Improvements to sources module

astrodb_utils/sources.py

@@ -11,7 +11,7 @@
 
 __all__ = [
     "find_source_in_db",
-    "ingest_names",
+    "ingest_name",
     "ingest_source",
 ]
 
@@ -28,7 +28,7 @@ def find_source_in_db(
     ra_col_name="ra_deg",
     dec_col_name="dec_deg",
     use_simbad=True,
-    fuzzy=False
+    fuzzy=False,
 ):
     """
     Find a source in the database given a source name and optional coordinates.
@@ -187,7 +187,7 @@ def coords_from_simbad(source):
 
 
 # NAMES
-def ingest_names(
+def ingest_name(
     db, source: str = None, other_name: str = None, raise_error: bool = None
 ):
     """
@@ -206,22 +206,26 @@ def ingest_names(
 
     Returns
     -------
-    None
+    other_name: str
+        Name of the source as it appears in the Names table
+
+    or None if name was not ingested
+
     """
-    names_data = [{"source": source, "other_name": other_name}]
+    source = strip_unicode_dashes(source)
+    other_name = strip_unicode_dashes(other_name)
+    name_data = [{"source": source, "other_name": other_name}]
     try:
         with db.engine.connect() as conn:
-            conn.execute(db.Names.insert().values(names_data))
+            conn.execute(db.Names.insert().values(name_data))
             conn.commit()
-        logger.info(f"Name added to database: {names_data}\n")
+        logger.info(f"Name added to database: {name_data}\n")
+        return other_name
     except sqlalchemy.exc.IntegrityError as e:
-        msg = f"Could not add {names_data} to Names."
-        if "UNIQUE constraint failed:" in str(e):
-            msg += " Other name is already present."
-        if raise_error:
-            raise AstroDBError(msg) from e
-        else:
-            logger.warning(msg)
+        msg = f"Could not add {name_data} to Names."
+        if "UNIQUE constraint failed: " in str(e):
+            msg += "Other name is already present."
+        exit_function(msg, raise_error)
 
 
 # SOURCES
@@ -286,6 +290,9 @@ def ingest_source(
 
     logger.debug(f"Trying to ingest source: {source}")
 
+    # change unicode dashes characters to `-`
+    source = strip_unicode_dashes(source)
+
     # Make sure reference is provided and in References table
     ref_check = find_publication(db, reference=reference)
     logger.debug(f"ref_check: {ref_check}")
@@ -323,7 +330,7 @@ def ingest_source(
 
         # One source match in the database, ingesting possible alt name
         if len(name_matches) == 1:
-            ingest_names(db, name_matches[0], source)
+            ingest_name(db, name_matches[0], source)
             msg2 = f"   Already in database as {name_matches[0]}. \n "
 
         # Multiple source matches in the database, unable to ingest source
@@ -375,18 +382,15 @@ def ingest_source(
         msg = f"Added {source_data}"
         logger.info(f"Added {source}")
         logger.debug(msg)
-    except sqlalchemy.exc.IntegrityError as e:
+    except sqlalchemy.exc.IntegrityError:
         msg = f"Not ingesting {source}. Not sure why. \n"
         msg2 = f"   {source_data} "
         logger.warning(msg)
         logger.debug(msg2)
-        if raise_error:
-            raise AstroDBError(msg + msg2) from e
-        else:
-            return
+        exit_function(msg + msg2, raise_error)
 
     # Add the source name to the Names table
-    ingest_names(db, source=source, other_name=source, raise_error=raise_error)
+    ingest_name(db, source=source, other_name=source, raise_error=raise_error)
 
     return
 
@@ -462,3 +466,23 @@ def find_survey_name_in_simbad(sources, desig_prefix, source_id_index=None):
         )
 
     return result_table
+
+
+def strip_unicode_dashes(source):
+    """
+    Function to remove unicode dashes from source names and replace with `-`
+    """
+
+    unicode_list = [
+        ("\u2013", "en dash"),
+        ("\u2014", "em dash"),
+        ("\u2212", "minus sign"),
+        ("\u2012", "figure dash"),
+    ]
+
+    for char, char_name in unicode_list:
+        if char in source:
+            source = source.replace(char, "-")
+            logger.info(f"replaced {char_name}({char}) with - in {source}")
+
+    return source

astrodb_utils/tests/conftest.py

@@ -5,7 +5,6 @@
 
 from astrodb_utils import load_astrodb, logger
 from astrodb_utils.publications import ingest_publication
-from astrodb_utils.sources import ingest_source
 
 logger.setLevel("DEBUG")
 
@@ -28,8 +27,6 @@ def db():
 
     logger.info("Loaded AstroDB Template database using load_astrodb function in conftest.py")
 
-
-
     ingest_publication(
         db,
         reference="Refr20",
@@ -40,8 +37,6 @@ def db():
 
     ingest_publication(db, doi="10.1086/161442", reference="Prob83")
 
-    ingest_source(db, "LHS 2924", reference="Prob83")
-
     return db
 
 

astrodb_utils/tests/test_sources.py

@@ -8,7 +8,9 @@
 from astrodb_utils.sources import (
     coords_from_simbad,
     find_source_in_db,
+    ingest_name,
     ingest_source,
+    strip_unicode_dashes,
 )
 
 
@@ -51,6 +53,14 @@
                 "raise_error": False,
             }
         ),
+             {
+                "source": "LHS 2924", # needed for test_find_source_in_db
+                "ra": None,
+                "dec": None,
+                "reference": "Prob83",
+                "raise_error": False,
+            }
+
     ],
 )
 @pytest.mark.filterwarnings(
@@ -187,3 +197,28 @@ def test_coords_from_simbad():
     coords = coords_from_simbad("Barnard Star")
     assert math.isclose(coords.ra.deg, 269.452, abs_tol=0.001)
     assert math.isclose(coords.dec.deg, 4.6933, abs_tol=0.001)
+
+
+def test_ingest_name(db):
+    result = ingest_name(db, "TWA 26", "WISE J113951.07-315921.6")
+    assert result == "WISE J113951.07-315921.6"
+
+    # try to ingest names that are already in the database
+    result = ingest_name(db, "Gl 229b", "HD 42581b", raise_error=False)
+    assert result is None
+
+    with pytest.raises(AstroDBError) as error_message:
+        ingest_name(db, "Gl 229b", "HD 42581b", raise_error=True)
+        assert "Other name is already present." in str(error_message.value)
+
+
+@pytest.mark.parametrize('input,expected', [
+    ('CWISE J221706.28–145437.6', 'CWISE J221706.28-145437.6'), #en dash 2013
+    ('2MASS J20115649—6201127', '2MASS J20115649-6201127'), # em dash 2014
+    ('1234−5678', '1234-5678'),  # minus sign 2212
+    ('9W34‒aou', '9W34-aou'), # figure dash 2012
+    ('should-work', 'should-work'), # no unicode dashes➖➖
+])
+def test_strip_unicode_dashes(input, expected):
+    result = strip_unicode_dashes(input)
+    assert result == expected