def build_report(report_data, request_data, report_property, sections):
""" Assembles report home folder, configures DRMAA and R related files
and spawns a new process for reports DRMAA job on cluster.
:param report_data: report info dictionary
:type report_data: dict
:param request_data: a copy of request object
:type request_data: HTTPrequest
:param report_property: report property form
:type report_property: breezeForms.ReportPropsForm
:param sections: a list of 'Rscripts' db objects
:type sections: list
:return: True
:rtype: bool
"""
from breeze.models import Project, UserProfile, ReportType, Report, ComputeTarget
from django.contrib.auth.models import User
log = logger.getChild('build_report')
assert isinstance(log, logging.getLoggerClass())
assert isinstance(request_data.user, User)
# get the request ReportType
rt = ReportType.objects.get(type=report_data['report_type'])
# list of users that will have access to this report
shared_users = aux.extract_users(request_data.POST.get('Groups'),
request_data.POST.get('Individuals'))
if shared_users == list() and request_data.POST.get('shared'):
shared_users = request_data.POST.getlist('shared')
# author
the_user = request_data.user
the_user.prof = UserProfile.objects.get(user=the_user)
assert isinstance(the_user.prof, UserProfile)
# target profile :
target = ComputeTarget.objects.get(pk=request_data.POST.get('target'))
assert target.id in rt.ready_id_list # TODO make a validator in the form section
# create initial instance so that we can use its db id
dbitem = Report(
_type=rt,
_name=report_data['instance_name'],
_author=the_user,
project=Project.objects.get(id=request_data.POST.get('project')),
_institute=the_user.prof.institute_info,
_breeze_stat=JobStat.INIT,
target=target,
rora_id=report_data['instance_id'])
dbitem.assemble(request_data=request_data,
shared_users=shared_users,
sections=sections)
dbitem.submit_to_cluster()
return True
def build_report(report_data, request_data, report_property, sections):
""" Assembles report home folder, configures DRMAA and R related files
and spawns a new process for reports DRMAA job on cluster.
:param report_data: report info dictionary
:type report_data: dict
:param request_data: a copy of request object
:type request_data: HTTPrequest
:param report_property: report property form
:type report_property: breezeForms.ReportPropsForm
:param sections: a list of 'Rscripts' db objects
:type sections: list
:return: True
:rtype: bool
"""
from breeze.models import Project, UserProfile, ReportType, Report
from django.contrib.auth.models import User
log = logger.getChild("build_report")
assert isinstance(log, logging.getLoggerClass())
assert isinstance(request_data.user, User)
# get the request ReportType
rt = ReportType.objects.get(type=report_data["report_type"])
# list of users that will have access to this report
shared_users = aux.extract_users(request_data.POST.get("Groups"), request_data.POST.get("Individuals"))
if shared_users == list() and request_data.POST.get("shared"):
shared_users = request_data.POST.getlist("shared")
# author
the_user = request_data.user
the_user.prof = UserProfile.objects.get(user=the_user)
assert isinstance(the_user.prof, UserProfile)
# create initial instance so that we can use its db id
dbitem = Report(
_type=rt,
_name=report_data["instance_name"],
_author=the_user,
project=Project.objects.get(id=request_data.POST.get("project")),
_institute=the_user.prof.institute_info,
_breeze_stat=JobStat.INIT,
rora_id=report_data["instance_id"],
)
dbitem.assemble(request_data=request_data, shared_users=shared_users, sections=sections)
dbitem.submit_to_cluster()
return True
def build_report(report_data, request_data, report_property, sections):
""" Assembles report home folder, configures DRMAA and R related files
and spawns a new process for reports DRMAA job on cluster.
:param report_data: report info dictionary
:type report_data: dict
:param request_data: a copy of request object
:type request_data: HTTPrequest
:param report_property: report property form
:type report_property: breezeForms.ReportPropsForm
:param sections: a list of 'Rscripts' db objects
:type sections: list
:return: True
:rtype: bool
"""
from breeze.models import Project, UserProfile, ReportType, Report, ComputeTarget
from django.contrib.auth.models import User
log = logger.getChild("build_report")
assert isinstance(log, logging.getLoggerClass())
assert isinstance(request_data.user, User)
# get the request ReportType
rt = ReportType.objects.get(type=report_data["report_type"])
# list of users that will have access to this report
shared_users = aux.extract_users(request_data.POST.get("Groups"), request_data.POST.get("Individuals"))
if shared_users == list() and request_data.POST.get("shared"):
shared_users = request_data.POST.getlist("shared")
# author
the_user = request_data.user
the_user.prof = UserProfile.objects.get(user=the_user)
assert isinstance(the_user.prof, UserProfile)
# target profile :
from django.core.exceptions import ObjectDoesNotExist
target_id = request_data.POST.get("target")
try:
# target = ComputeTarget.objects.get_ready().filter(pk=target_id)
target = ComputeTarget.objects.get(pk=target_id)
except ObjectDoesNotExist:
from django.contrib import messages
messages.add_message(request_data, messages.ERROR, "No such target %s" % target_id)
return False
if not target.is_ready:
from django.contrib import messages
messages.add_message(request_data, messages.ERROR, "target %s is either disable or not ready" % target)
return False
# target = ComputeTarget.objects.get(pk=request_data.POST.get('target'))
# if target.id not in rt.ready_id_list: # TODO make a validator in the form section
# if target not in ComputeTarget.objects.ready():
# from django.contrib import messages
# messages.add_message(request_data, messages.INFO, 'target %s is either disable or not ready' % target)
# return False
# create initial instance so that we can use its db id
dbitem = Report(
_type=rt,
_name=report_data["instance_name"],
_author=the_user,
project=Project.objects.get(id=request_data.POST.get("project")),
_institute=the_user.prof.institute_info,
_breeze_stat=JobStat.INIT,
target=target,
rora_id=report_data["instance_id"],
)
dbitem.assemble(request_data=request_data, shared_users=shared_users, sections=sections)
dbitem.submit_to_cluster()
return True
def build_report(report_data, request_data, report_property, sections):
""" Assembles report home folder, configures DRMAA and R related files
and spawns a new process for reports DRMAA job on cluster.
Arguments:
report_data -- report info dictionary
request_data -- a copy of request object
report_property -- report property form
sections -- a list of 'Rscripts' db objects
"""
# 'report_name' - report's headline
rt = breeze.models.ReportType.objects.get(type=report_data['report_type'])
report_name = report_data['report_type'] + ' Report' + ' :: ' + report_data[
'instance_name'] + ' <br> ' + str(rt.description)
# This trick is to extract users's names from the form
# buddies = list()
# for e in list(report_property.cleaned_data['share']):
# buddies.append( str(e) )
# shared_users = breeze.models.User.objects.filter(username__in=buddies)
shared_users = aux.extract_users(request_data.POST.get('Groups'),
request_data.POST.get('Individuals'))
insti = breeze.models.UserProfile.objects.get(
user=request_data.user).institute_info
# create initial instance so that we can use its db id
dbitem = breeze.models.Report(
type=breeze.models.ReportType.objects.get(
type=report_data['report_type']),
name=str(report_data['instance_name']),
author=request_data.user,
progress=0,
project=breeze.models.Project.objects.get(
id=request_data.POST.get('project')),
institute=insti
# project=breeze.models.Project.objects.get(name=report_property.cleaned_data['Project'])
)
dbitem.save()
if shared_users:
dbitem.shared = shared_users
# define location: that is report's folder name
path = slugify(
str(dbitem.id) + '_' + dbitem.name + '_' + dbitem.author.username)
loc = str(settings.MEDIA_ROOT) + str("reports/") + path
dochtml = loc + '/report'
dbitem.home = str("reports/") + path
dbitem.save()
# BUILD R-File
script_string = 'setwd(\"%s\")\n' % loc
script_string += 'require( Nozzle.R1 )\n\n'
script_string += 'path <- \"%s\"\n' % loc
script_string += 'report_name <- \"%s\"\n' % report_name
# define a function for exception handler
script_string += 'failed_fun_print <- function(section_name, error_report){\n'
script_string += ' Error_report_par <- newParagraph("<br>", asStrong( "Error Log Details: " ),"<br><br>",asCode(paste(error_report,collapse=""))); \n'
script_string += ' section_name <- addTo( section_name, newParagraph( "This section FAILED! Contact the development team... " ), Error_report_par )\n'
script_string += ' return (section_name)\n}\n\n'
script_string += dump_project_parameters(dbitem.project, dbitem)
script_string += dump_pipeline_config(rt, report_data['instance_id'])
script_string += 'REPORT <- newCustomReport(report_name)\n'
dummy_flag = False
for tag in sections:
secID = 'Section_dbID_' + str(tag.id)
if secID in request_data.POST and request_data.POST[secID] == '1':
tree = xml.parse(str(settings.MEDIA_ROOT) + str(tag.docxml))
script_string += '##### TAG: %s #####\n' % tag.name
if tag.name == "Import to FileMaker":
dummy_flag = True
# source main code segment
code_path = str(settings.MEDIA_ROOT) + str(tag.code)
script_string += '# <---------- body ----------> \n' + open(
code_path, 'r').read() + '\n'
script_string += '# <------- end of body --------> \n'
# input parameters definition
script_string += '# <---------- parameters ----------> \n'
script_string += gen_params_string(
tree, request_data.POST,
str(settings.MEDIA_ROOT) + dbitem.home, request_data.FILES)
script_string += '# <------- end of parameters --------> \n'
# final step - fire header
header_path = str(settings.MEDIA_ROOT) + str(tag.header)
script_string += '# <---------- header ----------> \n' + open(
header_path, 'r').read() + '\n\n'
script_string += 'new_section <- newSection( section_name )\n'
script_string += 'tag_section <- tryCatch({section_body(new_section)}, error = function(e){ failed_fun_print(new_section,e) })\n'
script_string += 'REPORT <- addTo( REPORT, tag_section )\n'
script_string += '# <------- end of header --------> \n'
script_string += '##### END OF TAG #####\n\n\n'
script_string += 'setwd(\"%s\")\n' % loc
else: # if tag disabled - do nothing
pass
# render report to file
script_string += '# Render the report to a file\n' + 'writeReport( REPORT, filename=toString(\"%s\"))\n' % dochtml
script_string += 'system("chmod -R 770 .")'
# save r-file
dbitem.rexec.save('script.r', base.ContentFile(script_string))
dbitem.save()
# configure shell-file
config_path = loc + '/sgeconfig.sh'
config = open(config_path, 'w')
# config should be executble
st = os.stat(config_path)
os.chmod(config_path, st.st_mode | stat.S_IEXEC)
command = '#!/bin/bash \n' + str(
settings.R_ENGINE_PATH) + 'CMD BATCH --no-save ' + str(
settings.MEDIA_ROOT) + str(dbitem.rexec)
config.write(command)
config.close()
# open report's folder for others
st = os.stat(loc)
os.chmod(loc, st.st_mode | stat.S_IRWXG)
# submit r-code
p = Process(target=run_report, args=(dbitem, dummy_flag))
#print(dbitem)
#run_report(dbitem,dummy_flag)
p.start()
return True
def build_report(report_data, request_data, report_property, sections):
""" Assembles report home folder, configures DRMAA and R related files
and spawns a new process for reports DRMAA job on cluster.
Arguments:
report_data -- report info dictionary
request_data -- a copy of request object
report_property -- report property form
sections -- a list of 'Rscripts' db objects
"""
# 'report_name' - report's headline
rt = breeze.models.ReportType.objects.get(type=report_data['report_type'])
report_name = report_data['report_type'] + ' Report' + ' :: ' + report_data['instance_name'] + ' <br> ' + str(rt.description)
# This trick is to extract users's names from the form
# buddies = list()
# for e in list(report_property.cleaned_data['share']):
# buddies.append( str(e) )
# shared_users = breeze.models.User.objects.filter(username__in=buddies)
shared_users = aux.extract_users(request_data.POST.get('Groups'), request_data.POST.get('Individuals'))
insti = breeze.models.UserProfile.objects.get(user=request_data.user).institute_info
# create initial instance so that we can use its db id
dbitem = breeze.models.Report(
type=breeze.models.ReportType.objects.get(type=report_data['report_type']),
name=str(report_data['instance_name']),
author=request_data.user,
progress=0,
project=breeze.models.Project.objects.get(id=request_data.POST.get('project')),
institute=insti
# project=breeze.models.Project.objects.get(name=report_property.cleaned_data['Project'])
)
dbitem.save()
if shared_users:
dbitem.shared = shared_users
# define location: that is report's folder name
path = slugify(str(dbitem.id) + '_' + dbitem.name + '_' + dbitem.author.username)
loc = str(settings.MEDIA_ROOT) + str("reports/") + path
dochtml = loc + '/report'
dbitem.home = str("reports/") + path
dbitem.save()
# BUILD R-File
script_string = 'setwd(\"%s\")\n' % loc
script_string += 'require( Nozzle.R1 )\n\n'
script_string += 'path <- \"%s\"\n' % loc
script_string += 'report_name <- \"%s\"\n' % report_name
# define a function for exception handler
script_string += 'failed_fun_print <- function(section_name){\n'
script_string += ' section_name <- addTo( section_name, newParagraph( "This section FAILED! Contact the development team... " ) )\n'
script_string += ' return (section_name)\n}\n\n'
script_string += dump_project_parameters(dbitem.project, dbitem)
script_string += dump_pipeline_config(rt, report_data['instance_id'])
script_string += 'REPORT <- newCustomReport(report_name)\n'
for tag in sections:
secID = 'Section_dbID_' + str(tag.id)
if secID in request_data.POST and request_data.POST[secID] == '1':
tree = xml.parse(str(settings.MEDIA_ROOT) + str(tag.docxml))
script_string += '##### TAG: %s #####\n' % tag.name
# source main code segment
code_path = str(settings.MEDIA_ROOT) + str(tag.code)
script_string += '# <---------- body ----------> \n' + open(code_path, 'r').read() + '\n'
script_string += '# <------- end of body --------> \n'
# input parameters definition
script_string += '# <---------- parameters ----------> \n'
script_string += gen_params_string(tree, request_data.POST, str(settings.MEDIA_ROOT) + dbitem.home, request_data.FILES)
script_string += '# <------- end of parameters --------> \n'
# final step - fire header
header_path = str(settings.MEDIA_ROOT) + str(tag.header)
script_string += '# <---------- header ----------> \n' + open(header_path, 'r').read() + '\n\n'
script_string += 'new_section <- newSection( section_name )\n'
script_string += 'tag_section <- tryCatch({section_body(new_section)}, error = function(e){ failed_fun_print(new_section) })\n'
script_string += 'REPORT <- addTo( REPORT, tag_section )\n'
script_string += '# <------- end of header --------> \n'
script_string += '##### END OF TAG #####\n\n\n'
script_string += 'setwd(\"%s\")\n' % loc
else: # if tag disabled - do nothing
pass
# render report to file
script_string += '# Render the report to a file\n' + 'writeReport( REPORT, filename=toString(\"%s\"))\n' % dochtml
script_string += 'system("chmod -R 770 .")'
# save r-file
dbitem.rexec.save('script.r', base.ContentFile(script_string))
dbitem.save()
# configure shell-file
config_path = loc + '/sgeconfig.sh'
config = open(config_path, 'w')
# config should be executble
st = os.stat(config_path)
os.chmod(config_path, st.st_mode | stat.S_IEXEC)
command = '#!/bin/bash \n' + str(settings.R_ENGINE_PATH) + 'CMD BATCH --no-save ' + str(settings.MEDIA_ROOT) + str(dbitem.rexec)
config.write(command)
config.close()
# open report's folder for others
st = os.stat(loc)
os.chmod(loc, st.st_mode | stat.S_IRWXG)
# submit r-code
p = Process(target=run_report, args=(dbitem,))
p.start()
return True
