" + \
"<b>Assigned name:</b> " + datasetName + "<br> ",
subSecId,4,0,1,1 )
pyrvapi.rvapi_add_data(
"hkl_data_" + str(body.dataSerialNo),
"Merged reflections",
# always relative to job_dir from job_dir/html
os.path.join("..", body.outputDir(), hkl.files[0]),
"hkl:hkl",
subSecId,
5,
0,
1,
1,
-1)
else:
body.file_stdout.write ( "\n\n ... Dataset " + hkl.dname + \
"\n was truncated and will substitute the " + \
"original one\n\n" )
mtzf = mtz.mtz_file(outFileName)
# ctruncate should create a single dataset here
for dset in mtzf:
dset.MTZ = os.path.basename(outFileName)
hkl_data = dtype_hkl.DType(body.job_id)
hkl_data.importMTZDataset(dset)
hkl_data.dname = hkl.dname
hkl_data.dataId = hkl.dataId
hkl_data.makeUniqueFNames(body.outputDir())
body.outputDataBox.add_data(hkl_data)
makeHKLTable(body, mtzTableId, subSecId, hkl,
hkl_data, 1, "", 0)
datasetName = hkl_data.dname
srf.putSRFDiagram(body, hkl_data, body.outputDir(),
body.reportDir(), subSecId, 3, 0,
1, 1, body.file_stdout,
body.file_stderr, None)
pyrvapi.rvapi_set_text (
" <br><hr/><h3>Created Reflection Data Set (merged)</h3>" + \
"<b>Assigned name:</b> " + datasetName + "<br> ",
subSecId,4,0,1,1 )
pyrvapi.rvapi_add_data(
"hkl_data_" + str(body.dataSerialNo),
"Merged reflections",
# always relative to job_dir from job_dir/html
os.path.join("..", body.outputDir(),
hkl_data.files[0]),
"hkl:hkl",
subSecId,
5,
0,
1,
1,
-1)
if body.summary_row_0 < 0:
body.putSummaryLine(f_orig, "HKL", datasetName)
else:
body.addSummaryLine("HKL", datasetName)
k += 1
pyrvapi.rvapi_flush()
if len(mf) <= 0:
body.putSummaryLine_red(f_orig, "UNKNOWN", "-- ignored")
body.file_stdout.write("... processed: " + f_orig + "\n ")
body.rvrow += 1
pyrvapi.rvapi_flush()
return
def write_output(items,
json_file=None,
xml_file=None,
xmlroot=None,
docid=None,
output=None):
# in non-i2 mode items are added to the output dictionary which is dumped to json
if json_file is not None:
if 'result' in items:
result = items['result']
for solution in output['solutions']:
if solution['id'] == result['id']:
solution.update({'acornCC': result['acornCC']})
else:
output.update(items)
temp_filename = json_file + '.tmp'
with open(temp_filename, 'w') as jsonfile:
print(json.dumps(output,
sort_keys=True,
indent=2,
separators=(',', ': ')),
file=jsonfile)
if os.path.exists(json_file):
import uuid
tmpfile = str(uuid.uuid4())
os.rename(json_file, tmpfile)
os.remove(tmpfile)
os.rename(temp_filename, json_file)
return output
elif xmlroot is None and xml_file is not None:
xmlroot = etree.Element('Fragon')
return xmlroot
elif docid is None:
jsrview_dir = os.path.join(os.environ['CCP4'], 'share', 'jsrview')
pyrvapi.rvapi_init_document('fragon_results', os.getcwd(),
'Fragon %s results' % items['Fragon'], 1,
7, jsrview_dir, None, None, None, None)
pyrvapi.rvapi_add_tab('tab1', 'Fragon results', True)
pyrvapi.rvapi_add_section('status', 'Current status', 'tab1', 0, 0, 1,
1, True)
pyrvapi.rvapi_add_text(
'The job is currently running. Updates will be shown here after fragment placement and density modification.',
'status', 0, 0, 1, 1)
pyrvapi.rvapi_flush()
output.update(items)
return 'tab1', output
elif xml_file is not None:
# in i2 mode new items are added to the etree as this preserves the order in the xml
for key in items:
if key == 'Fragon':
version_node = etree.SubElement(xmlroot, 'Version')
version_node.text = output['Fragon']
elif key == 'callback':
callback = items['callback']
if callback[0] == 'progress':
try:
progress_node = xmlroot.xpath(
'//Fragon/phaser_progress')[0]
except IndexError:
progress_node = etree.SubElement(
xmlroot, 'phaser_progress')
progress_node.text = callback[1]
elif callback[0] == 'Best LLG/TFZ':
best_llg_node = etree.SubElement(xmlroot, 'best_llg')
best_llg_node.text = callback[1]['llg']
best_tfz_node = etree.SubElement(xmlroot, 'best_tfz')
best_tfz_node.text = callback[1]['tfz']
elif key == 'solutions':
solutions = items['solutions']
try:
solutions_node = xmlroot.xpath('//Fragon/solutions')[0]
except IndexError:
solutions_node = etree.SubElement(xmlroot, 'solutions')
if len(solutions) > 0:
solutions_node.text = json.dumps(solutions)
else:
node = etree.SubElement(xmlroot, key)
node.text = items[key].__str__()
temp_filename = 'program.xml.tmp'
with open(temp_filename, 'w') as xmlfile:
xmlfile.write(etree.tostring(xmlroot, pretty_print=True))
if os.path.exists(xml_file):
import uuid
tmpfile = str(uuid.uuid4())
os.rename(xml_file, tmpfile)
os.remove(tmpfile)
os.rename(temp_filename, xml_file)
elif docid is not None:
for key in items:
if key == 'copies':
if items['copies'] > 1:
pyrvapi.rvapi_set_text(
'Running Phaser to place %d fragments' %
items['copies'], 'status', 0, 0, 1, 1)
else:
pyrvapi.rvapi_set_text(
'Running Phaser to place the fragment', 'status', 0, 0,
1, 1)
pyrvapi.rvapi_add_tab('tab2', 'Phaser log file', False)
pyrvapi.rvapi_append_content(output['root'] + '_Phaser.log',
True, 'tab2')
pyrvapi.rvapi_flush()
output.update(items)
elif key == 'callback':
callback = items['callback']
if callback[0] == 'progress':
pyrvapi.rvapi_set_text(
'Current Phaser stage: %s' % callback[1], 'status', 1,
0, 1, 1)
pyrvapi.rvapi_flush()
elif callback[0] == 'Best LLG':
pyrvapi.rvapi_set_text(
'Current best solution Log Likelihood Gain (LLG): %s Translation Function Z-score (TFZ): %s'
% (callback[1], output['best_tfz']), 'status', 2, 0, 1,
1)
pyrvapi.rvapi_flush()
elif callback[0] == 'Best TFZ':
output.update({'best_tfz': callback[1]})
elif key == 'solutions':
solutions = items['solutions']
top_llg = sorted(solutions,
key=lambda r: r['llg'],
reverse=True)[0]['llg']
top_tfz = sorted(solutions,
key=lambda r: r['llg'],
reverse=True)[0]['tfz']
top_acornCC = sorted([
solution['acornCC'] if solution['acornCC']
not in ['Running', '-', None] else None
for solution in solutions
],
reverse=True)[0]
if len(solutions) == 1:
pyrvapi.rvapi_set_text(
'Phaser has found a single solution with Log Likelihood Gain (LLG) of %0.2f and Translation Function Z-score (TFZ) of %0.2f'
% (top_llg, top_tfz), 'status', 0, 0, 1, 1)
else:
pyrvapi.rvapi_set_text(
'Phaser has found %d solutions. The top solution has Log Likelihood Gain (LLG) of %0.2f and Translation Function Z-score (TF Z-score) of %0.2f'
% (output['num_phaser_solutions'], top_llg, top_tfz),
'status', 0, 0, 1, 1)
if output['num_phaser_solutions'] > len(solutions):
pyrvapi.rvapi_set_text(
'Attempting to improve phases for the top %d solutions by density modification with ACORN'
% len(solns), 'status', 1, 0, 1, 1)
else:
pyrvapi.rvapi_set_text(
'Attempting to improve phases by density modification with ACORN',
'status', 1, 0, 1, 1)
if top_acornCC is not None:
pyrvapi.rvapi_set_text(
'The best solution so far has a correlation coefficient from density modification of %0.3f'
% top_acornCC, 'status', 2, 0, 1, 1)
else:
pyrvapi.rvapi_set_text('', 'status', 2, 0, 1, 1)
pyrvapi.rvapi_add_table('results_table', 'Phaser solutions',
'tab1', 1, 0, 1, 1, 1)
pyrvapi.rvapi_put_horz_theader('results_table',
'Solution number', '', 0)
pyrvapi.rvapi_put_horz_theader('results_table', 'Space group',
'', 1)
pyrvapi.rvapi_put_horz_theader('results_table', 'LLG',
'Phaser Log Likelihood Gain', 2)
pyrvapi.rvapi_put_horz_theader(
'results_table', 'TF Z-score',
'Phaser Translation Function Z-score', 3)
pyrvapi.rvapi_put_horz_theader(
'results_table', 'CC',
'CC from ACORN density modification', 4)
for solution in solutions:
pyrvapi.rvapi_put_table_string('results_table',
'%d' % solution['number'],
solution['number'] - 1, 0)
pyrvapi.rvapi_put_table_string('results_table',
solution['sg'],
solution['number'] - 1, 1)
pyrvapi.rvapi_put_table_string('results_table',
'%0.2f' % solution['llg'],
solution['number'] - 1, 2)
pyrvapi.rvapi_put_table_string('results_table',
'%0.2f' % solution['tfz'],
solution['number'] - 1, 3)
if solution['acornCC'] in ['Running', '-']:
pyrvapi.rvapi_put_table_string(
'results_table',
solution['acornCC'].replace('-', ''),
solution['number'] - 1, 4)
elif solution['acornCC'] is None:
pyrvapi.rvapi_put_table_string('results_table',
'Not tested',
solution['number'] - 1,
4)
else:
pyrvapi.rvapi_put_table_string(
'results_table', '%0.3f' % solution['acornCC'],
solution['number'] - 1, 4)
output.update(items)
pyrvapi.rvapi_flush()
elif key == 'cc_best':
solutions = output['solutions']
top_llg = sorted(solutions,
key=lambda r: r['llg'],
reverse=True)[0]['llg']
top_tfz = sorted(solutions,
key=lambda r: r['llg'],
reverse=True)[0]['tfz']
top_acornCC = sorted([
solution['acornCC'] if solution['acornCC']
not in ['Running', '-', None] else None
for solution in solutions
],
reverse=True)[0]
pyrvapi.rvapi_set_section_state('status', False)
pyrvapi.rvapi_add_section('results', 'Results', 'tab1', 2, 0,
1, 1, True)
pyrvapi.rvapi_add_text(
'Phaser found %d solutions. The top solution had Log Likelihood Gain (LLG) of %0.2f and Translation Function Z-score (TFZ) of %0.2f'
% (output['num_phaser_solutions'], top_llg, top_tfz),
'results', 0, 0, 1, 1)
pyrvapi.rvapi_add_text(
'The best solution has a correlation coefficient from density modification of %0.3f'
% top_acornCC, 'results', 1, 0, 1, 1)
if top_acornCC > 0.15:
pyrvapi.rvapi_add_text(
'This suggests the structure has been solved and the phases from ACORN will enable automated model building',
'results', 2, 0, 1, 1)
else:
pyrvapi.rvapi_add_text(
'Sorry this does not suggest a solution', 'results', 3,
0, 1, 1)
pyrvapi.rvapi_flush()
elif key == 'best_solution_id':
pdbout = output['name'] + '_phaser_solution.pdb'
mtzout = output['name'] + '_acorn_phases.mtz'
pyrvapi.rvapi_add_data(
'best', 'Best fragment placement and electron density',
pdbout, 'xyz', 'tab1', 3, 0, 1, 1, True)
pyrvapi.rvapi_append_to_data('best', mtzout, 'hkl:map')
else:
output.update(items)
return output
def wrapper(*args, **kwargs):
func(*args, **kwargs)
pyrvapi.rvapi_flush()
def run(body): # body is reference to the main Import class
files_mtz = []
for f_orig in body.files_all:
f_base, f_ext = os.path.splitext(f_orig)
if f_ext.lower() in ('.hkl', '.mtz'):
p_orig = os.path.join(body.importDir(), f_orig)
f_fmt = mtz.hkl_format(p_orig, body.file_stdout)
if f_fmt in ('xds_integrated', 'xds_scaled', 'mtz_integrated'):
files_mtz.append((f_orig, f_fmt))
if not files_mtz:
return
unmergedSecId = "unmerged_mtz_sec_" + str(body.widget_no)
body.widget_no += 1
k = 0
for f_orig, f_fmt in files_mtz:
try:
body.files_all.remove(f_orig)
p_orig = os.path.join(body.importDir(), f_orig)
p_mtzin = p_orig
if not f_fmt.startswith('mtz_'):
p_mtzin = os.path.splitext(f_orig)[0] + '.mtz'
sp = subprocess.Popen('pointless',
stdin=subprocess.PIPE,
stdout=body.file_stdout,
stderr=body.file_stderr)
sp.stdin.write('XDSIN ' + p_orig + '\nHKLOUT ' + p_mtzin +
'\nCOPY\n')
sp.stdin.close()
if sp.wait():
p_mtzin = None
if p_mtzin:
if k == 0:
body.file_stdout.write("\n" + "%" * 80 + "\n")
body.file_stdout.write("%%%%% UNMERGED DATA IMPORT\n")
body.file_stdout.write("%" * 80 + "\n")
pyrvapi.rvapi_add_section(unmergedSecId,
"Unmerged datasets",
body.report_page_id(),
body.rvrow, 0, 1, 1, False)
urow = 0
fileSecId = unmergedSecId
frow = 0
if len(files_mtz) > 1:
fileSecId = unmergedSecId + "_" + str(k)
pyrvapi.rvapi_add_section(fileSecId, "File " + f_orig,
unmergedSecId, urow, 0, 1, 1,
False)
urow += 1
pyrvapi.rvapi_set_text(
"<h2>Data analysis (Pointless)</h2>", fileSecId, frow,
0, 1, 1)
else:
pyrvapi.rvapi_set_text ( "<h2>Data analysis (Pointless)</h2>" + \
"<h3>File: " + f_orig + "</h3>",
fileSecId,frow,0,1,1 )
reportPanelId = fileSecId + "_report"
pyrvapi.rvapi_add_panel(reportPanelId, fileSecId, frow + 1, 0,
1, 1)
frow += 2
log_parser = pyrvapi_ext.parsers.generic_parser(
reportPanelId, False)
body.file_stdin = open(pointless_script(), 'w')
body.file_stdin.write (
"HKLIN " + p_mtzin + "\n" + \
"XMLOUT " + pointless_xml() + "\n"
)
body.file_stdin.close()
rc = command.call("pointless", [], "./", pointless_script(),
body.file_stdout, body.file_stderr,
log_parser)
body.unsetLogParser()
symmTablesId = fileSecId + "_" + symm_det()
pyrvapi.rvapi_add_section(symmTablesId,
"Symmetry determination tables",
fileSecId, frow, 0, 1, 1, True)
pyrvapi.rvapi_set_text(" ", fileSecId, frow + 1, 0, 1, 1)
frow += 2
#body.putSection ( symmTablesId,"Symmetry determination tables",True )
table_list = datred_utils.parse_xmlout(pointless_xml())
datred_utils.report(table_list, symmTablesId)
# dump_keyargs = dict(sort_keys=True, indent=4, separators=(',', ': '))
# print json.dumps(datred_utils.tabs_as_dict(tab_list), **dump_keyargs)
if rc.msg:
msg = "\n\n Pointless failed with message:\n\n" + \
rc.msg + \
"\n\n File " + f_orig + \
" cannot be processed.\n\n"
body.file_stdout.write(msg)
body.file_stderr.write(msg)
body.putSummaryLine_red(
f_orig, "UNMERGED",
"Failed to process/import, ignored")
else:
mf = mtz.mtz_file(p_mtzin)
dset_list = datred_utils.point_symm_datasets(
pointless_xml(), f_fmt)
body.summary_row_0 = -1 # to signal the beginning of summary row
for dataset in dset_list:
# make HKL dataset annotation
unmerged = dtype_unmerged.DType(body.job_id)
dataset["symm_summary"] = table_list
unmerged.importUnmergedData(mf, dataset)
body.dataSerialNo += 1
unmerged.makeDName(body.dataSerialNo)
outFileName = unmerged.dataId + ".mtz"
body.file_stdin = open(pointless_script(), 'w')
body.file_stdin.write (
"NAME PROJECT x CRYSTAL y DATASET z\n" + \
"HKLIN " + p_mtzin + "\n" + \
"HKLOUT " + os.path.join(body.outputDir(),outFileName) + "\n" + \
"COPY\n" + \
"ORIGINALLATTICE\n"
)
for offset, first, last in unmerged.dataset.runs:
body.file_stdin.write("RUN 1 FILE 1 BATCH " +
str(first) + " to " +
str(last) + "\n")
body.file_stdin.write("END\n")
body.file_stdin.close()
rc = command.call("pointless", [], "./",
pointless_script(), body.file_stdout,
body.file_stderr, None)
if rc.msg:
msg = "\n\n Pointless failed with message:\n\n" + \
rc.msg + \
"\n\n File " + outFileName + \
" cannot be processed.\n\n"
body.file_stdout.write(msg)
body.file_stderr.write(msg)
body.putSummaryLine_red(
outFileName, "UNMERGED",
"Failed to process/import, ignored")
else:
unmerged.files[0] = outFileName
subSecId = fileSecId
if len(dset_list) > 1:
subSecId = fileSecId + str(k)
pyrvapi.rvapi_add_section(
subSecId,
"Import " + unmerged.dataset.name,
fileSecId, frow, 0, 1, 1, False)
frow += 1
mtzTableId = "unmerged_mtz_" + str(k) + "_table"
unmerged.makeUniqueFNames(body.outputDir())
body.outputDataBox.add_data(unmerged)
makeUnmergedTable(body, mtzTableId, subSecId,
unmerged, 0)
pyrvapi.rvapi_set_text (
" <br><hr/><h3>Created Reflection Data Set (unmerged)</h3>" + \
"<b>Assigned name:</b> " + unmerged.dname + \
"<br> ",subSecId,frow,0,1,1 )
pyrvapi.rvapi_add_data(
"hkl_data_" + str(body.dataSerialNo),
"Unmerged reflections",
# always relative to job_dir from job_dir/html
os.path.join("..", body.outputDir(),
unmerged.files[0]),
"hkl:hkl",
subSecId,
frow + 1,
0,
1,
1,
-1)
frow += 2
if body.summary_row_0 < 0:
body.putSummaryLine(f_orig, "UNMERGED",
unmerged.dname)
else:
body.addSummaryLine("UNMERGED", unmerged.dname)
k += 1
pyrvapi.rvapi_flush()
# move imported file into output directory
os.rename(
p_mtzin,
os.path.join(body.outputDir(), os.path.basename(p_mtzin)))
body.file_stdout.write("... processed: " + f_orig + "\n ")
trace = ''
except:
trace = ''.join(traceback.format_exception(*sys.exc_info()))
body.file_stdout.write(trace)
if trace:
body.fail(trace, 'import failed')
body.rvrow += 1
pyrvapi.rvapi_flush()
return
def run(self):
# Prepare gesamt job
# Just in case (of repeated run) remove the output xyz file. When gesamt
# succeeds, this file is created.
if os.path.isfile(self.gesamt_xyz()):
os.remove(self.gesamt_xyz())
if os.path.isfile(self.gesamt_json()):
os.remove(self.gesamt_json())
# Prepare gesamt input
# fetch input data
xyz = self.input_data.data.xyz
nXYZ = len(xyz)
# make command-line parameters
cmd = []
for i in range(nXYZ):
cmd += [
os.path.join(self.inputDir(), xyz[i].files[0]), "-s",
xyz[i].chainSel
]
if nXYZ < 2:
if not "GESAMT_ARCHIVE" in os.environ:
self.fail ( "<b> *** Error: jsCofe is not configured to work " + \
"with GESAMT Archive</b><br>" + \
"<i> Please look for support</i><br>",
"No GESAMT Archive configured" )
cmd += [
"-archive", os.environ["GESAMT_ARCHIVE"], "-nthreads=auto",
"-min1=" +
self.getParameter(self.task.parameters.sec1.contains.MIN1),
"-min2=" +
self.getParameter(self.task.parameters.sec1.contains.MIN2),
"-trim-size=1", "-trim-Q=" +
self.getParameter(self.task.parameters.sec1.contains.QSCORE),
"--json",
self.gesamt_json()
]
self.rvrow += 1
pyrvapi.rvapi_add_grid(self.progress_grid_id(), False,
self.report_page_id(), self.rvrow, 0, 1, 1)
pyrvapi.rvapi_add_progress_bar(self.progress_bar_id(),
self.progress_grid_id(), 0, 0, 1, 1)
pyrvapi.rvapi_add_text(" ETR: ",
self.progress_grid_id(), 0, 1, 1, 1)
pyrvapi.rvapi_add_label(self.etr_label_id(),
self.progress_grid_id(), "--:--:--", 0, 2,
1, 1)
self.storeReportDocument(self.progress_bar_id() + ";" +
self.etr_label_id())
else:
cmd += [
"-o",
self.gesamt_xyz(), "-o-cs",
self.task.parameters.sec1.contains.MODE.value
]
if nXYZ == 2:
cmd += ["-domains"]
self.putPanel(self.gesamt_report_id())
self.storeReportDocument(
self.gesamt_report_id()) # self.job_id.zfill(4) )
r0 = self.getParameter(self.task.parameters.sec1.contains.R0)
if r0:
cmd += ["-r0=" + r0]
sigma = self.getParameter(self.task.parameters.sec1.contains.SIGMA)
if sigma:
cmd += ["-sigma=" + sigma]
cmd += ["--rvapi-rdoc", self.reportDocumentName()]
# run gesamt
self.runApp("gesamt", cmd)
if nXYZ < 2: # PDB scan
pyrvapi.rvapi_remove_widget(self.progress_grid_id())
pyrvapi.rvapi_reset_task()
pyrvapi.rvapi_flush()
if os.path.isfile(self.gesamt_json()):
hitlist = jsonut.readjObject(self.gesamt_json())
pyrvapi.rvapi_add_table(self.query_table_id(),
"Query structure",
self.report_page_id(), self.rvrow, 0,
1, 1, 0)
pyrvapi.rvapi_put_horz_theader(self.query_table_id(), "Name",
"Structure name", 0)
pyrvapi.rvapi_put_horz_theader(
self.query_table_id(), "Size",
"Structure size in number of residues", 1)
pyrvapi.rvapi_put_table_string(
self.query_table_id(), hitlist.query.file + " (" +
hitlist.query.selection + ")", 0, 0)
pyrvapi.rvapi_put_table_string(self.query_table_id(),
hitlist.query.size, 0, 1)
self.rvrow += 1
self.putMessage(" ")
querySize = float(hitlist.query.size)
nColumns = len(hitlist.columns)
if nColumns < 1 or not hasattr(hitlist.columns[0], "value"):
nHits = 0
elif type(hitlist.columns[0].value) is list:
nHits = min(
len(hitlist.columns[0].value),
self.task.parameters.sec1.contains.MAXHITS.value)
else:
nHits = 1
if nHits < 1:
self.putTitle("No PDB matches found")
self.putMessage(
"<i>Hint:</i> try to reduce report thresholds " +
"(ultimately down to 0) in order to see any hits;<br>"
+
"doing so will increase computation time and report " +
"lower-quality (less relevant) matches.")
else:
self.putSection(self.hits_table_sec_id(), "PDB Hits Table",
False)
pyrvapi.rvapi_add_table(self.hits_table_id(),
"PDB hits found",
self.hits_table_sec_id(), 0, 0, 1,
1, 100)
pyrvapi.rvapi_set_table_type(self.hits_table_id(), True,
True)
pyrvapi.rvapi_set_table_style(self.hits_table_id(), "",
"text-align:center;")
for j in range(nHits):
pyrvapi.rvapi_put_vert_theader(self.hits_table_id(),
str(j + 1),
"Hit number", j)
pyrvapi.rvapi_shape_vert_theader(
self.hits_table_id(), j, "text-align:right;", "",
1, 1)
for i in range(nColumns):
column = hitlist.columns[i]
pyrvapi.rvapi_put_horz_theader(self.hits_table_id(),
column.title,
column.tooltip, i)
if i == 0:
td_css = "font-family:courier;"
elif i == nColumns - 1:
td_css = "text-align:left;font-size:80%;"
pyrvapi.rvapi_shape_horz_theader(
self.hits_table_id(), i, td_css, "", 1, 1)
else:
td_css = ""
for j in range(nHits):
if nHits == 1:
pyrvapi.rvapi_put_table_string(
self.hits_table_id(), column.value, j, i)
else:
pyrvapi.rvapi_put_table_string(
self.hits_table_id(), column.value[j], j,
i)
if td_css:
pyrvapi.rvapi_shape_table_cell(
self.hits_table_id(), j, i, "", td_css, "",
1, 1)
pyrvapi.rvapi_add_button(
"hits_dnl_btn", "Export hit list", "{function}",
"window.parent.downloadJobFile(" +
self.job_id + ",'hits.txt')", False,
self.hits_table_sec_id(), 1, 0, 1, 1)
if nHits > 1:
self.putSection(self.hits_graph_sec_id(),
"Score Plots", False)
pyrvapi.rvapi_add_text("<h3>Alignment scores</h3>",
self.hits_graph_sec_id(), 0, 0,
1, 1)
pyrvapi.rvapi_add_graph(self.hits_graph_id(),
self.hits_graph_sec_id(), 1, 0,
1, 1)
pyrvapi.rvapi_set_graph_size(self.hits_graph_id(), 700,
400)
pyrvapi.rvapi_add_text(" <p><hr/>",
self.hits_graph_sec_id(), 2, 0,
1, 1)
pyrvapi.rvapi_add_text("<h3>Correlation plots</h3>",
self.hits_graph_sec_id(), 3, 0,
1, 1)
pyrvapi.rvapi_add_loggraph(self.corr_graph_id(),
self.hits_graph_sec_id(), 4,
0, 1, 1)
pyrvapi.rvapi_add_graph_data("data",
self.hits_graph_id(),
"Scores")
pyrvapi.rvapi_add_graph_data("data",
self.corr_graph_id(),
"Score correlations")
def addDatasets(ref, name):
pyrvapi.rvapi_add_graph_dataset(
ref, "data", self.hits_graph_id(), name, name)
pyrvapi.rvapi_add_graph_dataset(
ref, "data", self.corr_graph_id(), name, name)
return
addDatasets("hno", "Hit number")
addDatasets("qscore", "Q-score")
addDatasets("rmsd", "R.m.s.d.")
addDatasets("nalign", "Nalign/n0")
addDatasets("seqid", "Seq. Id.")
def addData(ref, value):
pyrvapi.rvapi_add_graph_real(
ref, "data", self.hits_graph_id(), value, "%g")
pyrvapi.rvapi_add_graph_real(
ref, "data", self.corr_graph_id(), value, "%g")
return
for j in range(nHits):
pyrvapi.rvapi_add_graph_int(
"hno", "data", self.hits_graph_id(), j)
addData("qscore",
float(hitlist.columns[2].value[j]))
addData("rmsd", float(hitlist.columns[3].value[j]))
addData(
"nalign",
float(hitlist.columns[4].value[j]) / querySize)
addData("seqid",
float(hitlist.columns[5].value[j]))
pyrvapi.rvapi_add_graph_plot("plot",
self.hits_graph_id(),
"Score profiles",
"Hit number", "Scores")
def addLine(xset, yset, color):
pyrvapi.rvapi_add_plot_line(
"plot", "data", self.hits_graph_id(), xset,
yset)
pyrvapi.rvapi_set_line_options(
yset, "plot", "data", self.hits_graph_id(),
color, "solid", "off", 2.5, True)
return
addLine("hno", "qscore", "#00008B")
addLine("hno", "rmsd", "#8B0000")
addLine("hno", "nalign", "#8B8B00")
addLine("hno", "seqid", "#008B00")
pyrvapi.rvapi_set_plot_legend("plot",
self.hits_graph_id(),
"e", "")
def addPlot(plotId, name, xname, yname, xset, yset,
color):
pyrvapi.rvapi_add_graph_plot(
plotId, self.corr_graph_id(), name, xname,
yname)
pyrvapi.rvapi_add_plot_line(
plotId, "data", self.corr_graph_id(), xset,
yset)
pyrvapi.rvapi_set_line_options(
yset, plotId, "data", self.corr_graph_id(),
color, "off", "filledCircle", 2.5, True)
return
addPlot("p1", "R.m.s.d. vs Seq. Id", "Seq. Id",
"R.m.s.d.", "seqid", "rmsd", "#8B0000")
addPlot("p2", "R.m.s.d. vs Q-score", "Q-score",
"R.m.s.d.", "qscore", "rmsd", "#8B0000")
addPlot("p3", "R.m.s.d. vs Nalign",
"Normalised alignment length", "R.m.s.d.",
"nalign", "rmsd", "#8B0000")
addPlot("p4", "Seq. Id. vs Q-score", "Q-score",
"Seq. Id.", "qscore", "seqid", "#008B00")
addPlot("p5", "Seq. Id. vs Nalign",
"Normalised alignment length", "Seq. Id.",
"nalign", "seqid", "#008B00")
addPlot("p6", "Nalign vs. Q-score", "Q-score",
"Normalised alignment length", "qscore",
"nalign", "#8B8B00")
else:
self.putTitle("No PDB matches found")
else: # pairwise or multiple alignment
self.rvrow += 1
if nXYZ == 2:
outFiles = self.restoreReportDocument().split("\n")
elif nXYZ > 2:
outFiles = [self.gesamt_xyz()]
if len(outFiles) > 0:
self.putTitle("Gesamt Output")
# register output data from temporary location (files will be moved
# to output directory by the registration procedure)
ensemble = self.registerEnsemble(
dtype_template.subtypeProtein(), outFiles[0])
if ensemble:
self.putEnsembleWidget("ensemble_btn",
"Superposed ensemble ",
ensemble, -1)
for i in range(1, len(outFiles) - 1):
self.rvrow += 1
ensemble = self.registerEnsemble(
dtype_template.subtypeProtein(), outFiles[i])
if ensemble:
self.putEnsembleWidget("ensemble_" + str(i) + "_btn",
"Superposed domain #" + str(i),
ensemble, -1)
else:
self.putTitle("No Output Files Generated")
# close execution logs and quit
self.success()
return
def run(body): # body is reference to the main Import class
files_xray = []
for f in body.files_all:
fl = f.lower()
if fl.endswith('.xray.link'):
files_xray.append(f)
if len(files_xray) <= 0:
return
body.file_stdout.write("\n" + "%" * 80 + "\n")
body.file_stdout.write("%%%%% IMPORT X-RAY DIFFRACTION IMAGES\n")
body.file_stdout.write("%" * 80 + "\n")
k = 0
for f in files_xray:
body.files_all.remove(f)
fpath = os.path.join(body.importDir(), f)
file = open(fpath, 'r')
dirpath = file.read()
file.close()
fname = os.path.basename(dirpath)
if os.path.isdir(dirpath):
if k == 0:
xraySecId = "xray_sec_" + str(body.widget_no)
body.widget_no += 1
pyrvapi.rvapi_add_section(xraySecId,
"X-Ray Diffraction Images",
body.report_page_id(), body.rvrow, 0,
1, 1, False)
subSecId = xraySecId
if len(files_xray) > 1:
subSecId = xraySecId + str(k)
pyrvapi.rvapi_add_section(subSecId, "Import " + fname,
xraySecId, k, 0, 1, 1, False)
xray = dtype_xrayimages.DType(body.job_id)
xray.setFile(f) # store link
body.dataSerialNo += 1
xray.makeDName(body.dataSerialNo)
body.outputDataBox.add_data(xray)
xrayTableId = "xray_" + str(k) + "_table"
body.putTable(xrayTableId, "", subSecId, 0)
jrow = 0
if len(files_xray) <= 1:
body.putTableLine(xrayTableId, "File name",
"Imported file name", fname, jrow)
jrow += 1
body.putTableLine(xrayTableId, "Assigned name",
"Assigned data name", xray.dname, jrow)
body.putTableLine(xrayTableId, "Contents", "File contents", "---",
jrow + 1)
os.rename(fpath, os.path.join(body.outputDir(), f))
body.putSummaryLine(fname, "X-Ray Images", xray.dname)
k += 1
else:
body.putSummaryLine_red(fname, "X-Ray Images",
"Directory not found -- ignored")
body.file_stdout.write("... processed: " + fname + "\n")
body.rvrow += 1
pyrvapi.rvapi_flush()
return
def exit_error(*args, **kwargs):
"""Exit on error collecting as much information as we can.
Parameters
----------
message : str, optional
A error message to print
Notes
-----
This previously accepted two arguments of a string to print as an error message and
an exception traceback.
We now just use sys.exch_info() so the messsage argument is no longer required but optional.
While we refactor the code, we'll use *args to get any argument parameters passed in
as the first argument.
"""
# Get the root logger
logger = logging.getLogger()
# An error may have occured before we started logging so we need to create one here
if not logger.handlers:
logging.basicConfig(format='%(message)s\n', level=logging.DEBUG)
logger = logging.getLogger()
exc_type, exc_value, exc_traceback = sys.exc_info()
msg = kwargs.get('message')
if msg is None:
if len(args) >= 1: # Fix for old cases
msg = args[0]
else:
msg = "{0}: {1}".format(exc_type.__name__, exc_value.message)
# header="**** AMPLE ERROR ****\n\n"
header = "*" * 70 + "\n"
header += "*" * 20 + " " * 10 + "AMPLE ERROR" + " " * 10 + "*" * 19 + "\n"
header += "*" * 70 + "\n\n"
# Create the Footer
footer = "\n\n" + "*" * 70 + "\n\n"
# Get the name of the debug log file
debug_log = _debug_logfile(logger)
if debug_log:
footer += "More information may be found in the debug log file: {0}\n".format(
debug_log)
footer += "\nIf you believe that this is an error with AMPLE, please email: [email protected]\n"
footer += "providing as much information as you can about how you ran the program.\n"
if debug_log:
footer += "\nPlease include the debug logfile with your email: {0}\n".format(
debug_log)
# String it all together
msg = header + msg + footer
# Print out main message
logger.critical(msg)
# If we were called without an exception being raised, we just print the current stack
if exc_traceback is None:
traceback_str = "".join(traceback.format_stack())
else:
traceback_str = "".join(
traceback.format_exception(exc_type, exc_value, exc_traceback))
msg = "AMPLE EXITING AT2..." + os.linesep + traceback_str
if debug_log:
logger.debug(msg)
else:
# If we don't have a debug file we want to output the traceback to the console
logger.info(msg)
# Make sure the error widget is updated
if pyrvapi:
pyrvapi.rvapi_flush()
sys.exit(1)
def __init__(self, rvapi_document, webserver_uri, display_gui, logfile, work_dir, ccp4i2_xml=None, tab_prefix=""):
self.rvapi_document = rvapi_document
self.webserver_uri = webserver_uri
self.display_gui = display_gui
self.logfile = logfile
self.work_dir = work_dir
self.ccp4i2 = bool(ccp4i2_xml)
self.tab_prefix = tab_prefix
self.jsrview_dir = None
self._webserver_start = None
self.log_tab_id = None
self.lattice_results_tab_id = None
self.lattice_df = None
self.contaminant_results_tab_id = None
self.contaminant_df = None
self.morda_db_results_tab_id = None
self.morda_db_df = None
self.summary_tab_id = None
self.summary_tab_results_sec_id = None
self.citation_tab_id = None
self.lattice_search_results_displayed = False
self.contaminant_results_displayed = False
self.morda_results_displayed = False
self.jscofe_mode = False
self.ccp4online_mode = False
self.rhs_tab_id = None
self.rvapi_meta = RvapiMetadata()
if self.display_gui or self.ccp4i2:
ccp4 = os.environ["CCP4"]
share_jsrview = os.path.join(ccp4, "share", "jsrview")
if self.rvapi_document:
pyrvapi.rvapi_restore_document2(rvapi_document)
self.rhs_tab_id = pyrvapi.rvapi_get_meta()
self.jscofe_mode = True
self.jsrview_dir = os.path.dirname(rvapi_document)
else:
self.jsrview_dir = os.path.join(work_dir, SIMBAD_PYRVAPI_SHAREDIR)
os.mkdir(self.jsrview_dir)
wintitle = "SIMBAD Results"
if ccp4i2_xml:
self.init_from_ccp4i2_xml(ccp4i2_xml, self.jsrview_dir, share_jsrview, wintitle)
else:
pyrvapi.rvapi_init_document("SIMBAD_results", self.jsrview_dir, wintitle, 1, 7, share_jsrview, None,
None, None, None)
self.rvapi_document = os.path.join(self.jsrview_dir, "index.html")
if webserver_uri:
self._webserver_start = len(self.jsrview_dir) - 7
self.ccp4online_mode = True
elif not ccp4i2_xml:
# We start our own browser
jsrview = os.path.join(ccp4, "libexec", "jsrview")
subprocess.Popen([jsrview, os.path.join(self.jsrview_dir, "index.html")])
pyrvapi.rvapi_add_header("SIMBAD Results")
if os.path.isfile(logfile) and not self.ccp4i2:
self.create_log_tab(logfile)
pyrvapi.rvapi_flush()
def flush(self):
pyrvapi.rvapi_flush()
return
def unsetLogParser(self):
self.file_stdout.flush()
self.log_parser = None
pyrvapi.rvapi_flush()
return
def run(body,
sectionTitle="Macromolecular sequences"
): # body is reference to the main Import class
files_seq = []
for f in body.files_all:
fl = f.lower()
if fl.endswith(('.seq', '.fasta', '.pir')):
files_seq.append(f)
if len(files_seq) <= 0:
return
annotation = None
try:
f = open('annotation.json', 'r')
annotation = jsonut.jObject(f.read()).annotation
except:
pass
body.file_stdout.write("\n" + "%" * 80 + "\n")
body.file_stdout.write("%%%%% IMPORT OF SEQUENCES\n")
body.file_stdout.write("%" * 80 + "\n")
if not annotation:
body.file_stdout.write(
"\n ******** Sequence annotation file NOT FOUND OR CORRUPT (error)\n"
)
body.file_stderr.write(
"\n ******** Sequence annotation file NOT FOUND OR CORRUPT (error)\n"
)
return
seqSecId = "seq_sec_" + str(body.widget_no)
body.widget_no += 1
pyrvapi.rvapi_add_section(seqSecId, sectionTitle, body.report_page_id(),
body.rvrow, 0, 1, 1, False)
k = 0
for f in files_seq:
body.files_all.remove(f)
annot = None
for a in annotation:
for item in a.items:
if item.rename == f:
annot = item
if not annot:
body.file_stdout.write(
"\n ******** Sequence annotation file DOES NOT MATCH UPLOAD (error)\n"
)
body.file_stderr.write(
"\n ******** Sequence annotation file DOES NOT MATCH UPLOAD (error)\n"
)
return
subSecId = seqSecId
if len(files_seq) > 1:
subSecId = seqSecId + str(k)
pyrvapi.rvapi_add_section(subSecId, "Import " + f, seqSecId, k, 0,
1, 1, False)
seq = dtype_sequence.DType(body.job_id)
seq.addSubtype(annot.type)
seq.setFile(f)
seq.convert2Seq(body.importDir(), body.outputDir())
body.dataSerialNo += 1
seq.makeDName(body.dataSerialNo)
os.rename(os.path.join(body.importDir(), f),
os.path.join(body.outputDir(), f))
seq.makeUniqueFNames(body.outputDir())
body.outputDataBox.add_data(seq)
seqTableId = "seq_" + str(k) + "_table"
body.putTable(seqTableId, "", subSecId, 0)
body.putTableLine(seqTableId, "File name", "Imported file name", f, 0)
body.putTableLine(seqTableId, "Assigned name", "Assigned data name",
seq.dname, 1)
body.putTableLine(seqTableId, "Type", "Polymer type", seq.subtype[0],
2)
lines = filter(None, (line.rstrip() for line in open(
os.path.join(body.outputDir(), seq.files[0]), "r")))
htmlLine = ""
body.file_stdout.write("\n")
weights = aaWeight
if annot.type != "protein":
weights = naWeight
for i in range(0, len(lines)):
if i > 0:
body.file_stdout.write(" ")
#body.file_stdout.write ( lines[i] + "\n" )
if i > 0:
htmlLine += "<br>"
seq.size += len(lines[i].strip())
for j in range(len(lines[i])):
if lines[i][j] in weights:
seq.weight += weights[lines[i][j]]
htmlLine += lines[i]
body.putTableLine(seqTableId, "Contents", "Data contents", htmlLine, 3)
body.putTableLine(seqTableId, "Length ", "Sequence length",
str(seq.size), 4)
body.putTableLine(seqTableId, "Weight ", "Molecular weight",
str(seq.weight), 5)
body.putSummaryLine(f, "SEQ", seq.dname)
body.file_stdout.write("\n... processed: " + f + "\n ")
k += 1
body.rvrow += 1
pyrvapi.rvapi_flush()
return
def __init__(self, rvapi_document, webserver_uri, display_gui, logfile, work_dir, ccp4i2_xml=None, tab_prefix=""):
self.rvapi_document = rvapi_document
self.webserver_uri = webserver_uri
self.display_gui = display_gui
self.logfile = logfile
self.work_dir = work_dir
self.ccp4i2 = bool(ccp4i2_xml)
self.tab_prefix = tab_prefix
self.jsrview_dir = None
self._webserver_start = None
self.log_tab_id = None
self.lattice_results_tab_id = None
self.lattice_df = None
self.contaminant_results_tab_id = None
self.contaminant_df = None
self.morda_db_results_tab_id = None
self.morda_db_df = None
self.summary_tab_id = None
self.summary_tab_results_sec_id = None
self.lattice_search_results_displayed = False
self.contaminant_results_displayed = False
self.morda_results_displayed = False
self.jscofe_mode = False
self.rhs_tab_id = None
self.rvapi_meta = RvapiMetadata()
if self.display_gui or self.ccp4i2:
ccp4 = os.environ["CCP4"]
share_jsrview = os.path.join(ccp4, "share", "jsrview")
if self.rvapi_document:
pyrvapi.rvapi_restore_document2(rvapi_document)
self.rhs_tab_id = pyrvapi.rvapi_get_meta()
self.jscofe_mode = True
self.jsrview_dir = os.path.dirname(rvapi_document)
else:
self.jsrview_dir = os.path.join(work_dir, SIMBAD_PYRVAPI_SHAREDIR)
os.mkdir(self.jsrview_dir)
wintitle = "SIMBAD Results"
if ccp4i2_xml:
self.init_from_ccp4i2_xml(ccp4i2_xml, self.jsrview_dir, share_jsrview, wintitle)
else:
pyrvapi.rvapi_init_document("SIMBAD_results", self.jsrview_dir, wintitle, 1, 7, share_jsrview, None,
None, None, None)
self.rvapi_document = os.path.join(self.jsrview_dir, "index.html")
if webserver_uri:
self._webserver_start = len(self.jsrview_dir) + 1
elif not ccp4i2_xml:
# We start our own browser
jsrview = os.path.join(ccp4, "libexec", "jsrview")
subprocess.Popen([jsrview, os.path.join(self.jsrview_dir, "index.html")])
pyrvapi.rvapi_add_header("SIMBAD Results")
if os.path.isfile(logfile) and not self.ccp4i2:
self.create_log_tab(logfile)
pyrvapi.rvapi_flush()
