def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
history = out_data.items()[0][1].history
if history == None:
print "unknown history!"
return
kingdom = param_dict.get('kingdom',None)
group = param_dict.get('group',None)
org = param_dict.get('org',None)
if not (kingdom or group or org):
print "Parameters are not available."
new_stdout = ""
split_stdout = stdout.split("\n")
basic_name = ""
for line in split_stdout:
fields = line.split("\t")
if fields[0] == "#File1":
description = fields[1]
chr = fields[2]
dbkey = fields[3]
file_type = fields[4]
name, data = out_data.items()[0]
basic_name = data.name
data.name = data.name + " (" + microbe_info[kingdom][group][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][group][org]['name']+":"+chr + ")"
data.dbkey = dbkey
data.info = data.name
datatypes.change_datatype( data, file_type )
data.init_meta()
data.set_peek()
app.model.flush()
elif fields[0] == "#NewFile":
description = fields[1]
chr = fields[2]
dbkey = fields[3]
filepath = fields[4]
file_type = fields[5]
newdata = app.model.Dataset()
newdata.extension = file_type
newdata.name = basic_name + " (" + microbe_info[kingdom][group][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][group][org]['name']+":"+chr + ")"
newdata.flush()
history.add_dataset( newdata )
newdata.flush()
app.model.flush()
try:
copyfile(filepath,newdata.file_name)
newdata.info = newdata.name
newdata.state = jobs.JOB_OK
except:
newdata.info = "The requested file is missing from the system."
newdata.state = jobs.JOB_ERROR
newdata.dbkey = dbkey
newdata.init_meta()
newdata.set_peek()
#
app.model.flush()
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout,
stderr):
history = out_data.items()[0][1].history
if history == None:
print "unknown history!"
return
new_stdout = ""
split_stdout = stdout.split("\n")
basic_name = ""
for line in split_stdout:
fields = line.split("\t")
if fields[0] == "#File1":
description = fields[1]
dbkey = fields[2]
file_type = fields[3]
name, data = out_data.items()[0]
basic_name = data.name
data.name = data.name + " (" + description + ")"
data.dbkey = dbkey
data.info = data.name
datatypes.change_datatype(data, file_type)
data.init_meta()
data.set_peek()
app.model.flush()
elif fields[0] == "#NewFile":
description = fields[1]
dbkey = fields[2]
filepath = fields[3]
file_type = fields[4]
newdata = app.model.Dataset()
newdata.extension = file_type
newdata.name = basic_name + " (" + description + ")"
newdata.flush()
history.add_dataset(newdata)
newdata.flush()
app.model.flush()
try:
copyfile(filepath, newdata.file_name)
newdata.info = newdata.name
newdata.state = jobs.JOB_OK
except:
newdata.info = "The requested file is missing from the system."
newdata.state = jobs.JOB_ERROR
newdata.dbkey = dbkey
newdata.init_meta()
newdata.set_peek()
#
app.model.flush()
def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
"""Sets the name of the data"""
outputType = param_dict.get( 'hgta_outputType', None )
if isinstance(outputType, list) and len(outputType)>0: outputType = outputType[-1]
items = out_data.items()
for name, data in items:
data.name = param_dict.get('display', data.name)
data.dbkey = param_dict.get('dbkey', '???')
if outputType == 'wigData':
ext = "wig"
elif outputType == 'maf':
ext = "maf"
elif outputType == 'gff':
ext = "gff"
else:
if 'hgta_doPrintSelectedFields' in param_dict:
ext = "interval"
elif 'hgta_doGetBed' in param_dict:
ext = "bed"
elif 'hgta_doGenomicDna' in param_dict:
ext = "fasta"
elif 'hgta_doGenePredSequence' in param_dict:
ext = "fasta"
else:
ext = "interval"
data = datatypes.change_datatype(data, ext)
out_data[name] = data
def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
"""Verifies the data after the run"""
items = out_data.items()
for name, data in items:
try:
err_msg, err_flag = 'Errors:', False
line_count = 0
num_lines = len(file(data.file_name).readlines())
for line in file(data.file_name):
line_count += 1
if line and line[0] == '-':
if line_count + 3 == num_lines and not err_flag:
err_flag = True
err_msg = "Warning: It appears that your results have been truncated by UCSC. View the bottom of your result file for details."
break
err_flag = True
err_msg = err_msg +" (line "+str(line_count)+")"+line
data.set_peek()
if isinstance(data.datatype, datatypes.interval.Interval) and data.missing_meta():
data = datatypes.change_datatype(data, 'tabular')
out_data[name] = data
if err_flag:
raise Exception(err_msg)
except Exception, exc:
data.info = data.info + "\n" + str(exc)
data.blurb = "error"
def exec_after_process(app, inp_data, out_data, param_dict,tool, stdout, stderr):
ext = param_dict.get('out_format', 'html')
items = out_data.items()
for name, data in items:
data = datatypes.change_datatype(data, ext)
data.flush()
app.model.flush()
def exec_before_job(trans, inp_data, out_data, param_dict, tool=None):
"""Sets the name of the data"""
outputType = param_dict.get('hgta_outputType', None)
if isinstance(outputType, list) and len(outputType) > 0:
outputType = outputType[-1]
items = out_data.items()
for name, data in items:
data.name = param_dict.get('display', data.name)
data.dbkey = param_dict.get('dbkey', '???')
if outputType == 'wigData':
ext = "wig"
elif outputType == 'maf':
ext = "maf"
elif outputType == 'gff':
ext = "gff"
else:
if 'hgta_doPrintSelectedFields' in param_dict:
ext = "interval"
elif 'hgta_doGetBed' in param_dict:
ext = "bed"
elif 'hgta_doGenomicDna' in param_dict:
ext = "fasta"
elif 'hgta_doGenePredSequence' in param_dict:
ext = "fasta"
else:
ext = "interval"
data = datatypes.change_datatype(data, ext)
out_data[name] = data
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
history = out_data.items()[0][1].history
if history == None:
print "unknown history!"
return
new_stdout = ""
split_stdout = stdout.split("\n")
basic_name = ""
for line in split_stdout:
fields = line.split("\t")
if fields[0] == "#File1":
description = fields[1]
dbkey = fields[2]
file_type = fields[3]
name, data = out_data.items()[0]
basic_name = data.name
data.name = data.name + " (" + description + ")"
data.dbkey = dbkey
data.info = data.name
datatypes.change_datatype(data, file_type)
data.init_meta()
data.set_peek()
app.model.flush()
elif fields[0] == "#NewFile":
description = fields[1]
dbkey = fields[2]
filepath = fields[3]
file_type = fields[4]
newdata = app.model.Dataset()
newdata.extension = file_type
newdata.name = basic_name + " (" + description + ")"
newdata.flush()
history.add_dataset(newdata)
newdata.flush()
app.model.flush()
try:
copyfile(filepath, newdata.file_name)
newdata.info = newdata.name
newdata.state = jobs.JOB_OK
except:
newdata.info = "The requested file is missing from the system."
newdata.state = jobs.JOB_ERROR
newdata.dbkey = dbkey
newdata.init_meta()
newdata.set_peek()
#
app.model.flush()
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout,
stderr):
ext = param_dict.get('out_format', 'html')
items = out_data.items()
for name, data in items:
data = datatypes.change_datatype(data, ext)
data.flush()
app.model.flush()
def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
"""Sets the name of the data"""
data_name = param_dict.get( 'name', 'Biomart query' )
data_type = param_dict.get( 'type', 'text' )
name, data = out_data.items()[0]
data = datatypes.change_datatype(data, data_type)
data.name = data_name
out_data[name] = data
def exec_before_job(trans, inp_data, out_data, param_dict, tool=None):
"""Sets the name of the data"""
data_name = param_dict.get('name', 'Biomart query')
data_type = param_dict.get('type', 'text')
name, data = out_data.items()[0]
data = datatypes.change_datatype(data, data_type)
data.name = data_name
out_data[name] = data
def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr):
#Properly set file formats before job run
#def exec_before_job(trans, inp_data, out_data, param_dict,tool):
#why isn't items an ordered list?
items = out_data.items()
#lets sort it ourselves....
items = sorted(items, key=operator.itemgetter(0))
#items is now sorted...
#normal filetype correction
data_count=1
for name, data in items:
outputType = param_dict.get( 'out_format'+str(data_count), None )
#print "data_count",data_count, "name", name, "outputType", outputType
if outputType !=None:
if outputType == 'ncbi':
outputType = "fasta"
elif outputType == 'excel':
outputType = "Tabular"
elif outputType == 'text':
outputType = "txt"
data = datatypes.change_datatype(data, outputType)
data.flush()
data_count+=1
#html filetype correction
data_count=1
for name, data in items:
wants_plot = param_dict.get( 'html_out'+str(data_count), None )
ext = "html"
if wants_plot == "yes":
data = datatypes.change_datatype(data, ext)
data.flush()
data_count+=1
#png file correction
data_count=1
for name, data in items:
wants_plot = param_dict.get( 'plot'+str(data_count), None )
ext = "png"
if wants_plot == "yes":
data = datatypes.change_datatype(data, ext)
data.flush()
data_count+=1
def copy_dataset(self, src, parent_id=None):
des = self.app.model.Dataset()
des.flush()
des = datatypes.change_datatype(des, src.ext)
des.name = src.name
des.info = src.info
des.blurb = src.blurb
des.peek = src.peek
des.extension = src.extension
des.dbkey = src.dbkey
des.state = src.state
des.metadata = src.metadata
des.hid = src.hid
des.parent_id = parent_id
shutil.copyfile(src.file_name,des.file_name)
des.hid = src.hid
des.designation = src.designation
des.flush()
return des
def copy_dataset(self, src, parent_id=None):
des = self.app.model.Dataset()
des.flush()
des = datatypes.change_datatype(des, src.ext)
des.name = src.name
des.info = src.info
des.blurb = src.blurb
des.peek = src.peek
des.extension = src.extension
des.dbkey = src.dbkey
des.state = src.state
des.metadata = src.metadata
des.hid = src.hid
des.parent_id = parent_id
shutil.copyfile(src.file_name, des.file_name)
des.hid = src.hid
des.designation = src.designation
des.flush()
return des
def exec_after_process(app,
inp_data,
out_data,
param_dict,
tool=None,
stdout=None,
stderr=None):
"""Verifies the data after the run"""
items = out_data.items()
for name, data in items:
try:
err_msg, err_flag = 'Errors:', False
line_count = 0
num_lines = len(file(data.file_name).readlines())
for line in file(data.file_name):
line_count += 1
if line and line[0] == '-':
if line_count + 3 == num_lines and not err_flag:
err_flag = True
err_msg = "Warning: It appears that your results have been truncated by UCSC. View the bottom of your result file for details."
break
err_flag = True
err_msg = err_msg + " (line " + str(
line_count) + ")" + line
data.set_peek()
if isinstance(data.datatype,
datatypes.interval.Interval) and data.missing_meta():
data = datatypes.change_datatype(data, 'tabular')
out_data[name] = data
if err_flag:
raise Exception(err_msg)
except Exception, exc:
data.info = data.info + "\n" + str(exc)
data.blurb = "error"
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout,
stderr):
for name, data in out_data.items():
if data.ext == "bed":
data = datatypes.change_datatype(data, "interval")
data.flush()
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout,
stderr):
history = out_data.items()[0][1].history
if history == None:
print "unknown history!"
return
kingdom = param_dict.get('kingdom', None)
group = param_dict.get('group', None)
org = param_dict.get('org', None)
if not (kingdom or group or org):
print "Parameters are not available."
new_stdout = ""
split_stdout = stdout.split("\n")
basic_name = ""
for line in split_stdout:
fields = line.split("\t")
if fields[0] == "#File1":
description = fields[1]
chr = fields[2]
dbkey = fields[3]
file_type = fields[4]
name, data = out_data.items()[0]
basic_name = data.name
data.name = data.name + " (" + microbe_info[kingdom][group][org][
'chrs'][chr]['data'][description][
'feature'] + " for " + microbe_info[kingdom][group][org][
'name'] + ":" + chr + ")"
data.dbkey = dbkey
data.info = data.name
datatypes.change_datatype(data, file_type)
data.init_meta()
data.set_peek()
app.model.flush()
elif fields[0] == "#NewFile":
description = fields[1]
chr = fields[2]
dbkey = fields[3]
filepath = fields[4]
file_type = fields[5]
newdata = app.model.Dataset()
newdata.extension = file_type
newdata.name = basic_name + " (" + microbe_info[kingdom][group][
org]['chrs'][chr]['data'][description][
'feature'] + " for " + microbe_info[kingdom][group][org][
'name'] + ":" + chr + ")"
newdata.flush()
history.add_dataset(newdata)
newdata.flush()
app.model.flush()
try:
copyfile(filepath, newdata.file_name)
newdata.info = newdata.name
newdata.state = jobs.JOB_OK
except:
newdata.info = "The requested file is missing from the system."
newdata.state = jobs.JOB_ERROR
newdata.dbkey = dbkey
newdata.init_meta()
newdata.set_peek()
#
app.model.flush()
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
for name, data in out_data.items():
if data.ext == "bed":
data = datatypes.change_datatype(data, "interval")
data.flush()
