def main():
from pychron.paths import paths
paths.build('_dev')
from pychron.core.helpers.logger_setup import logging_setup
from pychron.experiment.automated_run.spec import AutomatedRunSpec
logging_setup('dvcdb')
from pychron.dvc.dvc_database import DVCDatabase
from itertools import groupby
db = DVCDatabase(kind='mysql', host='localhost', username='******', name='pychronmeta', password='******')
db.connect()
identifiers = ['63290', '63291']
runs = [AutomatedRunSpec(identifier='63290', repository_identifier='Cather_McIntoshd')]
cr = ConflictResolver()
experiments = {}
cr.available_ids = db.get_repository_identifiers()
eas = db.get_associated_repositories(identifiers)
for idn, exps in groupby(eas, key=lambda x: x[1]):
experiments[idn] = [e[0] for e in exps]
conflicts = []
for ai in runs:
identifier = ai.identifier
es = experiments[identifier]
if ai.repository_identifier not in es:
conflicts.append((ai, es))
if conflicts:
cr.add_conflicts('Foo', conflicts)
if cr.conflicts:
info = cr.edit_traits(kind='livemodal')
if info.result:
cr.apply()
def main():
from pychron.paths import paths
paths.build('_dev')
from pychron.core.helpers.logger_setup import logging_setup
from pychron.experiment.automated_run.spec import AutomatedRunSpec
logging_setup('dvcdb')
from pychron.dvc.dvc_database import DVCDatabase
from itertools import groupby
db = DVCDatabase(kind='mysql',
host='localhost',
username='******',
name='pychronmeta',
password='******')
db.connect()
identifiers = ['63290', '63291']
runs = [
AutomatedRunSpec(identifier='63290',
repository_identifier='Cather_McIntoshd')
]
cr = ConflictResolver()
experiments = {}
with db.session_ctx():
cr.available_ids = db.get_repository_identifiers()
eas = db.get_associated_repositories(identifiers)
for idn, exps in groupby(eas, key=lambda x: x[1]):
experiments[idn] = [e[0] for e in exps]
conflicts = []
for ai in runs:
identifier = ai.identifier
es = experiments[identifier]
if ai.repository_identifier not in es:
conflicts.append((ai, es))
if conflicts:
cr.add_conflicts('Foo', conflicts)
if cr.conflicts:
info = cr.edit_traits(kind='livemodal')
if info.result:
cr.apply()
if prog:
# if prog and i % 25 == 0:
prog.change_message('Loading {}'.format(xi.record_id))
return xi
return progress_loader(ans, func, threshold=25, step=25)
def _load_entries(self):
p = paths.hidden_path('search_entries')
if os.path.isfile(p):
with open(p, 'r') as rfile:
self.search_entries = yaml.load(rfile)
def _search_entry_changed(self):
self.search()
if __name__ == '__main__':
db = DVCDatabase(bind=False, kind='mysql', host='localhost', username='******', name='pychrondvc_dev',
password='******')
db.connect()
# s = SearchParser(db=db)
# s.parse('s:FC-2')
# s.parse('s:=FC-2')
# s.parse('s=FC-2')
s = Searcher(db=db)
s.search_entry = 's:FC-2'
s.search()
# ============= EOF =============================================
dlg = FileDialog(action='open', default_directory=paths.irradiation_tray_maps_dir)
if dlg.open() == OK:
if dlg.path:
# verify this is a valid irradiation map file
if parse_irradiation_tray_map(dlg.path) is not None:
db = self.db
load_irradiation_map(db, dlg.path,
os.path.basename(dlg.path), overwrite_geometry=True)
if __name__ == '__main__':
paths.build('_dev')
logging_setup('le')
from pychron.dvc.dvc_database import DVCDatabase
dbt = DVCDatabase(kind='sqlite', path='/Users/ross/Programming/test3.sqlite')
dbt.connect()
# from pychron.dvc.meta_repo import MetaRepo
mr = MetaRepo()
mr.open_repo(paths.meta_root)
class Demo(HasTraits):
test = Button
traits_view = View('test')
def _test_fired(self):
e = LevelEditor(db=dbt,
meta_repo=mr,
irradiation='NM-274',
# verify this is a valid irradiation map file
if parse_irradiation_tray_map(dlg.path) is not None:
db = self.db
with db.session_ctx():
load_irradiation_map(db,
dlg.path,
os.path.basename(dlg.path),
overwrite_geometry=True)
if __name__ == '__main__':
paths.build('_dev')
logging_setup('le')
from pychron.dvc.dvc_database import DVCDatabase
dbt = DVCDatabase(kind='sqlite',
path='/Users/ross/Programming/test3.sqlite')
dbt.connect()
# from pychron.dvc.meta_repo import MetaRepo
mr = MetaRepo()
mr.open_repo(paths.meta_root)
class Demo(HasTraits):
test = Button
traits_view = View('test')
def _test_fired(self):
e = LevelEditor(db=dbt,
meta_repo=mr,
irradiation='NM-274',
name='H')
attr = getattr(tbl, attr)
if ',' in val:
f = attr.in_(val.split('.'))
else:
f = attr == val
filters.append(f)
else:
print('invalid table {}'.format(tbl))
return filters
if __name__ == '__main__':
db = DVCDatabase(
host='localhost',
username=os.environ.get('LOCALHOST_DB_USER'),
password=os.environ.get('LOCALHOST_DB_PWD'),
kind='mysql',
# echo=True,
name='pychrondvc_dev')
txt = '''project.name: Irradiation-NM-274
sample: FC-2'''
# txt = '''sample: FC-2'''
db.connect()
c = CustomAnalysisQuery(db=db)
q = c.generate_query(txt)
c.execute_query(q)
# ============= EOF =============================================
def _clone_central_db(self,
repositories,
analyses=None,
principal_investigators=None,
projects=None):
self.info('--------- Clone DB -----------')
# create an a sqlite database
from pychron.dvc.dvc_orm import Base
metadata = Base.metadata
from pychron.dvc.dvc_database import DVCDatabase
path = database_path()
if os.path.isfile(path):
if not self.confirmation_dialog(
'The database "{}" already exists. '
'Do you want to overwrite it'.format(
os.path.basename(path))):
path = self._get_new_path()
else:
os.remove(path)
if path:
progress = open_progress(n=20)
self.debug('--------- Starting db clone to {}'.format(path))
src = self.dvc
db = DVCDatabase(path=path, kind='sqlite')
db.connect()
with db.session_ctx(use_parent_session=False) as sess:
metadata.create_all(sess.bind)
tables = [
'MassSpectrometerTbl', 'ExtractDeviceTbl', 'VersionTbl',
'UserTbl'
]
for table in tables:
mod = __import__('pychron.dvc.dvc_orm', fromlist=[table])
progress.change_message('Cloning {}'.format(table))
self._copy_table(db, getattr(mod, table))
with src.session_ctx(use_parent_session=False):
from pychron.dvc.dvc_orm import RepositoryTbl
from pychron.dvc.dvc_orm import AnalysisTbl
from pychron.dvc.dvc_orm import AnalysisChangeTbl
from pychron.dvc.dvc_orm import RepositoryAssociationTbl
from pychron.dvc.dvc_orm import AnalysisGroupTbl
from pychron.dvc.dvc_orm import AnalysisGroupSetTbl
from pychron.dvc.dvc_orm import MaterialTbl
from pychron.dvc.dvc_orm import SampleTbl
from pychron.dvc.dvc_orm import IrradiationTbl
from pychron.dvc.dvc_orm import LevelTbl
from pychron.dvc.dvc_orm import IrradiationPositionTbl
from pychron.dvc.dvc_orm import PrincipalInvestigatorTbl
repos = [
src.db.get_repository(reponame)
for reponame in repositories
]
progress.change_message('Assembling Analyses 0/5')
st = time.time()
if analyses:
ans = analyses
ras = [
rai for ai in ans for rai in ai.repository_associations
]
else:
# at = time.time()
ras = [
ra for repo in repos
for ra in repo.repository_associations
]
# self.debug('association time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 1/5')
# at = time.time()
ans = [ri.analysis for ri in ras]
# self.debug('analysis time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 2/5')
# at = time.time()
ans_c = [ai.change for ai in ans]
# self.debug('change time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 3/5')
# at = time.time()
agss = [gi for ai in ans for gi in ai.group_sets]
# self.debug('agss time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 4/5')
# at = time.time()
ags = {gi.group for gi in agss}
# self.debug('ags time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 5/5')
self.debug(
'total analysis assembly time={}'.format(time.time() - st))
self._copy_records(progress, db, RepositoryTbl, repos)
self._copy_records(progress, db, RepositoryAssociationTbl, ras)
self._copy_records(progress, db, AnalysisTbl, ans)
self._copy_records(progress, db, AnalysisChangeTbl, ans_c)
self._copy_records(progress, db, AnalysisGroupTbl, ags)
self._copy_records(progress, db, AnalysisGroupSetTbl, agss)
if principal_investigators:
pis = [
src.get_principal_investigator(pp.name)
for pp in principal_investigators
]
else:
pis = {repo.principal_investigator for repo in repos}
self._copy_records(progress, db, PrincipalInvestigatorTbl, pis)
from pychron.dvc.dvc_orm import ProjectTbl
if projects:
prjs = [src.get_project(pp) for pp in projects]
else:
prjs = {
ai.irradiation_position.sample.project
for ai in ans
}
self._copy_records(progress, db, ProjectTbl, prjs)
ips = {ai.irradiation_position for ai in ans}
sams = {ip.sample for ip in ips}
mats = {si.material for si in sams}
self._copy_records(progress, db, MaterialTbl, mats)
self._copy_records(progress, db, SampleTbl, sams)
ls = {ip.level for ip in ips}
irs = {l.irradiation for l in ls}
self._copy_records(progress, db, IrradiationTbl, irs)
self._copy_records(progress, db, LevelTbl, ls)
self._copy_records(progress, db, IrradiationPositionTbl, ips)
self.debug('--------- db clone finished')
progress.close()
self.information_dialog('Database saved to "{}"'.format(path))
return path
def _clone_central_db(self, repositories, analyses=None, principal_investigators=None, projects=None):
self.info('--------- Clone DB -----------')
# create an a sqlite database
from pychron.dvc.dvc_orm import Base
metadata = Base.metadata
from pychron.dvc.dvc_database import DVCDatabase
path = database_path()
if os.path.isfile(path):
if not self.confirmation_dialog('The database "{}" already exists. '
'Do you want to overwrite it'.format(os.path.basename(path))):
path = self._get_new_path()
else:
os.remove(path)
if path:
progress = open_progress(n=20)
self.debug('--------- Starting db clone to {}'.format(path))
src = self.dvc
db = DVCDatabase(path=path, kind='sqlite')
db.connect()
with db.session_ctx(use_parent_session=False) as sess:
metadata.create_all(sess.bind)
tables = ['MassSpectrometerTbl', 'ExtractDeviceTbl', 'VersionTbl', 'UserTbl']
for table in tables:
mod = __import__('pychron.dvc.dvc_orm', fromlist=[table])
progress.change_message('Cloning {}'.format(table))
self._copy_table(db, getattr(mod, table))
with src.session_ctx(use_parent_session=False):
from pychron.dvc.dvc_orm import RepositoryTbl
from pychron.dvc.dvc_orm import AnalysisTbl
from pychron.dvc.dvc_orm import AnalysisChangeTbl
from pychron.dvc.dvc_orm import RepositoryAssociationTbl
from pychron.dvc.dvc_orm import AnalysisGroupTbl
from pychron.dvc.dvc_orm import AnalysisGroupSetTbl
from pychron.dvc.dvc_orm import MaterialTbl
from pychron.dvc.dvc_orm import SampleTbl
from pychron.dvc.dvc_orm import IrradiationTbl
from pychron.dvc.dvc_orm import LevelTbl
from pychron.dvc.dvc_orm import IrradiationPositionTbl
from pychron.dvc.dvc_orm import PrincipalInvestigatorTbl
repos = [src.db.get_repository(reponame) for reponame in repositories]
progress.change_message('Assembling Analyses 0/5')
st = time.time()
if analyses:
ans = analyses
ras = [rai for ai in ans
for rai in ai.repository_associations]
else:
# at = time.time()
ras = [ra for repo in repos for ra in repo.repository_associations]
# self.debug('association time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 1/5')
# at = time.time()
ans = [ri.analysis for ri in ras]
# self.debug('analysis time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 2/5')
# at = time.time()
ans_c = [ai.change for ai in ans]
# self.debug('change time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 3/5')
# at = time.time()
agss = [gi for ai in ans for gi in ai.group_sets]
# self.debug('agss time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 4/5')
# at = time.time()
ags = {gi.group for gi in agss}
# self.debug('ags time={}'.format(time.time()-at))
progress.change_message('Assembling Analyses 5/5')
self.debug('total analysis assembly time={}'.format(time.time()-st))
self._copy_records(progress, db, RepositoryTbl, repos)
self._copy_records(progress, db, RepositoryAssociationTbl, ras)
self._copy_records(progress, db, AnalysisTbl, ans)
self._copy_records(progress, db, AnalysisChangeTbl, ans_c)
self._copy_records(progress, db, AnalysisGroupTbl, ags)
self._copy_records(progress, db, AnalysisGroupSetTbl, agss)
if principal_investigators:
pis = [src.get_principal_investigator(pp.name) for pp in principal_investigators]
else:
pis = {repo.principal_investigator for repo in repos}
self._copy_records(progress, db, PrincipalInvestigatorTbl, pis)
from pychron.dvc.dvc_orm import ProjectTbl
if projects:
prjs = [src.get_project(pp) for pp in projects]
else:
prjs = {ai.irradiation_position.sample.project for ai in ans}
self._copy_records(progress, db, ProjectTbl, prjs)
ips = {ai.irradiation_position for ai in ans}
sams = {ip.sample for ip in ips}
mats = {si.material for si in sams}
self._copy_records(progress, db, MaterialTbl, mats)
self._copy_records(progress, db, SampleTbl, sams)
ls = {ip.level for ip in ips}
irs = {l.irradiation for l in ls}
self._copy_records(progress, db, IrradiationTbl, irs)
self._copy_records(progress, db, LevelTbl, ls)
self._copy_records(progress, db, IrradiationPositionTbl, ips)
self.debug('--------- db clone finished')
progress.close()
self.information_dialog('Database saved to "{}"'.format(path))
return path
def _db_default(self):
return DVCDatabase(kind='mysql',
username='******',
password='******',
host='localhost',
name='pychronmeta')
