#! /usr/bin/env python
##########################################################################
# NSAp - Copyright (C) CEA, 2013
# Distributed under the terms of the CeCILL-B license, as published by
# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
import re
# Cubicweb import
from cubicweb.web.action import Action
from cubicweb.predicates import is_instance
from cubicweb import ValidationError
from cubicweb.entities import AnyEntity
# Container import
from cubes.rql_download.config import CWSEARCH_RSET_CONTAINER
from cubes.rql_download.config import CWSEARCH_RESULT_CONTAINER
# Define global adaptor variables
RQL_DOWNLOAD_EXPORT_ENTITIES = ["Subject"]
RQL_DOWNLOAD_FSET_ENTITIES = ["Scan", "ProcessingRun", "GenomicMeasure"]
RQL_DOWNLOAD_ENTITIES = ["FileSet", "ExternalFile"]
class CWSearch(AnyEntity):
__regid__ = "CWSearch"
container_config = CWSEARCH_RSET_CONTAINER
[docs]class BaseIDownloadAdapter(Action):
""" Base adapter class.
.. note::
* A 'rql' method has to be implemented in child classes.
* We assume the database intergrity (ie. all file pathes inserted in
the db exist on the file system) and thus do not check in the hooks
to speed speed the search creation.
"""
__regid__ = "rqldownload-adapters"
__abstract__ = True
__rset_type__ = u"jsonexport"
[docs] def rql(self):
""" Method that return the completed RQL.
"""
raise NotImplementedError
[docs]class IFSetAdapter(BaseIDownloadAdapter):
""" Action to download ExternalFile entities to a FileSet entity.
.. warning::
* The adapted RQL must return the file pathes in the first item
of the rset.
"""
__regid__ = "rqldownload-adapters"
__select__ = BaseIDownloadAdapter.__select__ & is_instance("FileSet")
__rset_type__ = u"jsonexport"
[docs] def rql(self, rql, parameter_name, identifier=1):
""" Method that patch the rql.
.. note::
* reserved keys are 'PATH', 'FENTRIES' postfixed with the
identifier number.
* returned files are necessary at the beginning of the adapted rql.
Parameters
----------
rql: str (mandatory)
the request to adapt.
parameter_name: str (mandatory)
the label of the entity to adapt.
identifier: int (optional)
postfix the reserved keys with this identifier.
Returns
-------
global_rql: str
the adapted rql.
nb_files: int
the number of files returned at the begining of the result set.
"""
# Define reserved labels
reserved_labels = [
"PATH{0}".format(identifier),
"FENTRIES{0}".format(identifier)
]
# Check that reserved keys are not used
split_rql = re.split(r"[ ,]", rql)
for reserved_key in reserved_labels:
if reserved_key in split_rql:
raise ValidationError(
"CWSearch", {
"rql": _(
'cannot edit the rql "{0}", "{1}" is a reserved key, '
'choose another name.'.format(rql, reserved_key))})
# Remove the begining of the rql in order to complete it
formated_rql = " ".join(rql.split()[1:])
# Complete the rql in order to access file pathes
global_rql = (
"Any {0}, {1}, {2} external_files {3}, "
"{3} filepath {0}".format(reserved_labels[0], formated_rql,
parameter_name, reserved_labels[1]))
return global_rql, 1
class IFileAdapter(BaseIDownloadAdapter):
""" Action to download an ExternalFile entity.
.. warning::
* The adapted RQL must return the file pathes in the first item
of the rset.
"""
__regid__ = "rqldownload-adapters"
__select__ = BaseIDownloadAdapter.__select__ & is_instance("ExternalFile")
__rset_type__ = u"jsonexport"
def rql(self, rql, parameter_name, identifier=1):
""" Method that patch the rql.
.. note::
* reserved keys are 'PATH', postfixed with the identifier number.
* returned files are necessary at the beginning of the adapted rql.
Parameters
----------
rql: str (mandatory)
the request to adapt.
parameter_name: str (mandatory)
the label of the entity to adapt.
identifier: int (optional)
postfix the reserved keys with this identifier.
Returns
-------
global_rql: str
the adapted rql.
nb_files: int
the number of files returned at the begining of the result set.
"""
# Define reserved labels
reserved_labels = [
"PATH{0}".format(identifier),
]
# Check that reserved keys are not used
split_rql = re.split(r"[ ,]", rql)
for reserved_key in reserved_labels:
if reserved_key in split_rql:
raise ValidationError(
"CWSearch", {
"rql": _(
'cannot edit the rql "{0}", "{1}" is a reserved key, '
'choose another name.'.format(rql, reserved_key))})
# Remove the begining of the rql in order to complete it
formated_rql = " ".join(rql.split()[1:])
# Complete the rql in order to access file pathes
global_rql = (
"Any {0}, {1}, {2} filepath {0}".format(
reserved_labels[0], formated_rql, parameter_name))
return global_rql, 1
class IEntityFSetAdapter(BaseIDownloadAdapter):
""" Action to download entity objects related through a FileSet entity.
Add items in the global list 'RQL_DOWNLOAD_FSET_ENTITIES' to activate
such an action. The rset will be exported in json format.
.. warning::
* The adapted RQL must return the file pathes in the first item
of the rset.
"""
__regid__ = "rqldownload-adapters"
__select__ = BaseIDownloadAdapter.__select__ & is_instance(
*RQL_DOWNLOAD_FSET_ENTITIES)
__rset_type__ = u"jsonexport"
def rql(self, rql, parameter_name, identifier=1):
""" Method that patch the rql.
.. note::
* reserved keys are 'PATH', 'FENTRIES', 'FILES' postfixed with the
identifier number.
* returned files are necessary at the beginning of the adapted rql.
* detect if a filter is activated on the FileSets by checking
the unique 'filesets' relation: in this case the reserved
'FENTRIES' postfixed label is the label associated to the
FileSets.
Parameters
----------
rql: str (mandatory)
the request to adapt.
parameter_name: str (mandatory)
the label of the entity to adapt.
identifier: int (optional)
postfix the reserved keys with this identifier.
Returns
-------
global_rql: str
the adapted rql.
nb_files: int
the number of files returned at the begining of the result set.
"""
# Define reserved labels
reserved_labels = [
"PATH{0}".format(identifier),
"FILES{0}".format(identifier),
"FENTRIES{0}".format(identifier)
]
# Check that reserved keys are not used
split_rql = re.split(r"[ ,]", rql)
for reserved_key in reserved_labels:
if reserved_key in split_rql:
raise ValidationError(
"CWSearch", {
"rql": _(
'cannot edit the rql "{0}", "{1}" is a reserved key, '
'choose another name.'.format(rql, reserved_key))})
# Remove the begining of the rql in order to complete it
formated_rql = " ".join(rql.split()[1:])
# Complete the rql in order to access file pathes:
# case 1: a filter is activated on the FileSets
# case 2: download all the file sets associated files
if "filesets" in formated_rql:
fileset_label = formated_rql.split("filesets")[1].split(",")[0]
fileset_label = fileset_label.strip()
global_rql = (
"Any {0}, {1}, {2} external_files {3}, "
"{3} filepath {0}".format(reserved_labels[0], formated_rql,
fileset_label, reserved_labels[2]))
else:
global_rql = (
"Any {0}, {1}, {2} filesets {3}, {3} external_files {4}, "
"{4} filepath {0}".format(reserved_labels[0], formated_rql,
parameter_name, reserved_labels[1],
reserved_labels[2]))
return global_rql, 1
[docs]class IEntityAdapter(BaseIDownloadAdapter):
""" Action to download entity attributes.
Add items in the global list 'RQL_DOWNLOAD_EXPORT_ENTITIES' to activate
such an action. The rset will be exported in csv format.
"""
__select__ = BaseIDownloadAdapter.__select__ & is_instance(
*RQL_DOWNLOAD_EXPORT_ENTITIES)
__rset_type__ = u"ecsvexport"
[docs] def rql(self, rql, parameter_name, identifier=None):
""" Method that simply return the input rql.
"""
return rql, 1
