"""
All database tramsactions related to the instrumentattion and instrumentation journal go here.
Again, related templates for instruments and JEntres are inside this modul.
"""
from flask_sqlalchemy import SQLAlchemy
from werkzeug.utils import secure_filename
# from flask import g # This should not be needed here and be always a parameter for the function
from ResearchNotes.database import (
EntryType,
TemplateInstrumentationJournalEntry,
Instrument,
InstrumentationJournalEntry,
TemplateInstrument,
)
from .basics import Transaction
# =============================================================================
# entry.py - instrumentation journal entry management
# =============================================================================
[docs]def create_instrumentation_journal_entry(database: SQLAlchemy, entry_info: dict) -> int:
"""
Create an instrumentation journal entry.
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
entry_info: Dict
Information needed to initialize an Instrumentation Journal Entry object
Returns
-------
int
ID of the newly created jentry.
"""
new_entry = InstrumentationJournalEntry(
identifier=secure_filename(entry_info["identifier"]),
description=entry_info["description"],
creator_id=entry_info["creator_id"],
group_id=entry_info["group_id"],
instrument_id=entry_info["instrument_id"],
)
if entry_info["etype"] != 0:
new_entry.etype_id = entry_info["etype"]
with Transaction(database) as db_session:
db_session.add(new_entry)
return new_entry.id
[docs]def update_instrumentation_journal_entry(
database: SQLAlchemy, entry: InstrumentationJournalEntry, entry_info: dict
) -> None:
"""
Update an instrumentation journal entry
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
entry_info: Dict
Updated fields of an Instrumentation Journal Entry object
Returns
-------
None.
"""
with Transaction(database):
entry.identifier = secure_filename(entry_info["identifier"])
entry.description = entry_info["description"]
# if entry_info["etype"] != 0:
entry.etype_id = entry_info["etype"]
[docs]def create_etype(database: SQLAlchemy, etype_info: dict) -> None:
"""
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
etype_info: Dict
Instrumentation journal entry type information
Returns
-------
None
"""
new_etype = EntryType(
name=etype_info["name"],
instrument_id=etype_info["instrument_id"],
)
with Transaction(database) as db_session:
db_session.add(new_etype)
[docs]def update_etype(database: SQLAlchemy, etype: EntryType, etype_info: dict) -> None:
"""
Updates existing entry types.
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using
etype: EntryType
Instrumentation journal entry type to update
etype_info: Dict
Instrumentation journal entry type information
Returns
-------
None
"""
with Transaction(database):
etype.name = etype_info["name"]
# =============================================================================
# instruments.py - instruments/machines management
# =============================================================================
[docs]def create_instrument(database: SQLAlchemy, instrument_info: dict) -> int:
"""
Creates an instrument based on the data of a web form.
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
instrument_info: Dict
Information needed to initialize an Instrument object
Returns
-------
int
New instrument ID.
"""
new_instrument = Instrument(
identifier=secure_filename(instrument_info["identifier"]),
description=instrument_info["description"],
creator_id=instrument_info["creator_id"],
group_id=instrument_info["group_id"],
location_id=instrument_info["location_id"],
)
with Transaction(database) as db_session:
db_session.add(new_instrument)
return new_instrument.id
[docs]def update_instrument(
database: SQLAlchemy, instrument: Instrument, instrument_info: dict[str | int | None]
) -> None:
"""
Update the metadata associated with an instrument.
Pass a dict with the needed information (identifier, description, and
location_id).
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
sample: Sample
Entry of Sample object to be updated.
sample_data: dict
Containing the updated fields.
Returns
-------
None.
"""
with Transaction(database):
instrument.identifier = secure_filename(instrument_info["identifier"])
instrument.description = instrument_info["description"]
instrument.location_id = instrument_info["location_id"]
[docs]def deactivate_instrument(database: SQLAlchemy, instrument: Instrument) -> None:
"""
Deactivate an instrument.
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
instrument: Instrument
Instrument to be deactivated.
Returns
-------
None.
"""
with Transaction(database):
instrument.active = False
[docs]def activate_instrument(database: SQLAlchemy, instrument: Instrument) -> None:
"""
Activate an instrument.
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
instrument: Instrument
Instrument to be activated.
Returns
-------
None.
"""
with Transaction(database):
instrument.active = True
[docs]def update_default_instrument_templates(
database: SQLAlchemy,
instrument: Instrument,
default_ess: None | int,
default_ppm: None | int,
default_jentry: None | int,
) -> None:
"""
Update the default templates of the instrument.
Update the default templates for ESS, PPM and JEntry. If set to 0 or None, we set things to None in the database.
This should resolve the problems seen with more advanced databases and foreign key referring.
Parameters
----------
database
SQLAlchemy Database object to update.
instrument
Table to update (here Instruments)
default_ess : None|int
ID of the default EES template or None
default_ppm : None|int
ID of the default PPM template or None
default_jentry : None|int
ID of the default JEntry template or None
Returns
-------
"""
with Transaction(database):
if default_ess != 0:
instrument.default_ess_template_id = default_ess
else:
instrument.default_ess_template_id = None
if default_ppm != 0:
instrument.default_ppm_template_id = default_ppm
else:
instrument.default_ppm_template_id = None
if default_jentry != 0:
instrument.default_entry_template_id = default_jentry
else:
instrument.default_entry_template_id = None
# =============================================================================
# template.py - template management
# =============================================================================
[docs]def create_template_instrument(database: SQLAlchemy, template_info: dict) -> None:
"""
Create a template instrument.
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
template_info: Dict
Information needed to create a TemplateInstrument object
Returns
-------
None.
"""
instrument_template = TemplateInstrument(
tname=template_info["tname"],
identifier=secure_filename(template_info["identifier"]),
description=template_info["description"],
# location_id=template_info["location_id"],
creator_id=template_info["creator_id"],
group_id=template_info["group_id"],
)
with Transaction(database) as db_session:
db_session.add(instrument_template)
[docs]def update_template_instrument(
database: SQLAlchemy, template: TemplateInstrument, template_info: dict
) -> None:
"""
Update a instrument template based on the data of a web form.
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
template : TemplateSamples
temp_info: Dict
Returns
-------
None.
"""
with Transaction(database):
template.tname = template_info["tname"]
template.identifier = template_info["identifier"]
template.description = template_info["description"]
# template.location_id = template_info["location_id"]
[docs]def create_template_entry(database: SQLAlchemy, template_info: dict) -> None:
"""
Create a template instrumentation journal entry.
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
template_info: Dict
Information needed to create a TemplateInstrumentationJournalEntry object
Returns
-------
None.
"""
instrument_template = TemplateInstrumentationJournalEntry(
tname=template_info["tname"],
identifier=secure_filename(template_info["identifier"]),
description=template_info["description"],
creator_id=template_info["creator_id"],
group_id=template_info["group_id"],
etype_id=template_info.get("etype_id", None),
)
with Transaction(database) as db_session:
db_session.add(instrument_template)
[docs]def update_template_entry(
database: SQLAlchemy, template: TemplateInstrumentationJournalEntry, template_info: dict
) -> None:
"""
Update a instrumentation journal entry template based on the data of a web form.
Parameters
----------
database: FlaskSQLAlchemy class
Database handler that the Flask APP is using.
template : TemplateInstrumentationJournalEntry
template_info: Dict
Returns
-------
None.
"""
with Transaction(database):
template.tname = template_info["tname"]
template.identifier = template_info["identifier"]
template.description = template_info["description"]
template.etype_id = template_info["etype_id"]