Merge pull request #185 from Will-Cooper/updates

Updates on the issue log

Author: Will-Cooper

requirements.txt

@@ -1,18 +1,87 @@
-astrodbkit>=2.2
-astropy>=5.2.0,<6
-bokeh==3.0.2
-flask>=3.0,<4
-flask-cors>=4.0,<5
-flask-wtf>=1.2,<2
-markdown2>=2.4,<3
-multiprocess>=0.70,<1
-numpy>=1.24,<2
-pandas>=2.0,<2.1
-pysqlite3>=0.5,<1
-pytest>=8.0,<9
-requests>=2.31,<3
-specutils>=1.12,<2
-sqlalchemy>=2.0,<3
-tqdm>=4.66,<5
-werkzeug>=3.0,<4
-wtforms>=3.1,<4
+antiorm==1.2.1
+asdf==4.1.0
+asdf-astropy==0.7.0
+asdf_coordinates_schemas==0.3.0
+asdf_standard==1.1.1
+asdf_transform_schemas==0.5.0
+asdf_wcs_schemas==0.4.0
+astrodbkit==2.2
+astropy==5.3.4
+astroquery==0.4.9.post1
+attrs==25.1.0
+backports.tarfile==1.2.0
+beautifulsoup4==4.13.3
+blinker==1.9.0
+bokeh==3.7.3
+certifi==2025.1.31
+cffi==1.17.1
+charset-normalizer==3.4.1
+click==8.1.8
+contourpy==1.3.1
+cryptography==44.0.0
+db==0.1.1
+db-sqlite3==0.0.1
+dill==0.3.9
+distlib==0.3.9
+distro==1.9.0
+filelock==3.16.1
+Flask==3.1.0
+Flask-Cors==4.0.2
+Flask-WTF==1.2.2
+greenlet==3.1.1
+gwcs==0.21.0
+html5lib==1.1
+idna==3.10
+importlib_metadata==8.6.1
+iniconfig==2.0.0
+iniparse==0.5
+itsdangerous==2.2.0
+jaraco.classes==3.4.0
+jaraco.context==6.0.1
+jaraco.functools==4.1.0
+jeepney==0.8.0
+Jinja2==3.1.5
+jmespath==1.0.1
+keyring==25.6.0
+markdown2==2.5.3
+MarkupSafe==3.0.2
+more-itertools==10.6.0
+multiprocess==0.70.17
+narwhals==1.41.0
+ndcube==2.3.0
+numpy==1.26.4
+packaging==24.2
+pandas==2.0.3
+pathlib2==2.3.7.post1
+pillow==11.1.0
+platformdirs==4.3.6
+pluggy==1.5.0
+pycparser==2.22
+pyerfa==2.0.1.5
+PyMySQL==1.1.1
+pyOpenSSL==24.3.0
+pysqlite3==0.5.4
+pytest==8.3.4
+python-dateutil==2.9.0.post0
+pytz==2024.2
+pyvo==1.6
+PyYAML==6.0.2
+requests==2.32.3
+scipy==1.15.1
+SecretStorage==3.3.3
+semantic-version==2.10.0
+six==1.17.0
+soupsieve==2.6
+specutils==1.19.0
+SQLAlchemy==2.0.38
+tornado==6.4.2
+tqdm==4.67.1
+typing_extensions==4.12.2
+tzdata==2025.1
+urllib3==2.3.0
+virtualenv==20.28.0
+webencodings==0.5.1
+Werkzeug==3.1.3
+WTForms==3.2.1
+xyzservices==2025.1.0
+zipp==3.21.0

simple_app/app_simple.py

@@ -45,8 +45,8 @@ def search():
     if (query := form.search.data) is None:  # content in main searchbar
         query = ''
 
-    curdoc().template_variables['query'] = query  # add query to bokeh curdoc
-    curdoc().template_variables['ref_query'] = ref_query  # add query to bokeh curdoc
+    session['query'] = query  # add query to bokeh curdoc
+    session['ref_query'] = ref_query  # add query to bokeh curdoc
     db = SimpleDB(db_file)  # open database
 
     # object search function
@@ -96,7 +96,7 @@ def coordinate_query():
         if (query := form.query.data) is None:
             query = ''
 
-        curdoc().template_variables['query'] = query
+        session['query'] = query
         db = SimpleDB(db_file)
 
         # parse query into ra, dec, radius
@@ -127,7 +127,7 @@ def full_text_search():
         query = ''
         limmaxrows = True
 
-    curdoc().template_variables['query'] = query
+    session['query'] = query
     db = SimpleDB(db_file)
 
     # search through the tables using the given query
@@ -160,14 +160,14 @@ def raw_query():
         if (query := form.sqlfield.data) is None:
             query = ''
 
-        curdoc().template_variables['query'] = query
+        session['query'] = query
 
         # attempt to query the database
         try:
             results: Optional[pd.DataFrame] = db.sql_query(query, fmt='pandas')
 
         # catch any broken queries (should not activate as will be caught by validation)
-        except (ResourceClosedError, OperationalError, IndexError, SqliteWarning, BadSQLError):
+        except (ResourceClosedError, OperationalError, IndexError, SqliteWarning, BadSQLError, ProgrammingError):
             results = pd.DataFrame()
 
         results = reference_handle(results, db_file, True)
@@ -188,7 +188,7 @@ def solo_result(query: str):
     query: str
         The query -- full match to a main ID
     """
-    curdoc().template_variables['query'] = query
+    session['query'] = query
     db = SimpleDB(db_file)
 
     # search database for given object
@@ -199,6 +199,7 @@ def solo_result(query: str):
     except KeyError:
         abort(404, f'"{query}" does match any result in SIMPLE!')
         return
+    
     everything = Inventory(resultdict, db_file)
 
     # create camd and spectra plots
@@ -283,7 +284,7 @@ def create_file_for_download(key: str):
     key: str
         The dataframe string
     """
-    query = curdoc().template_variables['query']
+    query: str = session.get('query')
     db = SimpleDB(db_file)
 
     # search for a given object and a given key
@@ -305,7 +306,7 @@ def create_files_for_solo_download():
     """
     Creates and downloads all dataframes from solo results
     """
-    query = curdoc().template_variables['query']
+    query = session.get('query')
     db = SimpleDB(db_file)
 
     # search for a given object
@@ -328,7 +329,7 @@ def create_spectra_files_for_download():
     """
     Downloads the spectra files and zips together
     """
-    query = curdoc().template_variables['query']
+    query = session.get('query')
     db = SimpleDB(db_file)
 
     # search for a given object and specifically its spectra
@@ -346,13 +347,35 @@ def create_spectra_files_for_download():
     abort(400, 'Could not download fits')
 
 
+@app_simple.route('/write_multi_spectra', methods=['GET'])
+def create_multi_spectra_files_for_download():
+    """
+    Downloads the spectra files and zips together
+    """
+    query = session.get('query')
+    db = SimpleDB(db_file)
+
+    # search for the spectra within a given free search
+    resultdict: Dict[str, pd.DataFrame] = db.search_string(query, fmt='pandas', verbose=False)
+    spectra_df: pd.DataFrame = resultdict['Spectra']
+
+    # write all spectra for object to zipped file
+    zipped = write_spec_files(spectra_df.access_url.values)
+    if zipped is not None:
+        response = Response(zipped, mimetype='application/zip')
+        response = control_response(response, app_type='zip')
+        return response
+
+    abort(400, 'Could not download fits')
+
+
 @app_simple.route('/write_filt', methods=['GET'])
 def create_file_for_filtered_download():
     """
     Creates and downloads the shown dataframe when in filtered search
     """
-    query = curdoc().template_variables['query']
-    refquery = curdoc().template_variables['ref_query']
+    query = session.get('query')
+    refquery = session.get('ref_query')
     db = SimpleDB(db_file)
 
     # search for a given object and a full text search at the same time
@@ -375,7 +398,7 @@ def create_file_for_coordinate_download():
     """
     Creates and downloads the shown dataframe when in coordinate search
     """
-    query = curdoc().template_variables['query']
+    query = session.get('query')
     db = SimpleDB(db_file)
 
     # query the database for given coordinates and parse those coordinates
@@ -401,12 +424,12 @@ def create_file_for_full_download(key: str):
     key: str
         The dataframe string
     """
-    query = curdoc().template_variables['query']
+    query = session.get('query')
     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)
-
+    print(query, key, resultdict.keys())
     # write to csv
     if key in resultdict:
         results: pd.DataFrame = resultdict[key]
@@ -422,7 +445,7 @@ def create_files_for_multi_download():
     """
     Creates and downloads all dataframes from full results
     """
-    query = curdoc().template_variables['query']
+    query = session.get('query')
     db = SimpleDB(db_file)
 
     # search with full-text search
@@ -439,7 +462,7 @@ def create_file_for_sql_download():
     """
     Creates and downloads the shown dataframe when in sql query
     """
-    query = curdoc().template_variables['query']
+    query = session.get('query')
     db = SimpleDB(db_file)
 
     # query database via sql

simple_app/plots.py

@@ -333,14 +333,14 @@ def sky_plot() -> figure:
         _p_sky = figure(title='Sky Plot', outer_height=500,
                         active_scroll='wheel_zoom', active_drag='box_zoom',
                         tools='pan,wheel_zoom,box_zoom,box_select,reset',
-                        sizing_mode='stretch_width', x_range=[-180, 180], y_range=[-90, 90])
+                        sizing_mode='stretch_width', x_range=Range1d(-180, 180), y_range=Range1d(-90, 90))
 
         # background for skyplot
         _p_sky.ellipse(x=0, y=0, width=360, height=180, color='#444444', name='background')
 
         # scatter plot for sky plot
-        circle = _p_sky.circle(source=full_cds, x='ra_projected', y='dec_projected',
-                               size=6, name='circle', color='ghostwhite')
+        circle = _p_sky.scatter(marker='circle', source=full_cds, x='ra_projected', y='dec_projected',
+                                size=6, name='circle', color='ghostwhite')
 
         # bokeh tools for sky plot
         this_hover = HoverTool(renderers=[circle, ], tooltips=tooltips)
@@ -367,7 +367,8 @@ def colour_colour_plot() -> Tuple[figure, Toggle, Toggle, Select, Select]:
         _p_colour_colour = bokeh_formatter(_p_colour_colour)
 
         # scatter plot for colour-colour
-        full_plot = _p_colour_colour.circle(x=x_full_name, y=y_full_name, source=full_cds, size=6, color=cmap)
+        full_plot = _p_colour_colour.scatter(marker='circle', x=x_full_name, y=y_full_name, source=full_cds, size=6,
+                                             color=cmap)
 
         # colour bar for colour-colour plot
         cbar = ColorBar(color_mapper=cmap['transform'], label_standoff=12,
@@ -395,6 +396,8 @@ def colour_colour_plot() -> Tuple[figure, Toggle, Toggle, Select, Select]:
                                           args={'full_plot': full_plot, 'full_data': full_cds.data,
                                                 'y_button': _button_y_flip, 'y_axis': _p_colour_colour.yaxis[0],
                                                 'y_range': _p_colour_colour.y_range}))
+        _p_colour_colour.js_on_event('reset', CustomJS(args=dict(dropdown_x=_dropdown_x, dropdown_y=_dropdown_y),
+                                                       code=js_callbacks.reset_dropdown))
         return _p_colour_colour, _button_x_flip, _button_y_flip, _dropdown_x, _dropdown_y
 
     def colour_absolute_magnitude_diagram() -> Tuple[figure, Toggle, Toggle, Select, Select]:
@@ -413,7 +416,8 @@ def colour_absolute_magnitude_diagram() -> Tuple[figure, Toggle, Toggle, Select,
         _p_camd = bokeh_formatter(_p_camd)
 
         # scatter plot for camd
-        full_mag_plot = _p_camd.circle(x=x_full_name, y=y_full_name, source=full_cds, size=6, color=cmap)
+        full_mag_plot = _p_camd.scatter(marker='circle', x=x_full_name, y=y_full_name, source=full_cds, size=6,
+                                        color=cmap)
 
         # colour bar for camd
         cbar = ColorBar(color_mapper=cmap['transform'], label_standoff=12,
@@ -439,6 +443,8 @@ def colour_absolute_magnitude_diagram() -> Tuple[figure, Toggle, Toggle, Select,
                                                        args={'full_plot': full_mag_plot,
                                                              'full_data': full_cds.data, 'y_button': _button_mag_y_flip,
                                                              'y_axis': _p_camd.yaxis[0], 'y_range': _p_camd.y_range}))
+        _p_camd.js_on_event('reset', CustomJS(args=dict(dropdown_x=_dropdown_mag_x, dropdown_y=_dropdown_mag_y),
+                                              code=js_callbacks.reset_dropdown))
         return _p_camd, _button_mag_x_flip, _button_mag_y_flip, _dropdown_mag_x, _dropdown_mag_y
 
     # gather all necessary data including parallaxes, spectral types and bands
@@ -491,8 +497,8 @@ def colour_absolute_magnitude_diagram() -> Tuple[figure, Toggle, Toggle, Select,
     absmagnames = absmagnames[~np.isin(absmagnames, bad_cols)]
     absmag_shown_name = [name_simplifier(mag) for mag in absmagnames]
     dropdown_menu_mag = [*zip(absmagnames, absmag_shown_name)]
-    y_full_name = absmagnames[0]
-    y_shown_name = absmag_shown_name[0]
+    y_full_name = absmagnames[1]
+    y_shown_name = absmag_shown_name[1]
 
     # camd plot
     p_camd, button_mag_x_flip, button_mag_y_flip, dropdown_mag_x, dropdown_mag_y = colour_absolute_magnitude_diagram()
@@ -650,13 +656,13 @@ def camd_plot(query: str, everything: Inventory, all_bands: np.ndarray, all_resu
 
     # scatter plot for given object
     this_cds = ColumnDataSource(data=this_photometry)
-    this_plot = p.square(x=x_full_name, y=y_full_name, source=this_cds,
-                         color=cmap, size=20)  # plot for this object
+    this_plot = p.scatter(marker='square', x=x_full_name, y=y_full_name, source=this_cds,
+                          color=cmap, size=20)  # plot for this object
 
     # scatter plot for all data
     cds_full = ColumnDataSource(data=all_results_full)  # bokeh cds object
-    full_plot = p.circle(x=x_full_name, y=y_full_name, source=cds_full,
-                         color=cmap, alpha=0.5, size=6)  # plot all objects
+    full_plot = p.scatter(marker='circle', x=x_full_name, y=y_full_name, source=cds_full,
+                          color=cmap, alpha=0.5, size=6)  # plot all objects
     full_plot.level = 'underlay'  # put full plot underneath this plot
 
     # colour bar
@@ -683,6 +689,8 @@ def camd_plot(query: str, everything: Inventory, all_bands: np.ndarray, all_resu
                                               args={'full_plot': full_plot, 'this_plot': this_plot,
                                                     'full_data': cds_full.data, 'y_button': button_y_flip,
                                                     'y_axis': p.yaxis[0], 'y_range': p.y_range}))
+    p.js_on_event('reset', CustomJS(args=dict(dropdown_x=dropdown_x, dropdown_y=dropdown_y),
+                                    code=js_callbacks.reset_dropdown))
 
     # creating bokeh layout and html
     plots = column(p, row(dropdown_x,
@@ -705,6 +713,6 @@ def main_plots():
 
 
 if __name__ == '__main__':
-    ARGS, DB_FILE, PHOTOMETRIC_FILTERS, ALL_RESULTS, ALL_RESULTS_FULL, VERSION_STR,\
+    ARGS, DB_FILE, PHOTOMETRIC_FILTERS, ALL_RESULTS, ALL_RESULTS_FULL, VERSION_STR, \
         ALL_PHOTO, ALL_BANDS, ALL_PLX, ALL_SPTS = main_utils()
     NIGHTSKYTHEME, JSCALLBACKS = main_plots()

simple_app/simple_callbacks.js

@@ -289,4 +289,15 @@ function reset_slider (spectra_slide) {
     spectra_slide.value = [0.81, 0.82];
     spectra_slide.change.emit();
 
+}
+
+function reset_dropdown(dropdown_x, dropdown_y) {
+
+    // resetting the dropdown columns when reset button pressed
+    dropdown_x.value = dropdown_x.options[0][0];
+    dropdown_y.value = dropdown_y.options[1][0];
+
+    dropdown_x.change.emit();
+    dropdown_y.change.emit();
+
 }