from cubicweb import cwconfig
from cubicweb.dbapi import in_memory_repo_cnx
# Piws import
from cubes.piws.importer.users import CWUsers
from cubes.piws.importer.subjects import Subjects
from cubes.piws.importer.scans import Scans
from cubes.piws.importer.questionnaires import Questionnaires
from cubes.piws.importer.genetics import Genetics
from cubes.piws.importer.processings import Processings
# Define the output_directory
out_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)),
"source", "generated", "schemas")
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
# Generate the schemas
# > user
CWUsers.schema(outfname=os.path.join(out_dir, "users.png"))
# > subjects
Subjects.schema(outfname=os.path.join(out_dir, "subjects.png"))
# > scan
Scans.schema(outfname=os.path.join(out_dir, "scans.png"))
# > questionnaire
Questionnaires.schema(outfname=os.path.join(out_dir, "questionnaires.png"))
# > genetic
Genetics.schema(outfname=os.path.join(out_dir, "genetics.png"))
# > processings
Processings.schema(outfname=os.path.join(out_dir, "processings.png"))
use_store=False)
db_user_importer = CWUsers(session, USERS)
db_subject_importer = Subjects(
session, STUDY_NAME, subjects, use_store=False)
db_scan_importer = Scans(
session, STUDY_NAME, CENTER_NAME, scans, can_read=True, can_update=False,
data_filepath=demo_path, use_store=False)
db_questionnaire_importer = Questionnaires(
session, STUDY_NAME, CENTER_NAME, questionnaires, "Clinical",
can_read=True, can_update=False, data_filepath=demo_path, use_store=False,
use_openanswer=True)
db_genetic_importer = Genetics(
session, STUDY_NAME, CENTER_NAME, genetics, can_read=True,
can_update=False, data_filepath=demo_path, use_store=False)
db_processings_importer = Processings(
session, STUDY_NAME, CENTER_NAME, processings, "FreeSurfer", can_read=True,
can_update=False, data_filepath=demo_path, use_store=False)
# Execute in the appropriate order the importation scripts
# > groups
db_grp_importer.import_data()
db_grp_importer.cleanup()
# > users
db_user_importer.import_data()
db_user_importer.cleanup()
# > subjects
db_subject_importer.import_data()
db_subject_importer.cleanup()
# > scans
db_scan_importer.import_data()
db_scan_importer.cleanup()
from cubicweb import cwconfig
from cubicweb.dbapi import in_memory_repo_cnx
# Piws import
from cubes.piws.importer.users import CWUsers
from cubes.piws.importer.subjects import Subjects
from cubes.piws.importer.scans import Scans
from cubes.piws.importer.questionnaires import Questionnaires
from cubes.piws.importer.genetics import Genetics
from cubes.piws.importer.processings import Processings
# Define the output_directory
out_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), "source",
"generated", "schemas")
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
# Generate the schemas
# > user
CWUsers.schema(outfname=os.path.join(out_dir, "users.png"))
# > subjects
Subjects.schema(outfname=os.path.join(out_dir, "subjects.png"))
# > scan
Scans.schema(outfname=os.path.join(out_dir, "scans.png"))
# > questionnaire
Questionnaires.schema(outfname=os.path.join(out_dir, "questionnaires.png"))
# > genetic
Genetics.schema(outfname=os.path.join(out_dir, "genetics.png"))
# > processings
Processings.schema(outfname=os.path.join(out_dir, "processings.png"))
data_filepath=demo_path,
store_type=store_type,
use_openanswer=True)
db_genetic_importer = Genetics(session,
STUDY_NAME,
CENTER_NAME,
genetics,
can_read=True,
can_update=False,
data_filepath=demo_path,
store_type=store_type)
db_processings_importer = Processings(session,
STUDY_NAME,
CENTER_NAME,
processings,
"FreeSurfer",
can_read=True,
can_update=False,
data_filepath=demo_path,
store_type=store_type)
# Execute in the appropriate order the importation scripts
# > groups
db_grp_importer.import_data()
db_grp_importer.cleanup()
# > users
db_user_importer.import_data()
db_user_importer.cleanup()
# > subjects
db_subject_importer.import_data()
db_subject_importer.cleanup()
