Finish adding Radial Velocities table (#124)

* corrections to RV table

* add template RV data and tests

Author: kelle

data/reference/Publications.json

@@ -89,10 +89,23 @@
         "doi": "10.1093/mnras/stad343",
         "description": "The TIME Table: rotation and ages of cool exoplanet host stars"
     },
+    {
+        "reference": "Liu_13",
+        "bibcode": "2013ApJ...777L..20L",
+        "doi": "10.1088/2041-8205/777/2/L20",
+        "description": "The Extremely Red, Young L Dwarf PSO J318.5338-22.8603: A Free-floating Planetary-mass Analog to Directly Imaged Young Gas-giant Planets"
+    },
+    {
+        "reference": "Alle16",
+        "bibcode": "2016ApJ...819..133A",
+        "doi": "10.3847/0004-637X/819/2/133",
+        "description": "The Radial and Rotational Velocities of PSO J318.5338-22.8603, a Newly Confirmed Planetary-mass Member of the \u03b2 Pictoris Moving Group"
+    },
     {
         "reference": "vanL07",
         "bibcode": "2007A&A...474..653V",
         "doi": "10.1051/0004-6361:20078357",
         "description": "Validation of the new Hipparcos reduction"
+
     }
 ]

data/source/2mass_j21140802-2251358.json

@@ -0,0 +1,32 @@
+{
+    "Sources": [
+        {
+            "source": "2MASS J21140802-2251358",
+            "ra_deg": 318.533,
+            "dec_deg": -22.86,
+            "epoch_year": 2000.0,
+            "equinox": "J2000",
+            "shortname": null,
+            "reference": "Liu_13",
+            "other_references": null,
+            "comments": null
+        }
+    ],
+    "Names": [
+        {
+            "other_name": "2MASS J21140802-2251358"
+        },
+        {
+            "other_name": "PSO J318.5-22"
+        }
+    ],
+    "RadialVelocities": [
+        {
+            "rv_kms": -6.0,
+            "rv_error": 1.1,
+            "adopted": true,
+            "comments": "uncertainty reported as +0.8 and -1.1 km/s",
+            "reference": "Alle16"
+        }
+    ]
+}

schema/schema.yaml

@@ -9,6 +9,8 @@ description: "Template database for use by the AstroDB Toolkit"
 # - Comments length is 100 characters. ivoa:ucd: meta.note
 # - Reference is 30 characters
 # - Description is 100 characters. ivoa:ucd: meta.note
+# - Values are datatype: double
+# - Adopted: ivoa:ucd: meta.code
 ######################################################
 
 tables:
@@ -67,8 +69,9 @@ tables:
     - name: description
       "@id": "#Telescopes.description"
       datatype: string
-      length: 1000
+      length: 100
       description: Telescope description
+      ivoa:ucd: meta.note
     - name: reference
       "@id": "#Telescopes.reference"
       datatype: string
@@ -117,8 +120,9 @@ tables:
     - name: description
       "@id": "#Instruments.description"
       datatype: string
-      length: 1000
+      length: 100
       description: Instrument description
+      ivoa:ucd: meta.note
     - name: reference
       "@id": "#Instruments.reference"
       datatype: string
@@ -679,26 +683,27 @@ tables:
     - name: source
       "@id": "#RadialVelocities.source"
       datatype: string
-      length: 100
+      length: 50
       description: Main identifier for an object; links to Sources table
       ivoa:ucd: meta.id;meta.main
       nullable: false
-    - name: radial_velocity_kms
-      "@id": "#RadialVelocities.radial_velocity_kms"
+    - name: rv_kms
+      "@id": "#RadialVelocities.rv_kms"
       datatype: double
       description: Radial velocity value for this entry
       fits:tunit: km/s
       ivoa:ucd: spect.dopplerVeloc
-    - name: radial_velocity_error_kms
-      "@id": "#RadialVelocities.magnitude_error"
+    - name: rv_error
+      "@id": "#RadialVelocities.rv_error"
       datatype: double
-      description: Uncertainty of this parallax value
-      fits:tunit: mas
+      description: Uncertainty of the radial velocity value
+      fits:tunit: km/s
       ivoa:ucd: stat.error;spect.dopplerVeloc
     - name: adopted
       "@id": "#RadialVelocities.adopted"
       datatype: boolean
       description: Flag to indicate if this is the adopted entry
+      ivoa:ucd: meta.code
     - name: comments
       "@id": "#RadialVelocities.comments"
       datatype: string
@@ -741,7 +746,7 @@ tables:
         "@type": Check
         "@id": "#check_radial_velocity_error"
         description: Validate radial velocity error
-        expression: radial_velocity_error_kms >= 0
+        expression: rv_error >= 0
 
 
   - name: CompanionRelationships

scripts/ingest_gl229b.py

@@ -34,18 +34,17 @@
 
 
 def ingest_gl229b(db):
-    # ingest_publication(db, doi="10.1038/378463a0")
+    ingest_publication(db, doi="10.1038/378463a0")
     ingest_source(db, "Gl 229b", reference="Naka95")
 
-
-# ingest_publication(
-#     db,
-#     doi="10.1093/mnras/stad343",
-#     bibcode="2023MNRAS.520.5283G",
-#     reference="Gaid23",
-#     description="The TIME Table: rotation and ages of cool exoplanet host stars",
-#     ignore_ads=True,
-# )
+    ingest_publication(
+        db,
+        doi="10.1093/mnras/stad343",
+        bibcode="2023MNRAS.520.5283G",
+        reference="Gaid23",
+        description="The TIME Table: rotation and ages of cool exoplanet host stars",
+        ignore_ads=True,
+    )
 
 
 def ingest_companion(db):

scripts/ingest_pso0318

@@ -0,0 +1,68 @@
+from astrodb_utils import load_astrodb
+from astrodb_utils.sources import ingest_source, ingest_names
+from astrodb_utils.publications import ingest_publication
+
+# Load the database
+db_file = "tests/astrodb_template_tests.sqlite"
+felis_schema = "schema/schema.yaml"
+
+reference_tables = [
+    "Publications",
+    "Telescopes",
+    "Instruments",
+    "Versions",
+    "PhotometryFilters",
+    "Regimes",
+    "AssociationList",
+    "ParameterList",
+    "CompanionList",
+    "SourceTypeList",
+]
+
+db = load_astrodb(
+    db_file,
+    recreatedb=True,
+    felis_schema=felis_schema,
+    reference_tables=reference_tables,
+)
+
+def ingest_PSO_J318(db):
+    ingest_publication(
+        db,
+        doi="10.1088/2041-8205/777/2/L20",
+        bibcode="2013ApJ...777L..20L",
+        description="The Extremely Red, Young L Dwarf PSO J318.5338-22.8603: A Free-floating Planetary-mass Analog to Directly Imaged Young Gas-giant Planets",
+        reference="Liu_13",
+        ignore_ads=True,
+    )
+
+    ingest_source(db, "2MASS J21140802-2251358", reference="Liu_13")    
+
+    ingest_names(db, "2MASS J21140802-2251358", "PSO J318.5-22")
+
+def ingest_radial_velocity(db):
+    # Add radial velocity data for PSO J318.5
+    ingest_publication(db, doi="10.3847/0004-637X/819/2/133")
+
+    rv_data = [
+        {
+            "source": "2MASS J21140802-2251358",
+            "rv_kms": -6.0,
+            "rv_error": 1.1,
+            "adopted": True,
+            "comments": "uncertainty reported as +0.8 and -1.1 km/s",
+            "reference": "Alle16",
+        }
+    ]
+    with db.engine.connect() as conn:
+        conn.execute(db.RadialVelocities.insert().values(rv_data))
+        conn.commit()
+
+
+DB_SAVE = True
+
+ingest_PSO_J318(db)
+ingest_radial_velocity(db)
+
+if DB_SAVE:
+    db.save_database("data/")

tests/test_database.py

@@ -2,8 +2,8 @@
 Functions to test the database and example files
 """
 
-from astrodbkit.astrodb import or_
 from sqlalchemy.ext.automap import automap_base
+from sqlalchemy import func, or_
 
 
 def test_setup_db(db):
@@ -242,3 +242,51 @@ def test_companion_relationships(db):
     ), f"Found {len(t)} entries in the Companion Relationships table, expected {n_companion_relationships}"
 
 
+def test_radial_velocities(db):
+    # Test that Radial Velocities has expected number of entries
+    t = db.query(db.RadialVelocities.c.rv_kms).astropy()
+
+    n_radial_velocities = 1
+    assert (
+        len(t) == n_radial_velocities
+    ), f"Found {len(t)} entries in the Radial Velocities table, expected {n_radial_velocities}"
+
+    # Test that there is one adopted radial velocity measurement per source
+    t = (
+        db.query(
+            db.RadialVelocities.c.source,
+            func.sum(db.RadialVelocities.c.adopted).label("adopted_counts"),
+        )
+        .group_by(db.RadialVelocities.c.source)
+        .having(func.sum(db.RadialVelocities.c.adopted) != 1)
+        .astropy()
+    )
+
+    assert (
+        len(t) == 0
+    ), f"Found {len(t)} radial velocity measurements with incorrect 'adopted' labels"
+
+
+def test_proper_motions(db):
+    # Test that Radial Velocities has expected number of entries
+    t = db.query(db.ProperMotions.c.pm_ra).astropy()
+
+    n_proper_motions = 1
+    assert (
+        len(t) == n_proper_motions
+    ), f"Found {len(t)} entries in the Proper Motions table, expected {n_proper_motions}"
+
+    # Test that there is one adopted proper motion measurement per source
+    t = (
+        db.query(
+            db.ProperMotions.c.source,
+            func.sum(db.ProperMotions.c.adopted).label("adopted_counts"),
+        )
+        .group_by(db.ProperMotions.c.source)
+        .having(func.sum(db.ProperMotions.c.adopted) != 1)
+        .astropy()
+    )
+
+    assert (
+        len(t) == 0
+    ), f"Found {len(t)} proper motion measurements with incorrect 'adopted' labels"