small bug fixes, docs

progenetix · Feb 23, 2024 · ba533a3 · ba533a3
1 parent 9ade336
commit ba533a3
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Showing 6 changed files with 14 additions and 6 deletions.
diff --git a/bin/housekeeping.py b/bin/housekeeping.py
@@ -15,7 +15,6 @@
 from mongodb_utils import mongodb_update_indexes
 from doc_generator import doc_generator
 
-generated_docs_path = path.join( dir_path, pardir, "docs", "generated")
 services_conf_path = path.join( dir_path, "config" )
 services_lib_path = path.join( dir_path, pardir, "services", "lib" )
 sys.path.append( services_lib_path )
@@ -41,7 +40,11 @@ def housekeeping():
     read_service_prefs("housekeeping", services_conf_path, byc)
     run_beacon_init_stack(byc)
 
+    # TODO: rewrap, use config etc.
+    generated_docs_path = path.join( dir_path, pardir, "docs", "generated")
+    bycon_generated_docs_path = path.join( dir_path, pardir, pardir, "bycon", "docs", "generated")
     doc_generator(byc, generated_docs_path)
+    doc_generator(byc, bycon_generated_docs_path)
 
     if len(byc["dataset_ids"]) != 1:
         print("No single existing dataset was provided with -d ...")

diff --git a/bin/local/plot_defaults.yaml b/bin/local/plot_defaults.yaml
@@ -145,7 +145,7 @@ plot_parameters:
     description: >-
       * width of the plot image, in px
       * the plot area width is determined through
-        - plot_width - 2*plot_margins - plot_labelcol_width - plot_axislab_y_width - plot_dendrogram_width
+          - `plot_width - 2*plot_margins - plot_labelcol_width - plot_axislab_y_width - plot_dendrogram_width`
     type: integer
     default: 1024
 

diff --git a/docs/generated/argument_definitions.md b/docs/generated/argument_definitions.md
@@ -35,6 +35,7 @@ limit number of documents; a value of 0 sets to unlimited
 **description:**
 The requested granularity of the beacon    
 **cmdFlags:** `--requestedGranularity`    
+**default:** `record`    
 
 ### `request_entity_path_id` 
 **type:** string    
@@ -300,7 +301,11 @@ setting the number of documents reurned in test mode
 **type:** string    
 **cmdFlags:** `--output`    
 **description:**
-special output format; command line processing uses some predefined text as standard, but options are e.g. json or pgxseg    
+For defining a special output format, mostly for `byconaut` services use. Examples:
+
+* `cnvstats`, for `analyses`, to present some CNV statistics     
+* `pgxseg`, using the `.pgxseg` variant file format     
+* `text`, for some services to deliver a text table instead of JSON    
 
 ### `include_handovers` 
 **type:** boolean    

diff --git a/services/lib/bycon_plot.py b/services/lib/bycon_plot.py
@@ -138,7 +138,7 @@ def __get_plot_parameters(self):
         p_t_s = self.plot_types
 
         bps = {}
-        plot_pars = BYC_PARS.get("plot_pars", {})
+        plot_pars = BYC_PARS.get("plot_pars", "")
         for ppv in re.split(r'::|&', plot_pars):
             pp_pv = ppv.split('=')
             if len(pp_pv) == 2:

diff --git a/services/lib/geomap_utils.py b/services/lib/geomap_utils.py
@@ -188,7 +188,7 @@ def __update_geo_plot_params_from_form(byc):
     p_p.update({"inputfile": BYC_PARS.get("inputfile", "")})
 
     bps = {}
-    plot_pars = BYC_PARS.get("plot_pars", {})
+    plot_pars = BYC_PARS.get("plot_pars", "")
     for ppv in re.split(r'::|&', plot_pars):
         pp_pv = ppv.split('=')
         if len(pp_pv) == 2:

diff --git a/services/local/plot_defaults.yaml b/services/local/plot_defaults.yaml
@@ -145,7 +145,7 @@ plot_parameters:
     description: >-
       * width of the plot image, in px
       * the plot area width is determined through
-        - plot_width - 2*plot_margins - plot_labelcol_width - plot_axislab_y_width - plot_dendrogram_width
+          - `plot_width - 2*plot_margins - plot_labelcol_width - plot_axislab_y_width - plot_dendrogram_width`
     type: integer
     default: 1024