Stop storing absolute paths in the database

jwql/instrument_monitors/common_monitors/readnoise_monitor.py

@@ -413,7 +413,7 @@ def process(self, file_list):
             processed_file = file.replace("uncal", "refpix")
             if not os.path.isfile(processed_file):
                 files_to_calibrate.append(file)
-        
+
         # Run the files through the necessary pipeline steps
         outputs = run_parallel_pipeline(files_to_calibrate, "uncal", "refpix", self.instrument)
 
@@ -422,7 +422,7 @@ def process(self, file_list):
 
             # Get relevant header information for this file
             self.get_metadata(filename)
-            
+
             if filename in outputs:
                 processed_file = outputs[filename]
             else:
@@ -498,20 +498,23 @@ def process(self, file_list):
             # Construct new entry for this file for the readnoise database table.
             # Can't insert values with numpy.float32 datatypes into database
             # so need to change the datatypes of these values.
-            readnoise_db_entry = {'uncal_filename': filename,
+            #
+            # Store files as file name only (file path will be built at retrieval based
+            # on runtime configuration)
+            readnoise_db_entry = {'uncal_filename': os.path.basename(filename),
                                   'aperture': self.aperture,
                                   'detector': self.detector,
                                   'subarray': self.subarray,
                                   'read_pattern': self.read_pattern,
                                   'nints': self.nints,
                                   'ngroups': self.ngroups,
                                   'expstart': self.expstart,
-                                  'readnoise_filename': readnoise_outfile,
+                                  'readnoise_filename': os.path.basename(readnoise_outfile),
                                   'full_image_mean': float(full_image_mean),
                                   'full_image_stddev': float(full_image_stddev),
                                   'full_image_n': full_image_n.astype(float),
                                   'full_image_bin_centers': full_image_bin_centers.astype(float),
-                                  'readnoise_diff_image': readnoise_diff_png,
+                                  'readnoise_diff_image': os.path.basename(readnoise_diff_png),
                                   'diff_image_mean': float(diff_image_mean),
                                   'diff_image_stddev': float(diff_image_stddev),
                                   'diff_image_n': diff_image_n.astype(float),

jwql/website/apps/jwql/monitor_pages/monitor_readnoise_bokeh.py

@@ -31,6 +31,9 @@
 from jwql.database.database_interface import session
 from jwql.database.database_interface import FGSReadnoiseStats, MIRIReadnoiseStats, NIRCamReadnoiseStats, NIRISSReadnoiseStats, NIRSpecReadnoiseStats
 from jwql.utils.constants import FULL_FRAME_APERTURES, JWST_INSTRUMENT_NAMES_MIXEDCASE
+from jwql.utils.utils import get_config
+
+OUTPUTS_DIR = get_config()['outputs']
 
 
 class ReadnoiseMonitorData():
@@ -107,13 +110,16 @@ class ReadNoisePlotTab():
     def __init__(self, instrument, aperture):
         self.instrument = instrument
         self.aperture = aperture
+        self.ins_ap = "{}_{}".format(self.instrument.lower(), self.aperture.lower())
 
         self.db = ReadnoiseMonitorData(self.instrument, self.aperture)
 
         self.plot_readnoise_amplifers()
         self.plot_readnoise_difference_image()
         self.plot_readnoise_histogram()
 
+        self.file_path = os.path.join(OUTPUT_DIR, "readnoise_monitor", "data", self.ins_ap)
+
         self.tab = Panel(child=column(row(*self.amp_plots),
                                       self.diff_image_plot,
                                       self.readnoise_histogram),
@@ -133,7 +139,7 @@ def plot_readnoise_amplifers(self):
             else:
                 readnoise_vals = np.array(list())
 
-            filenames = [os.path.basename(result.uncal_filename).replace('_uncal.fits', '') for result in self.db.query_results]
+            filenames = [result.uncal_filename.replace('_uncal.fits', '') for result in self.db.query_results]
             expstarts_iso = np.array([result.expstart for result in self.db.query_results])
             expstarts = np.array([datetime.strptime(date, '%Y-%m-%dT%H:%M:%S.%f') for date in expstarts_iso])
             nints = [result.nints for result in self.db.query_results]
@@ -168,18 +174,16 @@ def plot_readnoise_difference_image(self):
                                       height=500, width=500, sizing_mode='scale_width')
 
         if len(self.db.query_results) != 0:
-            diff_image_png = self.db.query_results[-1].readnoise_diff_image
-            diff_image_png = os.path.join('/static', '/'.join(diff_image_png.split('/')[-6:]))
+            diff_image_png = os.path.join(self.file_path, self.db.query_results[-1].readnoise_diff_image)
             self.diff_image_plot.image_url(url=[diff_image_png], x=0, y=0, w=2048, h=2048, anchor="bottom_left")
-            
+
         self.diff_image_plot.xaxis.visible = False
         self.diff_image_plot.yaxis.visible = False
         self.diff_image_plot.xgrid.grid_line_color = None
         self.diff_image_plot.ygrid.grid_line_color = None
         self.diff_image_plot.title.text_font_size = '22px'
         self.diff_image_plot.title.align = 'center'
 
-
     def plot_readnoise_histogram(self):
         """Updates the readnoise histogram"""
 
@@ -200,12 +204,9 @@ def plot_readnoise_histogram(self):
                                           y_range=(hist_yr_start, hist_yr_end),
                                           sizing_mode='scale_width')
 
-        source = ColumnDataSource(data=dict(
-                        x=diff_image_bin_centers,
-                        y=diff_image_n,
-                        ))
+        source = ColumnDataSource(data=dict(x=diff_image_bin_centers, y=diff_image_n, ))
 
-        self.readnoise_histogram.add_tools(HoverTool(tooltips=[("Data (x, y)", "(@x, @y)"),]))
+        self.readnoise_histogram.add_tools(HoverTool(tooltips=[("Data (x, y)", "(@x, @y)"), ]))
 
         self.readnoise_histogram.circle(x='x', y='y', source=source)