Ingest BONES spectra

.gitignore

@@ -13,4 +13,5 @@ build/
 simple/version.py
 *.zip
 *.fits
-*sty2054_supplemental_files/
+*.txt
+*.csv

scripts/ingests/bones_archive/ingest_BONES_spectra.py

@@ -0,0 +1,171 @@
+import logging
+import csv
+from datetime import datetime
+import pandas as pd
+from pathlib import Path
+from astropy.io import fits
+from astrodb_utils.spectra import ingest_spectrum
+from astrodb_utils.instruments import ingest_instrument
+from astrodb_utils.publications import ingest_publication
+from simple import REFERENCE_TABLES
+from astrodb_utils import AstroDBError, load_astrodb
+
+"""
+This script ingest new created spectra FITS files into the SIMPLE database
+"""
+
+# Set the loggging level of the astrodb_utils logger
+astrodb_utils_logger = logging.getLogger("astrodb_utils")
+astrodb_utils_logger.setLevel(logging.INFO)
+
+# Set up the logging for this ingest script.
+logger = logging.getLogger("astrodb_utils.bones") 
+logger.setLevel(logging.INFO)
+
+# Load Database
+SAVE_DB = False
+RECREATE_DB = True
+SCHEMA_PATH = "simple/schema.yaml"
+db = load_astrodb(
+    "SIMPLE.sqlite",
+    recreatedb=RECREATE_DB,
+    reference_tables=REFERENCE_TABLES,
+    felis_schema=SCHEMA_PATH,
+)
+
+# Paths
+spreadsheet_url = "https://docs.google.com/spreadsheets/d/e/2PACX-1vRtZ_Sl9hSi-JdIimRxbRLSTTYozlLOStmlzzcoAM7yB-duaMtzSqAIITI2ioMqlSIc6en8eiZDnUGe/pub?gid=0&single=true&output=csv"
+data = pd.read_csv(spreadsheet_url)
+fits_file = "/Users/guanying/SIMPLE db/SIMPLE-db/scripts/spectra_convert/BONES Archive/Processed BONES/"
+SKIP_FILES = [
+    "2MASS J12270506-0447207",
+    "WISEA J135501.90−825838.9",
+    "ULAS J124947.04+095019.8",
+    "SDSS J133837.01-022908.4",
+    "LHS 377",
+    "2MASS J16262034+3925190",
+    "2MASS J06453153−6646120",
+    "SDSS J010448.46+153501.8",
+    "ULAS J020858.62+020657.0",
+    "ULAS J021642.96+004005.7",
+    "ULAS J024035.36+060629.3",
+    "ULAS J130710.22+151103.4",
+    "ULAS J135058.86+081506.8",
+    "2MASS J14120397+1216100",
+    "ULAS J151913.03-000030.0",
+    "ULAS J223302.03+062030.8",
+    "ULAS J230711.01+014447.1",
+]
+def add_instruments():
+    INSTRUMENT=[
+        {
+            "name": "BCSpec",
+            "mode": "spectroscopy",
+            "telescope": "LCO du Pont",
+        },
+        {
+            "name": "DSpec",
+            "mode":"spectroscopy",
+            "telescope": "Palomar Hale",
+        },
+        {
+            "name":"MOSFIRE",
+            "mode":"Imaging",
+            "telescope":"Keck I",
+        },
+        {
+            "name":"OSIRIS",
+            "mode":"Missing",
+            "telescope":"SOAR",
+        }
+    ]
+    for inst in INSTRUMENT:
+        try:
+            ingest_instrument(
+                db,
+                instrument=inst["name"],
+                mode=inst["mode"],
+                telescope=inst["telescope"]
+            )
+        except AstroDBError as e:
+            logger.error(f"Failed to ingest instrument {inst['name']}: {e}")
+
+
+def add_publications():
+    try:
+        ingest_publication(
+            db,
+            reference="Burg25.79",
+            bibcode="2025ApJ...982...79B",
+            doi="10.3847/1538-4357/adb39f",
+            description="New Cold Subdwarf Discoveries from Backyard Worlds and a Metallicity Classification System for T Subdwarfs"
+        )
+    except AstroDBError as e:
+        logger.error(f"Failed to ingest publication Burg25.79: {e}")
+
+def modify_date(obs_date):
+    if not obs_date:
+        return None
+
+    return datetime.fromisoformat(str(obs_date)) # example: 2004-04-17 04:40:11.761000
+
+def add_access_url(filename):
+
+    filename = filename.replace(".txt", "_SIMPLE.fits")
+    filename = filename.replace(".csv", "_SIMPLE.fits")
+    filename = filename.replace('+', '%2B')
+
+    access_url = (
+        "https://bdnyc.s3.us-east-1.amazonaws.com/bones/"
+        + filename
+    )
+
+    return access_url
+
+def ingest_spectra():
+    added_files = 0
+    failed_files = 0
+
+    for _, row in data.iloc[1:83].iterrows():
+
+        if row['NAME'] in SKIP_FILES:
+            logger.info(f"Skipping {row['Filename']} due to known issues.")
+            continue
+
+        print(f"Processing {row['NAME']}...")
+
+        filename = str(row['Filename'])
+        access_url = add_access_url(filename)
+        original_spectrum = filename # To be updated
+
+        obs_date = modify_date(row['DATE-OBS'])
+
+        try:
+            ingest_spectrum(
+                db,
+                source=row['SIMPLE Name'],
+                spectrum=access_url,
+                # original_spectrum=original_spectrum,
+                regime= row['Regime'],
+                instrument=row['INSTRUME'],
+                telescope=row['TELESCOP'],
+                mode=row['mode'],
+                obs_date=obs_date,
+                reference=row['Reference'],
+            )
+            logger.info(f"Ingesting spectrum for {row['NAME']}...")
+            print(f"Successfully ingest spectrum for {row['NAME']}")
+            added_files += 1
+        except AstroDBError as e:
+            logger.error(f"Failed to ingest spectrum for {row['NAME']}: {e}")
+            failed_files += 1
+    print(f"Total spectra added: {added_files}")
+    print(f"Total failed spectra: {failed_files}")
+
+add_instruments()
+add_publications()
+ingest_spectra()
+
+if SAVE_DB:
+    db.save_database(directory="data/")
+    logger.info("Database saved as SIMPLE.sqlite")