Python MassSpecDatabaseAdapter Examples

Example #1

File: mass_spec_reverter.py Project: NMGRL/pychron

 def setup_destination(self):
     dest = MassSpecDatabaseAdapter()
     dest.trait_set(name='massspecdata_crow',
                    kind='mysql',
                    username='******',
                    password=os.environ.get('DB_PWD'))
     self.destination = dest

Example #2

File: mass_spec_reverter.py Project: ael-noblegas/pychron

 def setup_destination(self):
     dest = MassSpecDatabaseAdapter()
     dest.trait_set(name='massspecdata_crow',
                    kind='mysql',
                    username='******',
                    password=os.environ.get('DB_PWD'))
     self.destination = dest

Example #3

File: mass_spec_irradiation_exporter.py Project: NMGRL/pychron

    def setup(self):
        """
            return True if connection to dest made
        """
        dest = MassSpecDatabaseAdapter(bind=False)
        dest.trait_set(**self.destination_spec)
        self.destination = dest

        return self.destination.connect()

Example #4

File: mass_spec_irradiation_exporter.py Project: stephen-e-cox/pychron

    def setup(self):
        """
            return True if connection to dest made
        """
        dest = MassSpecDatabaseAdapter(bind=False)
        dest.trait_set(**self.destination_spec)
        self.destination = dest

        return self.destination.connect()

Example #5

File: analysis_modifier.py Project: stephen-e-cox/pychron

    def _secondary_db_default(self):
        from apptools.preferences.preference_binding import bind_preference

        db = MassSpecDatabaseAdapter()
        prefid = 'pychron.massspec.database'
        bind_preference(db, 'host', '{}.host'.format(prefid))
        bind_preference(db, 'username', '{}.username'.format(prefid))
        bind_preference(db, 'name', '{}.name'.format(prefid))
        bind_preference(db, 'password', '{}.password'.format(prefid))
        return db

Example #6

def massspec_db_factory(path, remove=True):
    from pychron.mass_spec.database.massspec_database_adapter import MassSpecDatabaseAdapter
    from pychron.mass_spec.database.massspec_orm import Base

    if remove and os.path.isfile(path):
        os.remove(path)

    db = MassSpecDatabaseAdapter()
    # db.verbose_retrieve_query = True
    db.trait_set(kind='sqlite', path=path)
    db.connect()

    metadata = Base.metadata
    db.create_all(metadata)
    return db

Example #7

File: test_helpers.py Project: NMGRL/pychron

def massspec_db_factory(path, remove=True):
    from pychron.mass_spec.database.massspec_database_adapter import MassSpecDatabaseAdapter
    from pychron.mass_spec.database.massspec_orm import Base

    if remove and os.path.isfile(path):
        os.remove(path)

    db = MassSpecDatabaseAdapter()
    # db.verbose_retrieve_query = True
    db.trait_set(kind='sqlite', path=path)
    db.connect()

    metadata = Base.metadata
    db.create_all(metadata)
    return db

Example #8

# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# ===============================================================================

# ============= enthought library imports =======================
import os

# ============= standard library imports ========================
# ============= local library imports  ==========================
os.environ['MassSpecDBVersion'] = '16'
from pychron.mass_spec.database.massspec_database_adapter import MassSpecDatabaseAdapter
from pychron.mass_spec.database.massspec_orm import AnalysesTable, IsotopeTable, DetectorTable

db = MassSpecDatabaseAdapter(bind=False)
db.host = '129.138.12.160'
db.name = 'massspecdata'
db.username = '******'
db.password = '******'
db.kind = 'mysql'
db.connect(test=False)


def fix_reference_detector(rd, aid):
    with db.session_ctx() as sess:
        q = sess.query(AnalysesTable)
        q = q.filter(AnalysesTable.AnalysisID == aid)
        record = q.one()

        q = sess.query(DetectorTable)

Example #9

File: mass_spec_utilities.py Project: ael-noblegas/pychron

# See the License for the specific language governing permissions and
# limitations under the License.
# ===============================================================================

# ============= enthought library imports =======================
from __future__ import absolute_import
from __future__ import print_function
import os

# ============= standard library imports ========================
# ============= local library imports  ==========================
os.environ['MassSpecDBVersion'] = '16'
from pychron.mass_spec.database.massspec_database_adapter import MassSpecDatabaseAdapter
from pychron.mass_spec.database.massspec_orm import AnalysesTable, IsotopeTable, DetectorTable

db = MassSpecDatabaseAdapter(bind=False)
db.host = '129.138.12.160'
db.name = 'massspecdata'
db.username = '******'
db.password = '******'
db.kind = 'mysql'
db.connect(test=False)


def fix_reference_detector(rd, aid):
    q = db.session.query(AnalysesTable)
    q = q.filter(AnalysesTable.AnalysisID == aid)
    record = q.one()

    q = db.session.query(DetectorTable)
    q = q.join(IsotopeTable)

Example #10

File: mass_spec_database_importer.py Project: tdurieux/BugSwarm-dissection

    def _db_default(self):
        db = MassSpecDatabaseAdapter(kind='mysql', autoflush=False)

        return db