Helper functions to check and get things from lookup tables (#152)

* get_db_publication and test

* get_db_regime and tests

* get_db_instrument and tests

* ingest_instrument improvements

Author: kelle

astrodb_utils/__init__.py

@@ -5,7 +5,6 @@
 from .utils import (  # noqa: F401
     AstroDBError,
     exit_function,
-    ingest_instrument,
     internet_connection,
     load_astrodb,
 )
@@ -15,7 +14,7 @@
 
 
 
-logger = logging.getLogger("astrodb_utils")
+logger = logging.getLogger(__name__) # Sets up the parent "astrodb_utils" logger
 
 LOGFORMAT = logging.Formatter(
     "%(levelname)-8s - %(name)-15s - %(message)s")
@@ -30,7 +29,7 @@
 handler.setFormatter(LOGFORMAT)
 logger.addHandler(handler)
 
-logger.info(f"Logger initialized: {logger.name}")
-logger.info(f"Logger level: {logging.getLevelName(logger.getEffectiveLevel()) }")
+logger.setLevel(logging.INFO)  # Set the default logging level to INFO
+logger.debug(f"Logger level: {logging.getLevelName(logger.getEffectiveLevel()) }")
 
 warnings.filterwarnings("ignore", module="astroquery.simbad")

astrodb_utils/instruments.py

@@ -0,0 +1,154 @@
+import logging
+
+import sqlalchemy.exc
+from sqlalchemy import and_
+
+from astrodb_utils import AstroDBError, exit_function
+
+__all__ = [
+    "ingest_instrument",
+    "get_db_instrument"
+]
+
+logger = logging.getLogger(__name__)
+
+
+def ingest_instrument(db, *, telescope=None, instrument=None, mode=None, raise_error=True):
+    """
+    Script to ingest instrumentation
+    TODO: Add option to ingest references for the telescope and instruments
+
+    Parameters
+    ----------
+    db: astrodbkit.astrodb.Database
+        Database object created by astrodbkit
+    telescope: str
+    instrument: str
+    mode: str
+
+    Returns
+    -------
+
+    None
+
+    """
+
+    # Make sure enough inputs are provided
+    if telescope is None and (instrument is None or mode is None):
+        msg = "Telescope, Instrument, and Mode must be provided"
+        logger.error(msg)
+        raise AstroDBError(msg)
+
+    msg_search = f"Searching for {telescope}, {instrument}, {mode} in database"
+    logger.debug(msg_search)
+
+    # Search for the inputs in the database
+    telescope_db = (
+        db.query(db.Telescopes).filter(db.Telescopes.c.telescope == telescope).table()
+    )
+    mode_db = (
+        db.query(db.Instruments)
+        .filter(
+            and_(
+                db.Instruments.c.mode == mode,
+                db.Instruments.c.instrument == instrument,
+                db.Instruments.c.telescope == telescope,
+            )
+        )
+        .table()
+    )
+
+    if len(telescope_db) == 1 and len(mode_db) == 1:
+        msg_found = (
+            f"{telescope}-{instrument}-{mode} is already in the database. Nothing added."
+        )
+        logger.info(msg_found)
+        return
+
+    # Ingest telescope entry if not already present
+    if telescope is not None and len(telescope_db) == 0:
+        telescope_add = [{"telescope": telescope}]
+        try:
+            with db.engine.connect() as conn:
+                conn.execute(db.Telescopes.insert().values(telescope_add))
+                conn.commit()
+            msg_telescope = f"{telescope} was successfully ingested in the database"
+            logger.info(msg_telescope)
+        except sqlalchemy.exc.IntegrityError as e:  # pylint: disable=invalid-name
+            msg =f"Telescope could not be ingested: {telescope}"
+            logger.error(msg)
+            raise AstroDBError(msg) from e
+
+    # Ingest instrument+mode (requires telescope) if not already present
+    if (
+        telescope is not None
+        and instrument is not None
+        and mode is not None
+        and len(mode_db) == 0
+    ):
+        instrument_add = [
+            {"instrument": instrument, "mode": mode, "telescope": telescope}
+        ]
+        try:
+            with db.engine.connect() as conn:
+                conn.execute(db.Instruments.insert().values(instrument_add))
+                conn.commit()
+            msg_instrument = f"{telescope}-{instrument}-{mode} was successfully ingested in the database."
+            logger.info(msg_instrument)
+        except sqlalchemy.exc.IntegrityError as e:  # pylint: disable=invalid-name
+            msg = "Instrument/Mode could not be ingested: {telescope}-{instrument}-{mode} "
+            logger.error(msg)
+            raise AstroDBError(msg) from e
+
+    return
+
+
+def get_db_instrument(db, instrument=None, mode=None, telescope=None):
+    instrument_table = (
+        db.query(db.Instruments)
+        .filter(
+            and_(
+                db.Instruments.c.instrument.contains(instrument),
+                db.Instruments.c.telescope.contains(telescope),
+            )
+        )
+        .table()
+    )
+
+    if len(instrument_table) > 1: # constrain query with instrument mode
+        instrument_table = (
+            db.query(db.Instruments)
+            .filter(
+                and_(
+                    db.Instruments.c.instrument.contains(instrument),
+                    db.Instruments.c.mode.ilike(mode),
+                    db.Instruments.c.telescope.contains(telescope),
+                )
+            )
+            .table()
+        )
+
+    if len(instrument_table) == 1:
+        if (
+            instrument_table["instrument"][0] != instrument
+            or instrument_table["mode"][0] != mode
+            or instrument_table["telescope"][0] != telescope
+        ):
+            msg = (
+                f"Instrument {instrument} with mode {mode} and telescope {telescope} "
+                f"matched to {instrument_table['instrument'][0]}-{instrument_table['mode'][0]}-{instrument_table['telescope'][0]}. "
+            )
+            logger.warning(msg) 
+
+        return (
+            instrument_table["instrument"][0],
+            instrument_table["mode"][0],
+            instrument_table["telescope"][0],
+        )
+
+    if len(instrument_table) == 0:
+        msg = f"{telescope}-{instrument}-{mode}, not found in database. Please add it to the Instruments table."
+    else:
+        msg = f"Multiple matches found for {telescope}-{instrument}-{mode}. Please check the Instruments table."
+
+    exit_function(msg, raise_error=True, return_value=None)

astrodb_utils/photometry.py

@@ -12,9 +12,9 @@
 
 from astrodb_utils import (
     AstroDBError,
-    ingest_instrument,
     internet_connection,
 )
+from astrodb_utils.instruments import ingest_instrument
 from astrodb_utils.publications import find_publication
 from astrodb_utils.sources import find_source_in_db