def user_delete(user_id):
"""
Delete the user with the provided id in the database
"""
from core.model.project import Project
u = User.from_id(user_id)
if u:
Project.delete(u.sandbox_id)
Session().query(User).filter_by(id=user_id).delete(synchronize_session=False)
def user_delete(user_id):
"""
Delete the user with the provided id in the database
"""
from core.model.project import Project
u = User.from_id(user_id)
if u:
Project.delete(u.sandbox_id)
Session().query(User).filter_by(id=user_id).delete(
synchronize_session=False)
def analaysis_get_fullpath(self):
"""
Return the list of project from the root to the last one where the analysis is stored
"""
from core.model import Project
fullpath = []
project = Project.from_id(self.project_id)
while project is not None:
fullpath.insert(0,{"id": project.id, "name":project.name})
project = None if not project.parent_id else Project.from_id(project.parent_id)
return fullpath
def analaysis_get_fullpath(self):
"""
Return the list of project from the root to the last one where the analysis is stored
"""
from core.model import Project
fullpath = []
project = Project.from_id(self.project_id)
while project is not None:
fullpath.insert(0, {"id": project.id, "name": project.name})
project = None if not project.parent_id else Project.from_id(
project.parent_id)
return fullpath
def user_init(self, loading_depth=0, force=False):
"""
Init properties of an user :
- id : int : the unique id of the user in the database
- login : str : the login of the user
- firstname : str : firstname of the user
- lastname : str : lastname of the user
- email : str : email
- function : str : the function of the user
- location : str : the location of the user
- is_admin : bool : is the user an admin or not
- is_activated : bool : is the user activated or not
- sandbox_id : int : this id refer to the sandbox project of the user
- update_date : datetime : the last time that the object have been updated
- create_date : datetime : the date when the object have been created
If loading_depth is > 0, Following properties fill be loaded : (Max depth level is 2)
- sandbox : Project : The sandbox project of the user
"""
from core.model.project import Project
# Avoid recursion infinit loop
if hasattr(self, "loading_depth") and not force:
return
else:
self.loading_depth = min(2, loading_depth)
try:
self.sandbox = None
if self.loading_depth > 0:
self.sandbox = Project.from_id(self.sandbox_id,
self.loading_depth - 1)
except Exception as ex:
raise RegovarException("User data corrupted (id={}).".format(self.id),
"", ex)
def user_init(self, loading_depth=0, force=False):
"""
Init properties of an user :
- id : int : the unique id of the user in the database
- login : str : the login of the user
- firstname : str : firstname of the user
- lastname : str : lastname of the user
- email : str : email
- function : str : the function of the user
- location : str : the location of the user
- is_admin : bool : is the user an admin or not
- is_activated : bool : is the user activated or not
- sandbox_id : int : this id refer to the sandbox project of the user
- update_date : datetime : the last time that the object have been updated
- create_date : datetime : the date when the object have been created
If loading_depth is > 0, Following properties fill be loaded : (Max depth level is 2)
- sandbox : Project : The sandbox project of the user
"""
from core.model.project import Project
# Avoid recursion infinit loop
if hasattr(self, "loading_depth") and not force:
return
else:
self.loading_depth = min(2, loading_depth)
try:
self.sandbox = None
if self.loading_depth > 0:
self.sandbox = Project.from_id(self.sandbox_id, self.loading_depth-1)
except Exception as ex:
raise RegovarException("User data corrupted (id={}).".format(self.id), "", ex)
def analysis_init(self, loading_depth=0, force_refresh=False):
"""
Init properties of an analysis :
- id : int : the unique id of the analysis in the database
- project_id : int : the id of the project that owns this analysis
- name : str : the name of the analysis
- comment : str : an optional comment
- settings : json : parameters used to init the analysis
- fields : [str] : The list of field's id to display
- filter : json : The last current filter to applied
- order : [str] : The list of field's id to used to order result
- selection : [str] : The list of ids of selected variants
- create_date : datetime : The date when the analysis have been created
- update_date : datetime : The last time that the analysis have been updated
- total_variants : int : The total number of variant in this analysis
- reference_id : int : Refer to the id of the reference used for this analysis
- computing_progress: json : Used when the working table is computed to store the current progress, error, messages, ...
- status : enum : The status of the analysis : 'empty', 'computing', 'ready', 'error'
- filters_ids : [int] : The list of ids of filters saved for this analysis
- samples_ids : [int] : The list of ids of samples used for analysis
- files_ids : [int] : The list of ids of files associated to the analysis (via analysis_file table)
- attributes : json : The list of attributes defined for this analysis
- fullpath : [json] : The list of folder from root to the analyses [{"id":int, "name":str},...]
- statistics : json : Statistics about the analysis
If loading_depth is > 0, Following properties fill be loaded : (Max depth level is 2)
- project : Project : The that own the analysis
- samples : [Sample] : The list of samples owns by the analysis
- filters : [Filter] : The list of Filter created in the analysis
- files : [File] : The list of File associated to the analysis (via analysis_file table)
"""
from core.model.project import Project
# With depth loading, sqlalchemy may return several time the same object. Take care to not erase the good depth level)
# Avoid recursion infinit loop
if hasattr(self, "loading_depth") and not force_refresh and self.loading_depth >= loading_depth:
return
else:
self.loading_depth = min(2, loading_depth)
try:
if not self.filter: self.filter = ANALYSIS_DEFAULT_FILTER
self.filters_ids = self.get_filters_ids()
self.samples_ids = AnalysisSample.get_samples_ids(self.id)
self.attributes = self.get_attributes()
self.files_ids = AnalysisFile.get_files_ids(self.id)
self.fullpath = self.get_fullpath()
self.project = None
self.samples = []
self.filters = []
self.files = []
self.panels = []
if self.loading_depth > 0:
self.project = Project.from_id(self.project_id, self.loading_depth-1)
self.samples = AnalysisSample.get_samples(self.id, self.loading_depth-1)
self.filters = self.get_filters(self.loading_depth-1)
self.files = AnalysisFile.get_files(self.id, self.loading_depth-1)
except Exception as ex:
raise RegovarException("Analysis data corrupted (id={}).".format(self.id), "", ex)
def user_new(login=None):
"""
Return a new user object
"""
from core.model.project import Project
# Check login or create a fake one if not provided
if not login:
login = "******".format(User.count() + 1)
# create sandbox project
sandbox = Project.new()
sandbox.load({"comment": "My sandbox"})
u = User(login=login, sandbox_id=sandbox.id)
try:
u.save()
except Exception as ex:
raise RegovarException(
"Unable to create new user with provided informations.", "", ex)
return u
def user_new(login=None):
"""
Return a new user object
"""
from core.model.project import Project
# Check login or create a fake one if not provided
if not login:
login = "******".format(User.count() + 1)
# create sandbox project
sandbox = Project.new()
sandbox.load({"comment": "My sandbox", "is_sandbox": True})
u = User(login=login, sandbox_id=sandbox.id)
try:
u.save()
except Exception as ex:
raise RegovarException("Unable to create new user with provided informations.", "", ex)
u.init()
return u
def subject_get_projects(self, loading_depth=0):
"""
Return the list of projects linked to the subject
"""
from core.model.project import Project
return Project.from_ids(self.get_projects_ids(), loading_depth)
def analysis_init(self, loading_depth=0, force_refresh=False):
"""
Init properties of an analysis :
- id : int : the unique id of the analysis in the database
- project_id : int : the id of the project that owns this analysis
- name : str : the name of the analysis
- comment : str : an optional comment
- settings : json : parameters used to init the analysis
- fields : [str] : The list of field's id to display
- filter : json : The last current filter to applied
- order : [str] : The list of field's id to used to order result
- selection : [str] : The list of ids of selected variants
- create_date : datetime : The date when the analysis have been created
- update_date : datetime : The last time that the analysis have been updated
- total_variants : int : The total number of variant in this analysis
- reference_id : int : Refer to the id of the reference used for this analysis
- computing_progress: json : Used when the working table is computed to store the current progress, error, messages, ...
- status : enum : The status of the analysis : 'empty', 'computing', 'ready', 'error'
- filters_ids : [int] : The list of ids of filters saved for this analysis
- samples_ids : [int] : The list of ids of samples used for analysis
- files_ids : [int] : The list of ids of files associated to the analysis (via analysis_file table)
- attributes : json : The list of attributes defined for this analysis
- fullpath : [json] : The list of folder from root to the analyses [{"id":int, "name":str},...]
- statistics : json : Statistics about the analysis
If loading_depth is > 0, Following properties fill be loaded : (Max depth level is 2)
- project : Project : The that own the analysis
- samples : [Sample] : The list of samples owns by the analysis
- filters : [Filter] : The list of Filter created in the analysis
- files : [File] : The list of File associated to the analysis (via analysis_file table)
"""
from core.model.project import Project
# With depth loading, sqlalchemy may return several time the same object. Take care to not erase the good depth level)
# Avoid recursion infinit loop
if hasattr(self, "loading_depth"
) and not force_refresh and self.loading_depth >= loading_depth:
return
else:
self.loading_depth = min(2, loading_depth)
try:
if not self.filter: self.filter = ANALYSIS_DEFAULT_FILTER
self.filters_ids = self.get_filters_ids()
self.samples_ids = AnalysisSample.get_samples_ids(self.id)
self.attributes = self.get_attributes()
self.files_ids = AnalysisFile.get_files_ids(self.id)
self.fullpath = self.get_fullpath()
self.project = None
self.samples = []
self.filters = []
self.files = []
self.panels = []
if self.loading_depth > 0:
self.project = Project.from_id(self.project_id,
self.loading_depth - 1)
self.samples = AnalysisSample.get_samples(self.id,
self.loading_depth - 1)
self.filters = self.get_filters(self.loading_depth - 1)
self.files = AnalysisFile.get_files(self.id,
self.loading_depth - 1)
except Exception as ex:
raise RegovarException(
"Analysis data corrupted (id={}).".format(self.id), "", ex)
def analysis_load(self, data):
"""
Helper to update several paramters at the same time. Note that dynamics properties (project, samples, files, attributes)
cannot be updated with this method. However, you can update project_id .
To update sample you must used dedicated models object : AnalysisSample
"""
from core.model.project import Project
settings = False
need_to_clean_db = False
try:
if "name" in data.keys(): self.name = check_string(data['name'])
if "project_id" in data.keys():
self.project_id = check_int(data['project_id'])
if "comment" in data.keys():
self.comment = check_string(data['comment'])
if "create_date" in data.keys():
self.create_date = check_date(data['create_date'])
if "update_date" in data.keys():
self.update_date = check_date(data['update_date'])
if "fields" in data.keys(): self.fields = data["fields"]
if "filter" in data.keys(): self.filter = data["filter"]
if "selection" in data.keys(): self.selection = data["selection"]
if "order" in data.keys(): self.order = data["order"]
if "total_variants" in data.keys():
self.total_variants = check_int(data["total_variants"])
if "reference_id" in data.keys():
self.reference_id = check_int(data["reference_id"])
if "computing_progress" in data.keys():
self.computing_progress = check_float(data["computing_progress"])
if "status" in data.keys():
self.status = check_string(data["status"],
"empty") if data["status"] else "empty"
if "attributes" in data.keys(): self.attributes = data["attributes"]
if "statistics" in data.keys(): self.statistics = data["statistics"]
if "files_ids" in data.keys():
self.files_ids = data['files_ids']
# Remove old
for fid in self.files_ids:
if fid not in data["files_ids"]:
AnalysisFile.delete(self.id, fid)
# Add new samples
for fid in data["files_ids"]:
if fid not in self.files_ids:
AnalysisFile.new(self.id, sid)
if "settings" in data.keys():
# When settings change, need to regenerate working table
self.settings = data["settings"]
self.status = "empty"
self.computing_progress = None
need_to_clean_db = True
if "samples_ids" in data.keys():
# Remove old
for sid in self.samples_ids:
if sid not in data["samples_ids"]:
AnalysisSample.delete(self.id, sid)
# Add new samples
for sid in data["samples_ids"]:
if sid not in self.samples_ids:
AnalysisSample.new(self.id, sid)
# When settings change, need to regenerate working table
self.status = "empty"
self.computing_progress = None
need_to_clean_db = True
# If settings empty, init it with informations from samples
if len(self.settings["annotations_db"]) == 0:
settings = self.settings
from core.model.sample import Sample
dbuids = []
for sid in data["samples_ids"]:
sample = Sample.from_id(sid)
if sample and sample.default_dbuid:
for dbuid in sample.default_dbuid:
if dbuid not in dbuids:
dbuids.append(dbuid)
self.status = "empty"
settings["annotations_db"] = dbuids
self.settings = settings
if need_to_clean_db:
execute(
"DROP TABLE IF EXISTS wt_{0} CASCADE; DROP TABLE IF EXISTS wt_{0}_var CASCADE;"
.format(self.id))
# check to reload dynamics properties
if self.loading_depth > 0:
self.project = Project.from_id(self.project_id,
self.loading_depth - 1)
self.samples = AnalysisSample.get_samples(self.id,
self.loading_depth - 1)
self.filters = self.get_filters(self.loading_depth - 1)
self.files = AnalysisFile.get_files(self.id,
self.loading_depth - 1)
self.save()
# FIXME : why sqlalchemy don't care about json settings the first time ?
if settings:
self.settings = settings
self.save()
# END FIXME
except Exception as ex:
raise RegovarException('Invalid input data to load.', "", ex)
return self
def analysis_load(self, data):
"""
Helper to update several paramters at the same time. Note that dynamics properties (project, samples, files, attributes)
cannot be updated with this method. However, you can update project_id .
To update sample you must used dedicated models object : AnalysisSample
"""
from core.model.project import Project
settings = False
need_to_clean_db = False
try:
if "name" in data.keys(): self.name = check_string(data['name'])
if "project_id" in data.keys(): self.project_id = check_int(data['project_id'])
if "comment" in data.keys(): self.comment = check_string(data['comment'])
if "create_date" in data.keys(): self.create_date = check_date(data['create_date'])
if "update_date" in data.keys(): self.update_date = check_date(data['update_date'])
if "fields" in data.keys(): self.fields = data["fields"]
if "filter" in data.keys(): self.filter = data["filter"]
if "selection" in data.keys(): self.selection = data["selection"]
if "order" in data.keys(): self.order = data["order"]
if "total_variants" in data.keys(): self.total_variants = check_int(data["total_variants"])
if "reference_id" in data.keys(): self.reference_id = check_int(data["reference_id"])
if "computing_progress" in data.keys(): self.computing_progress = check_float(data["computing_progress"])
if "status" in data.keys(): self.status = check_string(data["status"], "empty") if data["status"] else "empty"
if "attributes" in data.keys(): self.attributes = data["attributes"]
if "statistics" in data.keys(): self.statistics = data["statistics"]
if "files_ids" in data.keys():
self.files_ids = data['files_ids']
# Remove old
for fid in self.files_ids:
if fid not in data["files_ids"]:
AnalysisFile.delete(self.id, fid)
# Add new samples
for fid in data["files_ids"]:
if fid not in self.files_ids:
AnalysisFile.new(self.id, sid)
if "settings" in data.keys():
# When settings change, need to regenerate working table
self.settings = data["settings"]
self.status = "empty"
self.computing_progress = None
need_to_clean_db = True
if "samples_ids" in data.keys():
# Remove old
for sid in self.samples_ids:
if sid not in data["samples_ids"]:
AnalysisSample.delete(self.id, sid)
# Add new samples
for sid in data["samples_ids"]:
if sid not in self.samples_ids:
AnalysisSample.new(self.id, sid)
# When settings change, need to regenerate working table
self.status = "empty"
self.computing_progress = None
need_to_clean_db = True
# If settings empty, init it with informations from samples
if len(self.settings["annotations_db"]) == 0:
settings = self.settings
from core.model.sample import Sample
dbuids = []
for sid in data["samples_ids"]:
sample = Sample.from_id(sid)
if sample and sample.default_dbuid:
for dbuid in sample.default_dbuid:
if dbuid not in dbuids:
dbuids.append(dbuid)
self.status = "empty"
settings["annotations_db"] = dbuids
self.settings = settings
if need_to_clean_db:
execute("DROP TABLE IF EXISTS wt_{0} CASCADE; DROP TABLE IF EXISTS wt_{0}_var CASCADE;".format(self.id))
# check to reload dynamics properties
if self.loading_depth > 0:
self.project = Project.from_id(self.project_id, self.loading_depth-1)
self.samples = AnalysisSample.get_samples(self.id, self.loading_depth-1)
self.filters = self.get_filters(self.loading_depth-1)
self.files = AnalysisFile.get_files(self.id, self.loading_depth-1)
self.save()
# FIXME : why sqlalchemy don't care about json settings the first time ?
if settings:
self.settings = settings
self.save()
# END FIXME
except Exception as ex:
raise RegovarException('Invalid input data to load.', "", ex)
return self
def subject_get_projects(self, loading_depth=0):
"""
Return the list of projects linked to the subject
"""
from core.model.project import Project
return Project.from_ids(self.get_projects_ids(), loading_depth)