Ingest parallax function and ingest data from Ultracool sheet (#528)

* updated ingest_parallax to return flags
* formatting fixes and made logger stream to stdout
* improved tests
* refactored keyword arguments

scripts/ingests/ultracool_sheet/Ingest_Parallax.py

@@ -0,0 +1,130 @@
+from astrodb_utils import load_astrodb, find_source_in_db, AstroDBError
+import sys
+
+sys.path.append(".")
+import logging
+from astropy.io import ascii
+from simple.schema import Photometry
+from simple.schema import REFERENCE_TABLES
+from math import isnan
+from simple.utils.astrometry import ingest_parallax
+from scripts.ingests.ultracool_sheet.references import uc_ref_to_simple_ref
+
+
+logger = logging.getLogger(__name__)
+
+# Logger setup
+# This will stream all logger messages to the standard output and
+# apply formatting for that
+logger.propagate = False  # prevents duplicated logging messages
+LOGFORMAT = logging.Formatter(
+    "%(asctime)s %(levelname)s: %(message)s", datefmt="%m/%d/%Y %I:%M:%S%p"
+)
+ch = logging.StreamHandler(stream=sys.stdout)
+ch.setFormatter(LOGFORMAT)
+# To prevent duplicate handlers, only add if they haven't been set previously
+if len(logger.handlers) == 0:
+    logger.addHandler(ch)
+logger.setLevel(logging.INFO)
+
+DB_SAVE = False
+RECREATE_DB = True
+db = load_astrodb(
+    "SIMPLE.sqlite", recreatedb=RECREATE_DB, reference_tables=REFERENCE_TABLES
+)
+
+
+# Load Ultracool sheet
+doc_id = "1i98ft8g5mzPp2DNno0kcz4B9nzMxdpyz5UquAVhz-U8"
+sheet_id = "361525788"
+link = (
+    f"https://docs.google.com/spreadsheets/d/{doc_id}/export?format=csv&gid={sheet_id}"
+)
+
+# read the csv data into an astropy table
+uc_sheet_table = ascii.read(
+    link,
+    format="csv",
+    data_start=1,
+    header_start=0,
+    guess=False,
+    fast_reader=False,
+    delimiter=",",
+)
+
+no_sources = 0
+multiple_sources = 0
+ingested = 0
+already_exists = 0
+no_data = 0
+
+# Ingest loop
+for source in uc_sheet_table:
+    if isnan(source["plx_lit"]):  # skip if no data
+        no_data += 1
+        continue
+    uc_sheet_name = source["name"]
+    match = find_source_in_db(
+        db,
+        uc_sheet_name,
+        ra=source["ra_j2000_formula"],
+        dec=source["dec_j2000_formula"],
+    )
+
+    if len(match) == 1:
+        # 1 Match found. INGEST!
+        simple_source = match[0]
+        logger.debug(f"Match found for {uc_sheet_name}: {simple_source}")
+
+        try:
+            references = source["ref_plx_lit"].split(";")
+            reference = uc_ref_to_simple_ref(db, references[0])
+
+            comment = None
+            if len(references) > 1:
+                comment = f"other references: {uc_ref_to_simple_ref(db, references[1])}"
+            ingest_parallax(
+                db,
+                source=simple_source,
+                parallax_mas=source["plx_lit"],
+                parallax_err_mas=source["plxerr_lit"],
+                reference=reference,
+                comment=comment,
+            )
+            ingested += 1
+        except AstroDBError as e:
+            msg = "ingest failed with error: " + str(e)
+            if "Duplicate measurement exists" in str(e):
+                already_exists += 1
+            else:
+                logger.warning(msg)
+                raise AstroDBError(msg) from e
+
+    elif len(match) == 0:
+        no_sources += 1
+    elif len(match) > 1:
+        multiple_sources += 1
+    else:
+        msg = "Unexpected situation occured"
+        logger.error(msg)
+        raise AstroDBError(msg)
+
+
+# 1108 data points in UC sheet in total
+logger.info(f"ingested:{ingested}")  # 1014 ingested
+logger.info(f"already exists:{already_exists}")  # skipped 6 due to preexisting data
+logger.info(f"no sources:{no_sources}")  # skipped 86 due to 0 matches
+logger.info(f"multiple sources:{multiple_sources}")  # skipped 2 due to multiple matches
+logger.info(f"no data: {no_data}")  # 2782
+logger.info(
+    f"data points tracked:{ingested+already_exists+no_sources+multiple_sources}"
+)  # 1108
+total = ingested + already_exists + no_sources + multiple_sources + no_data
+logger.info(f"total: {total}")  # 3890
+
+if total != len(uc_sheet_table):
+    msg = "data points tracked inconsistent with UC sheet"
+    logger.error(msg)
+    raise AstroDBError(msg)
+elif DB_SAVE:
+    db.save_database(directory="data/")

scripts/ingests/ultracool_sheet/Ingest_spitzer_photometry.py

@@ -17,7 +17,7 @@
 logger = logging.getLogger("AstroDB")
 logger.setLevel(logging.INFO)
 
-DB_SAVE = True
+DB_SAVE = False
 RECREATE_DB = True
 db = load_astrodb(
     "SIMPLE.sqlite", recreatedb=RECREATE_DB, reference_tables=REFERENCE_TABLES

scripts/ingests/ultracool_sheet/references.py

@@ -27,6 +27,8 @@
 
 
 def uc_ref_to_simple_ref(db, ref):
+    if ref == "Harr15":  # Reference with no ADS.
+        return ref
     t = (
         db.query(db.Publications)
         .filter(db.Publications.c.bibcode == uc_ref_to_ADS[ref])