class BcbioPBSPROEngineSetLauncher(PBSPROLauncher,
launcher.BatchClusterAppMixin):
"""Launch Engines using PBSPro"""
batch_file_name = Unicode(u'pbspro_engines',
config=True,
help="batch file name for the engine(s) job.")
tag = traitlets.Unicode("", config=True)
cores = traitlets.Integer(1, config=True)
mem = traitlets.Unicode("", config=True)
array_cmd = traitlets.Unicode("", config=True)
default_template = Unicode(u"""#!/bin/sh
#PBS -V
#PBS -N {tag}-e
{resources}
{array_cmd}
cd $PBS_O_WORKDIR
%s %s --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote,
engine_cmd_argv)), ' '.join(timeout_params)))
def start(self, n):
"""Start n engines by profile or profile_dir."""
resources = "#PBS -l select=1:ncpus=%d" % self.cores
if self.mem:
resources += ":mem=%smb" % int(float(self.mem) * 1024)
self.context["resources"] = resources
self.context["cores"] = self.cores
self.context["tag"] = self.tag if self.tag else "bcbio"
self.context["array_cmd"] = "" if n == 1 else "#PBS -J 1-%i" % n
return super(BcbioPBSPROEngineSetLauncher, self).start(n)
class BcbioTORQUEControllerLauncher(TORQUELauncher,
launcher.BatchClusterAppMixin):
"""Launch a controller using Torque."""
batch_file_name = Unicode(unicode("torque_controller" + str(uuid.uuid4())),
config=True,
help="batch file name for the engine(s) job.")
cores = traitlets.Integer(1, config=True)
tag = traitlets.Unicode("", config=True)
resources = traitlets.Unicode("", config=True)
default_template = Unicode("""#!/bin/sh
#PBS -V
#PBS -N {tag}-c
#PBS -j oe
#PBS -l nodes=1:ppn={cores}
{resources}
cd $PBS_O_WORKDIR
%s --ip=* --log-to-file --profile-dir="{profile_dir}" --cluster-id="{cluster_id}" %s
""" % (' '.join(map(pipes.quote,
controller_cmd_argv)), ' '.join(controller_params)))
def start(self):
"""Start the controller by profile or profile_dir."""
try:
self.context["cores"] = self.cores
self.context["tag"] = self.tag if self.tag else "bcbio"
self.context["resources"] = "\n".join(
_prep_torque_resources(self.resources))
return super(BcbioTORQUEControllerLauncher, self).start(1)
except:
self.log.exception("Controller start failed")
class BcbioPBSEngineSetLauncher(launcher.PBSEngineSetLauncher):
"""Custom launcher handling heterogeneous clusters on PBS.
"""
batch_file_name = Unicode(unicode("pbs_engines" + str(uuid.uuid4())))
cores = traitlets.Integer(1, config=True)
mem = traitlets.Unicode("", config=True)
tag = traitlets.Unicode("", config=True)
pename = traitlets.Unicode("", config=True)
resources = traitlets.Unicode("", config=True)
default_template = traitlets.Unicode("""#PBS -V
#PBS -j oe
#PBS -S /bin/sh
#PBS -q {queue}
#PBS -N {tag}-e
#PBS -t 1-{n}
{mem}
%s %s --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote, engine_cmd_argv)),
' '.join(timeout_params)))
def start(self, n):
self.context["cores"] = self.cores
self.context["pename"] = str(self.pename)
if self.mem:
self.context["mem"] = "#PBS -l mem=%smb" % int(float(self.mem) * 1024)
else:
self.context["mem"] = ""
self.context["tag"] = self.tag if self.tag else "bcbio"
return super(BcbioPBSEngineSetLauncher, self).start(n)
class BcbioSGEControllerLauncher(launcher.SGEControllerLauncher):
batch_file_name = Unicode(unicode("sge_controller" + str(uuid.uuid4())))
tag = traitlets.Unicode("", config=True)
resources = traitlets.Unicode("", config=True)
queue_template = Unicode('')
default_template = traitlets.Unicode(u"""#$ -V
#$ -cwd
#$ -w w
#$ -S /bin/sh
#$ -N {tag}-c
{queue}
{resources}
%s --ip=* --log-to-file --profile-dir="{profile_dir}" --cluster-id="{cluster_id}" %s
""" % (' '.join(map(pipes.quote, controller_cmd_argv)),
' '.join(controller_params)))
def start(self):
self.context["tag"] = self.tag if self.tag else "bcbio"
self.context["resources"] = "\n".join([_prep_sge_resource(r)
for r in str(self.resources).split(";")
if r.strip()])
if self.queue:
self.context["queue"] = "#$ -q %s" % self.queue
else:
self.context["queue"] = ""
return super(BcbioSGEControllerLauncher, self).start()
class BcbioOLDSLURMEngineSetLauncher(SLURMLauncher,
launcher.BatchClusterAppMixin):
"""Launch engines using SLURM for version < 2.6"""
machines = traitlets.Integer(1, config=True)
account = traitlets.Unicode("", config=True)
timelimit = traitlets.Unicode("", config=True)
batch_file_name = Unicode(unicode("SLURM_engines" + str(uuid.uuid4())),
config=True,
help="batch file name for the engine(s) job.")
default_template = Unicode(u"""#!/bin/sh
#SBATCH -A {account}
#SBATCH --job-name ipengine
#SBATCH -N {machines}
#SBATCH -t {timelimit}
srun -N {machines} -n {n} %s %s --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote,
engine_cmd_argv)), ' '.join(timeout_params)))
def start(self, n):
"""Start n engines by profile or profile_dir."""
self.context["machines"] = self.machines
self.context["account"] = self.account
self.context["timelimit"] = self.timelimit
return super(BcbioOLDSLURMEngineSetLauncher, self).start(n)
class D3Sankey(widgets.DOMWidget):
# the name of the requirejs module (no .js!)
_view_module = traitlets.Unicode(
'nbextensions/ipythond3sankey/js/widget_d3sankey',
sync=True)
# the name of the Backbone.View subclass to be used
_view_name = traitlets.Unicode(
'D3SankeyView',
sync=True
)
# the name of the CSS file to load with this widget
_view_style = traitlets.Unicode(
'nbextensions/ipythond3sankey/css/widget_d3sankey',
sync=True
)
# the actual value: lists of nodes and links
nodes = traitlets.List(sync=True)
links = traitlets.List(sync=True)
# margins & size
margin_top = traitlets.Float(1, sync=True)
margin_right = traitlets.Float(1, sync=True)
margin_bottom = traitlets.Float(6, sync=True)
margin_left = traitlets.Float(1, sync=True)
width = traitlets.Float(960, sync=True)
height = traitlets.Float(500, sync=True)
unit = traitlets.Unicode('', sync=True)
class Tangle(TangleBase):
"""
The base Tangle class: subclass this if you know your way around
`traitlets`.
Otherwise, check out `tangle`.
"""
_view_name = traitlets.Unicode("TangleView", sync=True)
_view_module = traitlets.Unicode(
"/nbextensions/ipytangle/js/tangle_view.js", sync=True)
# compatibilty with core types (interact)
description = traitlets.Unicode("Tangle", sync=True)
value = traitlets.Instance(sync=True, klass=TangleBase)
# for the future?
_tangle_prefix = traitlets.Unicode("", sync=True)
_tangle_upstream_traits = traitlets.Tuple(sync=True)
_tangle_cell_hiding = traitlets.Bool(sync=True)
def __init__(self, *args, **kwargs):
_dummy = widgets.DOMWidget()
kwargs["_tangle_upstream_traits"] = tuple(_dummy.trait_names())
super(Tangle, self).__init__(*args, **kwargs)
self.value = self
self.on_trait_change(self._notify_value)
def _notify_value(self, name, old, new):
if name != "value":
self._notify_trait("value", self, self)
class BcbioTORQUEEngineSetLauncher(TORQUELauncher, launcher.BatchClusterAppMixin):
"""Launch Engines using Torque"""
cores = traitlets.Integer(1, config=True)
mem = traitlets.Unicode("", config=True)
tag = traitlets.Unicode("", config=True)
resources = traitlets.Unicode("", config=True)
batch_file_name = Unicode(unicode("torque_engines" + str(uuid.uuid4())),
config=True, help="batch file name for the engine(s) job.")
default_template = Unicode(u"""#!/bin/sh
#PBS -V
#PBS -j oe
#PBS -N {tag}-e
#PBS -t 1-{n}
#PBS -l nodes=1:ppn={cores}
{mem}
{resources}
cd $PBS_O_WORKDIR
%s %s --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote, engine_cmd_argv)),
' '.join(timeout_params)))
def start(self, n):
"""Start n engines by profile or profile_dir."""
try:
self.context["cores"] = self.cores
if self.mem:
self.context["mem"] = "#PBS -l mem=%smb" % int(float(self.mem) * 1024)
else:
self.context["mem"] = ""
self.context["tag"] = self.tag if self.tag else "bcbio"
self.context["resources"] = "\n".join(_prep_torque_resources(self.resources))
return super(BcbioTORQUEEngineSetLauncher, self).start(n)
except:
self.log.exception("Engine start failed")
class Result(documents.Document):
title = traitlets.Unicode()
smalltitle = traitlets.Unicode()
value = traitlets.Any()
date = traitlets.Instance(datetime.datetime)
def __init__(self, *args, **kwargs):
super(Result, self).__init__(*args, **kwargs)
if self.date is None:
self.date = datetime.datetime.now()
def _result_html(self):
if hasattr(self.value, '__html__'):
return self.value.__html__()
if hasattr(self.value, '__repr_html__'):
return self.value.__repr_html__()
elif isinstance(self.value, sympy.Expr):
return sympy.latex(self.value)
else:
return str(self.value)
def __repr_html__(self):
template = env.get_template('base_report.html')
return template.render(report = self)
class BcbioLSFEngineSetLauncher(launcher.LSFEngineSetLauncher):
"""Custom launcher handling heterogeneous clusters on LSF.
"""
batch_file_name = Unicode(unicode("lsf_engine" + str(uuid.uuid4())))
cores = traitlets.Integer(1, config=True)
mem = traitlets.Unicode("", config=True)
tag = traitlets.Unicode("", config=True)
resources = traitlets.Unicode("", config=True)
job_array_template = Unicode('')
queue_template = Unicode('')
default_template = traitlets.Unicode("""#!/bin/sh
#BSUB -q {queue}
#BSUB -J {tag}-e[1-{n}]
#BSUB -oo bcbio-ipengine.bsub.%%J
#BSUB -n {cores}
#BSUB -R "span[hosts=1]"
{mem}
{resources}
%s %s --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote, engine_cmd_argv)),
' '.join(timeout_params)))
def start(self, n):
self.context["cores"] = self.cores
if self.mem:
# scale memory to kb
mem = int(float(self.mem) * 1024.0 * 1024.0)
self.context["mem"] = "#BSUB -M %s" % mem
else:
self.context["mem"] = ""
self.context["tag"] = self.tag if self.tag else "bcbio"
self.context["resources"] = _format_lsf_resources(self.resources)
return super(BcbioLSFEngineSetLauncher, self).start(n)
class IPythonProgressWidget(widgets.DOMWidget):
"""IPython widget for displaying a progress bar."""
# pylint: disable=too-many-public-methods
_view_name = traitlets.Unicode('NengoProgressBar', sync=True)
progress = traitlets.Float(0., sync=True)
text = traitlets.Unicode(u'', sync=True)
FRONTEND = '''
require(["widgets/js/widget", "widgets/js/manager"],
function(widget, manager) {
if (typeof widget.DOMWidgetView == 'undefined') {
widget = IPython;
}
if (typeof manager.WidgetManager == 'undefined') {
manager = IPython;
}
var NengoProgressBar = widget.DOMWidgetView.extend({
render: function() {
// $el is the DOM of the widget
this.$el.css({width: '100%', marginBottom: '0.5em'});
this.$el.html([
'<div style="',
'width: 100%;',
'border: 1px solid #cfcfcf;',
'border-radius: 4px;',
'text-align: center;',
'position: relative;">',
'<div class="pb-text" style="',
'position: absolute;',
'width: 100%;">',
'0%',
'</div>',
'<div class="pb-bar" style="',
'background-color: #bdd2e6;',
'width: 0%;',
'transition: width 0.1s linear;">',
' ',
'</div>',
'</div>'].join(''));
},
update: function() {
this.$el.css({width: '100%', marginBottom: '0.5em'});
var progress = 100 * this.model.get('progress');
var text = this.model.get('text');
this.$el.find('div.pb-bar').width(progress.toString() + '%');
this.$el.find('div.pb-text').text(text);
},
});
manager.WidgetManager.register_widget_view(
'NengoProgressBar', NengoProgressBar);
});'''
@classmethod
def load_frontend(cls):
"""Loads the JavaScript front-end code required by then widget."""
get_ipython().run_cell_magic('javascript', '', cls.FRONTEND)
class HeatmapWidget(W.DOMWidget):
_view_name = T.Unicode('HeatmapView', sync=True)
heatmap_data = T.List(sync=True)
row_labels = T.List(sync=True)
col_labels = T.List(sync=True)
hcrow = T.List(sync=True)
hccol = T.List(sync=True)
minval = T.Float(sync=True)
maxval = T.Float(sync=True)
html_style = T.Unicode(sync=True)
class BcbioPBSControllerLauncher(launcher.PBSControllerLauncher):
batch_file_name = Unicode(unicode("pbs_controller" + str(uuid.uuid4())))
tag = traitlets.Unicode("", config=True)
default_template = traitlets.Unicode(u"""#PBS -V
#PBS -S /bin/sh
#PBS -N {tag}-c
%s --ip=* --log-to-file --profile-dir="{profile_dir}" --cluster-id="{cluster_id}" %s
""" % (' '.join(map(pipes.quote, controller_cmd_argv)),
' '.join(controller_params)))
def start(self):
self.context["tag"] = self.tag if self.tag else "bcbio"
return super(BcbioPBSControllerLauncher, self).start()
class VariationDataProperties(JsonTraits):
info_text = "Variation data properties"
num_snps = Numeric(0, desc="Number of SNPs")
num_individuals = Integer(0, desc="Number of individuals")
snp_effect_annotation = tls.Unicode(
"", desc="Flag for SNP annotation: yes or no")
individual_names = tls.List(tls.Unicode)
class BcbioLSFControllerLauncher(launcher.LSFControllerLauncher):
batch_file_name = Unicode(unicode("lsf_controller" + str(uuid.uuid4())))
tag = traitlets.Unicode("", config=True)
resources = traitlets.Unicode("", config=True)
job_array_template = Unicode('')
queue_template = Unicode('')
default_template = traitlets.Unicode("""#!/bin/sh
#BSUB -q {queue}
#BSUB -J {tag}-c
#BSUB -oo bcbio-ipcontroller.bsub.%%J
{resources}
%s --ip=* --log-to-file --profile-dir="{profile_dir}" --cluster-id="{cluster_id}" %s
""" % (' '.join(map(pipes.quote, controller_cmd_argv)),
' '.join(controller_params)))
def start(self):
self.context["tag"] = self.tag if self.tag else "bcbio"
self.context["resources"] = _format_lsf_resources(self.resources)
return super(BcbioLSFControllerLauncher, self).start()
class BcbioLSFControllerLauncher(launcher.LSFControllerLauncher):
default_template = traitlets.Unicode("""#!/bin/sh
#BSUB -J bcbio-ipcontroller
#BSUB -oo bcbio-ipcontroller.bsub.%%J
%s --ip=* --log-to-file --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote, launcher.ipcontroller_cmd_argv))))
def start(self):
return super(BcbioLSFControllerLauncher, self).start()
class BcbioSGEControllerLauncher(launcher.SGEControllerLauncher):
default_template = traitlets.Unicode(u"""#$ -V
#$ -S /bin/sh
#$ -N ipcontroller
%s --ip=* --log-to-file --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote, launcher.ipcontroller_cmd_argv))))
def start(self):
return super(BcbioSGEControllerLauncher, self).start()
class BcbioOLDSLURMControllerLauncher(SLURMLauncher, launcher.BatchClusterAppMixin):
"""Launch a controller using SLURM for versions < 2.6"""
account = traitlets.Unicode("", config=True)
timelimit = traitlets.Unicode("", config=True)
batch_file_name = Unicode(unicode("SLURM_controller" + str(uuid.uuid4())),
config=True, help="batch file name for the engine(s) job.")
default_template = Unicode("""#!/bin/sh
#SBATCH -A {account}
#SBATCH --job-name ipcontroller
#SBATCH -t {timelimit}
%s --ip=* --log-to-file --profile-dir="{profile_dir}" --cluster-id="{cluster_id}" %s
""" % (' '.join(map(pipes.quote, controller_cmd_argv)),
' '.join(controller_params)))
def start(self):
"""Start the controller by profile or profile_dir."""
self.context["account"] = self.account
self.context["timelimit"] = self.timelimit
return super(BcbioOLDSLURMControllerLauncher, self).start(1)
class BcbioSLURMControllerLauncher(SLURMLauncher, launcher.BatchClusterAppMixin):
batch_file_name = Unicode(unicode("SLURM_controller" + str(uuid.uuid4())))
account = traitlets.Unicode("", config=True)
timelimit = traitlets.Unicode("", config=True)
mem = traitlets.Unicode("", config=True)
tag = traitlets.Unicode("", config=True)
resources = traitlets.Unicode("", config=True)
default_template = traitlets.Unicode("""#!/bin/sh
#SBATCH -J {tag}-c
#SBATCH -o bcbio-ipcontroller.out.%%j
#SBATCH -e bcbio-ipcontroller.err.%%j
#SBATCH -A {account}
#SBATCH -t {timelimit}
{mem}
{resources}
%s --ip=* --log-to-file --profile-dir="{profile_dir}" --cluster-id="{cluster_id}" %s
""" % (' '.join(map(pipes.quote, controller_cmd_argv)),
' '.join(controller_params)))
def start(self):
self.context["account"] = self.account
self.context["timelimit"] = self.timelimit
self.context["mem"] = "#SBATCH --mem=%d" % (8 * DEFAULT_MEM_PER_CPU)
self.context["tag"] = self.tag if self.tag else "bcbio"
self.context["resources"] = "\n".join(["#SBATCH --%s" % r.strip()
for r in str(self.resources).split(";")
if r.strip()])
return super(BcbioSLURMControllerLauncher, self).start(1)
class BcbioLSFEngineSetLauncher(launcher.LSFEngineSetLauncher):
"""Custom launcher handling heterogeneous clusters on LSF.
"""
batch_file_name = Unicode(unicode("lsf_engine" + str(uuid.uuid4())))
cores = traitlets.Integer(1, config=True)
numengines = traitlets.Integer(1, config=True)
mem = traitlets.Unicode("", config=True)
tag = traitlets.Unicode("", config=True)
resources = traitlets.Unicode("", config=True)
job_array_template = Unicode('')
queue_template = Unicode('')
default_template = traitlets.Unicode("""#!/bin/sh
#BSUB -q {queue}
#BSUB -J {tag}-e[1-{n}]
#BSUB -oo bcbio-ipengine.bsub.%%J
#BSUB -n {cores}
#BSUB -R "span[hosts=1]"
{mem}
{resources}
{cmd}
""")
def start(self, n):
self.context["cores"] = self.cores * self.numengines
if self.mem:
# lsf.conf can specify nonstandard units for memory reservation
lsf_unit = lsf.get_lsf_units(resource=True)
mem = utils.convert_mb(float(self.mem) * 1024, lsf_unit)
# check if memory reservation is per core or per job
if lsf.per_core_reservation():
mem = mem / self.cores
mem = mem * self.numengines
self.context["mem"] = '#BSUB -R "rusage[mem=%s]"' % mem
else:
self.context["mem"] = ""
self.context["tag"] = self.tag if self.tag else "bcbio"
self.context["resources"] = _format_lsf_resources(self.resources)
self.context["cmd"] = get_engine_commands(self.context,
self.numengines)
return super(BcbioLSFEngineSetLauncher, self).start(n)
class Icon(InstallerMixin, widgets.DOMWidget):
"""
A widget which can show one or more icons
"""
icons = traitlets.List(sync=True)
size = traitlets.Enum(Size, sync=True)
context = traitlets.Enum(bs.Context, sync=True)
_view_name = traitlets.Unicode('ipbs/IconView', sync=True)
def __init__(self, *args, **kwargs):
kwargs["icons"] = list(args) + kwargs.pop("icons", [])
super(Icon, self).__init__(**kwargs)
class VariationDataset(JsonTraits):
info_text = "Variation dataset"
name = tls.Unicode("no name", desc="Name")
description = tls.Unicode("none", desc="Description")
file_format = tls.Unicode("vcf", desc="File format")
comments = tls.Unicode("", desc="Comments")
kbase_genome_id = tls.Unicode("", desc="Genome identifier")
kbase_genome_name = tls.Unicode("", desc="Genome name")
shock_node_id = tls.Unicode("", desc="Shock node ID")
properties = tls.Instance(VariationDataProperties, ())
command_used = tls.Unicode("unspecified", desc="Command")
def __repr__(self):
return json.dumps(self.as_json())
class BcbioSGEEngineSetLauncher(launcher.SGEEngineSetLauncher):
"""Custom launcher handling heterogeneous clusters on SGE.
"""
batch_file_name = Unicode(unicode("sge_engine" + str(uuid.uuid4())))
cores = traitlets.Integer(1, config=True)
pename = traitlets.Unicode("", config=True)
resources = traitlets.Unicode("", config=True)
mem = traitlets.Unicode("", config=True)
tag = traitlets.Unicode("", config=True)
default_template = traitlets.Unicode("""#$ -V
#$ -cwd
#$ -b y
#$ -j y
#$ -S /bin/sh
#$ -q {queue}
#$ -N {tag}-e
#$ -t 1-{n}
#$ -pe {pename} {cores}
{mem}
{resources}
echo \($SGE_TASK_ID - 1\) \* 0.5 | bc | xargs sleep
%s %s --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote, engine_cmd_argv)),
' '.join(timeout_params)))
def start(self, n):
self.context["cores"] = self.cores
if self.mem:
self.context["mem"] = "#$ -l mem_free=%sM" % int(float(self.mem) * 1024)
else:
self.context["mem"] = ""
self.context["tag"] = self.tag if self.tag else "bcbio"
self.context["pename"] = str(self.pename)
self.context["resources"] = "\n".join(["#$ -l %s" % r.strip()
for r in str(self.resources).split(";")
if r.strip()])
return super(BcbioSGEEngineSetLauncher, self).start(n)
class FileUpload(Question):
encoding = traits.Unicode("b")
def check(self, responses, student_id=None):
if responses[0]:
filename = os.path.join(
FILE_UPLOAD_DIR,
self.__class__.__name__ + "_" + str(student_id))
fout = open(filename, 'w' + self.encoding)
fout.write(responses[0])
fout.close()
responses[0] = "File uploaded successfully!"
else:
responses[0] = ""
return {"scores": [""], "comments": [responses[0]]}
class Report(documents.Document):
title = traitlets.Unicode()
results = traitlets.List(documents.Reference(Result))
date = traitlets.Instance(datetime.datetime)
def __init__(self, *args, **kwargs):
super(Report, self).__init__(*args, **kwargs)
if self.date is None:
self.date = datetime.datetime.now()
def __html__(self):
template = env.get_template('report_base.html')
return template.render(report = self)
def make_report(self, report_folder,openbrowser = True):
save_html_report(self.__html__(), report_folder,
openbrowser=openbrowser)
class BcbioLSFEngineSetLauncher(launcher.LSFEngineSetLauncher):
"""Custom launcher handling heterogeneous clusters on LSF.
"""
cores = traitlets.Integer(1, config=True)
default_template = traitlets.Unicode("""#!/bin/sh
#BSUB -q {queue}
#BSUB -J bcbio-ipengine[1-{n}]
#BSUB -oo bcbio-ipengine.bsub.%%J
#BSUB -n {cores}
#BSUB -R "span[hosts=1]"
%s %s --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(
pipes.quote, launcher.ipengine_cmd_argv)), ' '.join(timeout_params)))
def start(self, n):
self.context["cores"] = self.cores
return super(BcbioLSFEngineSetLauncher, self).start(n)
class BcbioPBSPROEngineSetLauncher(PBSPROLauncher, launcher.BatchClusterAppMixin):
"""Launch Engines using PBSPro"""
batch_file_name = Unicode(u'pbspro_engines', config=True,
help="batch file name for the engine(s) job.")
tag = traitlets.Unicode("", config=True)
default_template = Unicode(u"""#!/bin/sh
#PBS -V
#PBS -N {tag}-e
cd $PBS_O_WORKDIR
%s %s --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote, engine_cmd_argv)),
' '.join(timeout_params)))
def start(self, n):
"""Start n engines by profile or profile_dir."""
self.context["tag"] = self.tag if self.tag else "bcbio"
return super(BcbioPBSPROEngineSetLauncher, self).start(n)
class BcbioPBSPROControllerLauncher(PBSPROLauncher, launcher.BatchClusterAppMixin):
"""Launch a controller using PBSPro."""
batch_file_name = Unicode(u'pbspro_controller', config=True,
help="batch file name for the controller job.")
tag = traitlets.Unicode("", config=True)
default_template = Unicode("""#!/bin/sh
#PBS -V
#PBS -N {tag}-c
cd $PBS_O_WORKDIR
%s --ip=* --log-to-file --profile-dir="{profile_dir}" --cluster-id="{cluster_id}" %s
""" % (' '.join(map(pipes.quote, controller_cmd_argv)),
' '.join(controller_params)))
def start(self):
"""Start the controller by profile or profile_dir."""
self.context["tag"] = self.tag if self.tag else "bcbio"
return super(BcbioPBSPROControllerLauncher, self).start(1)
class MultiPartQuestion(Question):
"""
Question with multiple parts (which are themselves questions)
"""
active_parts = traits.List()
list_type = traits.Unicode("a")
def _parts_changed(self):
self.active_parts = []
self.max_pts = []
for part in self.parts:
part.seed = self.seed
self.active_parts.append(part)
self.max_pts.extend(part.max_pts)
def to_JSON(self, solution=False):
data = {
"type": self.type,
"text": self.text,
"parts": [p.to_JSON(solution) for p in self.active_parts],
"list_type": self.list_type
}
if solution: data['solution'] = {}
return data
def check(self, responses, student_id=None):
scores = []
comments = []
end = 0
for i, part in enumerate(self.active_parts):
# extract responses corresponding to current part
start = end
end = start + part.num_answers
resp = responses[start:end]
# call the check method for that part
out = part.check(resp)
scores.extend(out['scores'])
comments.extend(out['comments'])
# write any changes to the answer back
responses[start:end] = resp
return {"scores": scores, "comments": comments}
class BcbioSGEEngineSetLauncher(launcher.SGEEngineSetLauncher):
"""Custom launcher handling heterogeneous clusters on SGE.
"""
cores = traitlets.Integer(1, config=True)
default_template = traitlets.Unicode("""#$ -V
#$ -cwd
#$ -b y
#$ -j y
#$ -S /bin/sh
#$ -q {queue}
#$ -N bcbio-ipengine
#$ -t 1-{n}
#$ -pe threaded {cores}
%s %s --profile-dir="{profile_dir}" --cluster-id="{cluster_id}"
""" % (' '.join(map(pipes.quote,
launcher.ipengine_cmd_argv)), ' '.join(timeout_params)))
def start(self, n):
self.context["cores"] = self.cores
return super(BcbioSGEEngineSetLauncher, self).start(n)