def process():
from looper import build_parser as blp
actions = get_positional_args(blp(), sort=True)
try:
globs.selected_project, globs.selected_project_id, globs.current_subproj = \
select_project(request.form.get('select_project'))
except TypeError:
app.logger.info("No project selected, redirecting to the index page.")
flash("No project was selected, choose one from the list below.")
return redirect(url_for('index'))
config_file = str(os.path.expandvars(os.path.expanduser(globs.selected_project)))
if globs.p is None:
globs.p = Project(config_file, subproject=globs.current_subproj)
try:
# subproject related logic can be removed with the introduction of direct subproject selection in the index
subprojects = globs.p.subprojects.keys()
except AttributeError:
subprojects = None
# populating project/subproject metadata and date are treated individually since when the project is activated
# we want its subprojects data to be populated but not the dates
with globs.cc as x:
x.populate_project_metadata(paths=globs.selected_project,
sp=globs.current_subproj if globs.current_subproj else None)
x.project_date(globs.selected_project, globs.current_subproj)
get_navbar_summary_links()
return render_template('process.html', p_info=project_info_dict(globs.p), change=None,
selected_subproject=globs.p.subproject, actions=actions, subprojects=subprojects,
interval=globs.status_check_interval)
def prj(self, tmpdir, prj_data, anns_file, iface_paths):
""" Provide basic Project. """
prj_data["pipeline_interfaces"] = iface_paths
prj_data["metadata"][SAMPLE_ANNOTATIONS_KEY] = anns_file
prj_file = tmpdir.join("pconf.yaml").strpath
with open(prj_file, 'w') as f:
yaml.dump(prj_data, f)
return Project(prj_file)
def prj(self, tmpdir, prj_data, anns_file, iface_paths):
""" Provide basic Project. """
prj_data[PIPELINE_INTERFACES_KEY] = iface_paths
prj_data[METADATA_KEY][SAMPLE_ANNOTATIONS_KEY] = anns_file
prj_file = tmpdir.join("pconf.yaml").strpath
with open(prj_file, 'w') as f:
yaml.dump(prj_data, f)
return Project(prj_file)
def interactive(prj_lines=PROJECT_CONFIG_LINES,
iface_lines=PIPELINE_INTERFACE_CONFIG_LINES,
merge_table_lines=MERGE_TABLE_LINES,
annotation_lines=SAMPLE_ANNOTATION_LINES,
project_kwargs=None,
logger_kwargs=None):
"""
Create Project and PipelineInterface instances from default or given data.
This is intended to provide easy access to instances of fundamental looper
object for interactive test-authorship-motivated work in an iPython
interpreter or Notebook. Test authorship is simplified if we provide
easy access to viable instances of these objects.
:param Iterable[str] prj_lines: project config lines
:param Iterable[str] iface_lines: pipeline interface config lines
:param Iterable[str] merge_table_lines: lines for a merge table file
:param Iterable[str] annotation_lines: lines for a sample annotations file
:param str | int loglevel: level at which to attend to log messages
:param dict project_kwargs: keyword arguments for Project constructor
:param dict logger_kwargs: keyword arguments for logging configuration
:param bool devmode: whether logging should be done in development mode;
this implies a more verbose level setting and a more information-rich
template for logging message formatting
:param str logfile: path to file to which to write logging messages
:return Project, PipelineInterface: one Project and one PipelineInterface,
"""
# Establish logging for interactive session.
looper_logger_kwargs = {"level": "DEBUG"}
looper_logger_kwargs.update(logger_kwargs or {})
setup_looper_logger(**looper_logger_kwargs)
# TODO: don't work with tempfiles once ctors tolerate Iterable.
dirpath = tempfile.mkdtemp()
path_conf_file = _write_temp(prj_lines,
dirpath=dirpath,
fname=P_CONFIG_FILENAME)
path_iface_file = _write_temp(iface_lines,
dirpath=dirpath,
fname="pipeline_interface.yaml")
path_merge_table_file = _write_temp(merge_table_lines,
dirpath=dirpath,
fname=MERGE_TABLE_FILENAME)
path_sample_annotation_file = _write_temp(annotation_lines,
dirpath=dirpath,
fname=ANNOTATIONS_FILENAME)
prj = Project(path_conf_file, **(project_kwargs or {}))
iface = PipelineInterface(path_iface_file)
for path in [
path_conf_file, path_iface_file, path_merge_table_file,
path_sample_annotation_file
]:
os.unlink(path)
return prj, iface
def test_looper_command_templates_hooks(self, prep_temp_pep, cmd):
tp = prep_temp_pep
for path in {
piface["pipe_iface_file"]
for piface in Project(tp).pipeline_interfaces
}:
with mod_yaml_data(path) as piface_data:
piface_data[PRE_SUBMIT_HOOK_KEY][PRE_SUBMIT_CMD_KEY] = [cmd]
stdout, stderr, rc = subp_exec(tp, "run")
sd = os.path.join(get_outdir(tp), "submission")
print(stderr)
assert rc == 0
verify_filecount_in_dir(sd, "test.txt", 3)
def test_looper_other_plugins(self, prep_temp_pep, plugin, appendix):
tp = prep_temp_pep
for path in {
piface["pipe_iface_file"]
for piface in Project(tp).pipeline_interfaces
}:
with mod_yaml_data(path) as piface_data:
piface_data[PRE_SUBMIT_HOOK_KEY][PRE_SUBMIT_PY_FUN_KEY] = [
plugin
]
stdout, stderr, rc = subp_exec(tp, "run")
sd = os.path.join(get_outdir(tp), "submission")
print(stderr)
assert rc == 0
verify_filecount_in_dir(sd, appendix, 3)
def process():
from looper import build_parser as blp
actions = get_positional_args(blp(), sort=True)
# this try-except block is used to determine whether the user should be redirected to the index page
# to select the project when they land on the process subpage from the set_comp_env subpage
if globs.selected_project is None and request.form.get(
'select_project') is None:
app.logger.info(
"The project is not selected, redirecting to the index page.")
flash("No project was selected, choose one from the list below.")
return redirect(url_for('index'))
else:
new_selected_project = request.form.get('select_project')
if new_selected_project is not None and globs.selected_project != new_selected_project:
globs.selected_project = new_selected_project
config_file = str(
os.path.expandvars(os.path.expanduser(globs.selected_project)))
if globs.p is None:
globs.p = Project(config_file)
try:
subprojects = list(globs.p.subprojects.keys())
except AttributeError:
subprojects = None
# TODO: p_info will be removed altogether in the future version
get_navbar_summary_links()
p_info = {
"name": globs.p.name,
"config_file": globs.p.config_file,
"sample_count": globs.p.num_samples,
"output_dir": globs.p.metadata.output_dir,
"subprojects": ",".join(subprojects)
}
globs.reset_btn = True
return render_template('process.html',
p_info=p_info,
change=None,
selected_subproject=globs.p.subproject,
actions=actions,
subprojects=subprojects)