add reference table to SIMPLEDB class super

simple_app/app_simple.py

@@ -47,7 +47,7 @@ def search():
 
     curdoc().template_variables['query'] = query  # add query to bokeh curdoc
     curdoc().template_variables['ref_query'] = ref_query  # add query to bokeh curdoc
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})  # open database
+    db = SimpleDB(db_file)  # open database
 
     # object search function
     try:
@@ -97,7 +97,7 @@ def coordinate_query():
             query = ''
 
         curdoc().template_variables['query'] = query
-        db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+        db = SimpleDB(db_file)
 
         # parse query into ra, dec, radius
         ra, dec, radius = form.multi_param_str_parse(query)
@@ -127,7 +127,7 @@ def full_text_search():
         limmaxrows = True
 
     curdoc().template_variables['query'] = query
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # search through the tables using the given query
     results: Dict[str, pd.DataFrame] = db.search_string(query, fmt='pandas', verbose=False)
@@ -150,7 +150,7 @@ def raw_query():
     """
     Page for raw sql query, returning all tables
     """
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})  # open database
+    db = SimpleDB(db_file)  # open database
     form = SQLForm(db_file=db_file)  # main query form
 
     # checks that the SQL is valid, then submits form
@@ -187,12 +187,16 @@ def solo_result(query: str):
         The query -- full match to a main ID
     """
     curdoc().template_variables['query'] = query
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # search database for given object
-    resultdict: dict = db.inventory(query)
-    if not len(resultdict):
+    try:
+        resultdict: dict = db.inventory(query)
+        if not len(resultdict):
+            raise KeyError
+    except KeyError:
         abort(404, f'"{query}" does match any result in SIMPLE!')
+        return
     everything = Inventory(resultdict)
 
     # create camd and spectra plots
@@ -278,7 +282,7 @@ def create_file_for_download(key: str):
         The dataframe string
     """
     query = curdoc().template_variables['query']
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # search for a given object and a given key
     resultdict: dict = db.inventory(query)
@@ -300,7 +304,7 @@ def create_files_for_solo_download():
     Creates and downloads all dataframes from solo results
     """
     query = curdoc().template_variables['query']
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # search for a given object
     resultdict: dict = db.inventory(query)
@@ -323,7 +327,7 @@ def create_spectra_files_for_download():
     Downloads the spectra files and zips together
     """
     query = curdoc().template_variables['query']
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # search for a given object and specifically its spectra
     resultdict: dict = db.inventory(query)
@@ -347,7 +351,7 @@ def create_file_for_filtered_download():
     """
     query = curdoc().template_variables['query']
     refquery = curdoc().template_variables['ref_query']
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # search for a given object and a full text search at the same time
     results: Optional[pd.DataFrame] = db.search_object(query, fmt='pandas')
@@ -370,7 +374,7 @@ def create_file_for_coordinate_download():
     Creates and downloads the shown dataframe when in coordinate search
     """
     query = curdoc().template_variables['query']
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # query the database for given coordinates and parse those coordinates
     form = CoordQueryForm(db_file=db_file)
@@ -396,7 +400,7 @@ def create_file_for_full_download(key: str):
         The dataframe string
     """
     query = curdoc().template_variables['query']
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # search database with a free-text search and specific table
     resultdict: Dict[str, pd.DataFrame] = db.search_string(query, fmt='pandas', verbose=False)
@@ -417,7 +421,7 @@ def create_files_for_multi_download():
     Creates and downloads all dataframes from full results
     """
     query = curdoc().template_variables['query']
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # search with full-text search
     resultdict: Dict[str, pd.DataFrame] = db.search_string(query, fmt='pandas', verbose=False)
@@ -434,7 +438,7 @@ def create_file_for_sql_download():
     Creates and downloads the shown dataframe when in sql query
     """
     query = curdoc().template_variables['query']
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # query database via sql
     results: Optional[pd.DataFrame] = db.sql_query(query, fmt='pandas')

simple_app/plots.py

@@ -129,7 +129,7 @@ def normalise() -> np.ndarray:
         return flux / fluxmed
 
     # query the database for the spectra
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})  # open database
+    db = SimpleDB(db_file)  # open database
     t_spectra: Table = db.query(db.Spectra).\
         filter(db.Spectra.c.source == query).\
         table(spectra=['spectrum'])

simple_app/tests/test_utils.py

@@ -10,15 +10,15 @@
 # local packages
 from ..utils import *
 
-db_name = 'temp.db'
+db_name = 'temp.sqlite'
 db_cs = f'sqlite:///{db_name}'
 
 
 @pytest.fixture(scope='module')
 def db():
     if os.path.exists(db_name):
         os.remove(db_name)
-    copy('SIMPLE.db', db_name)
+    copy('SIMPLE.sqlite', db_name)
     assert os.path.exists(db_name)
     # Connect to the new database and confirm it has the Sources table
     db = SimpleDB(db_cs)

simple_app/utils.py

@@ -39,6 +39,12 @@ class SimpleDB(Database):  # this keeps pycharm happy about unresolved reference
     SpectralTypes = None
     CompanionRelationships = None
 
+    def __init__(self, connection_string):
+        super().__init__(connection_string,
+                         reference_tables=REFERENCE_TABLES,
+                         connection_arguments={'check_same_thread': False})
+
+
 
 class Inventory:
     """
@@ -276,7 +282,7 @@ def validate_query(self, field):
 
         """
         # split search bar into 3 components (ra, dec, radius)
-        db = SimpleDB(self.db_file, connection_arguments={'check_same_thread': False})  # open database
+        db = SimpleDB(self.db_file)  # open database
         ra, dec, radius = self.multi_param_str_parse(field.data)
 
         if not ra:  # i.e. empty string, bad parse
@@ -332,7 +338,7 @@ def validate_sqlfield(self, field):
             The data within the query form
         """
         forbidden = ('update', 'drop', 'truncate', 'grant', 'commit', 'create', 'replace', 'alter', 'insert', 'delete')
-        db = SimpleDB(self.db_file, connection_arguments={'check_same_thread': False})  # open database
+        db = SimpleDB(self.db_file)  # open database
 
         # check query field has data within
         if (query := field.data) is None or query.strip() == '':  # content in main searchbar
@@ -429,7 +435,7 @@ def get_all_sources(db_file: str):
     full_results
         The full dataframe of all the sources
     """
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # get the full Sources table and just the main id list
     full_results: pd.DataFrame = db.query(db.Sources).pandas()
@@ -451,7 +457,7 @@ def get_version(db_file: str) -> str:
     vstr
         The stringified version formatted
     """
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # query Versions table and extract active version before pretty-printing
     v: pd.DataFrame = db.query(db.Versions).pandas()
@@ -655,7 +661,7 @@ def get_all_photometry(db_file: str, photometric_filters: pd.DataFrame):
     all_bands: np.ndarray
         The unique passbands to create dropdowns by
     """
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # query all photometry and extract the unique bands
     all_photometry: pd.DataFrame = db.query(db.Photometry).pandas()
@@ -678,7 +684,7 @@ def get_all_parallaxes(db_file: str):
     all_parallax: pd.DataFrame
         The dataframe of all the parallaxes
     """
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # query the database for the parallaxes and only take necessary columns
     all_parallaxes: pd.DataFrame = db.query(db.Parallaxes).pandas()
@@ -695,7 +701,7 @@ def get_all_spectral_types(db_file: str):
     all_spts: pd.DataFrame
         The dataframe of all the spectral type numbers
     """
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # query the database for the spectral types and only take necessary columns
     all_spts: pd.DataFrame = db.query(db.SpectralTypes).pandas()
@@ -982,7 +988,7 @@ def get_filters(db_file: str) -> pd.DataFrame:
     phot_filters: pd.DataFrame
         All of the filters, access as: phot_filters.loc['effective_wavelength', <bandname>]
     """
-    db = SimpleDB(db_file, connection_arguments={'check_same_thread': False})
+    db = SimpleDB(db_file)
 
     # query the database for all of the PhotometryFilters
     phot_filters: pd.DataFrame = db.query(db.PhotometryFilters).pandas().set_index('band').T