for issue #195, allowing notes field to be populated and added to the…

… top of the report
polio-nanopore · Nov 27, 2023 · 83497f0 · 83497f0
1 parent 858b5b6
commit 83497f0
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Showing 4 changed files with 12 additions and 2 deletions.
diff --git a/piranha/command.py b/piranha/command.py
@@ -78,6 +78,7 @@ def main(sysargs = sys.argv[1:]):
     misc_group.add_argument('--runname',action="store",help=f"Run name to appear in report. Default: {VALUE_RUNNAME}")
     misc_group.add_argument('--username',action="store",help="Username to appear in report. Default: no user name")
     misc_group.add_argument('--institute',action="store",help="Institute name to appear in report. Default: no institute name")
+    misc_group.add_argument('--notes',action="store",help="Miscellaneous notes to appear at top of report. Default: no notes")
     misc_group.add_argument('--orientation',action="store",help="Orientation of barcodes in wells on a 96-well plate. If `well` is supplied as a column in the barcode.csv, this default orientation will be overwritten. Default: `vertical`. Options: `vertical` or `horizontal`.")
     misc_group.add_argument('-t', '--threads', action='store',dest="threads",type=int,help="Number of threads. Default: 1")
     misc_group.add_argument("--verbose",action="store_true",help="Print lots of stuff to screen")
@@ -154,6 +155,7 @@ def main(sysargs = sys.argv[1:]):
                                 args.username,
                                 args.institute,
                                 args.runname,
+                                args.notes,
                                 config)
     # runs qc checks on the phylo input options and configures the phylo settings
     # now need tempdir for this parsing, so run after directory_setup

diff --git a/piranha/data/report.mako b/piranha/data/report.mako
@@ -609,6 +609,11 @@
       %if config["institute"]!="":
         <h3><strong>${LANGUAGE_CONFIG["6"]}</strong> | ${config["institute"].lstrip("'").rstrip("'")}</h3>
       %endif
+      %if config["notes"]!="":
+        <hr>
+        <p>${config["notes"].lstrip("'").rstrip("'")}</p>
+        <hr>
+      %endif
       <div class="info_box">
         <p>${LANGUAGE_CONFIG["52"]}</p>
       </div>

diff --git a/piranha/input_parsing/initialising.py b/piranha/input_parsing/initialising.py
@@ -70,9 +70,10 @@ def get_defaults():
                     KEY_POSITIVE:VALUE_POSITIVE,
                     KEY_NEGATIVE:VALUE_NEGATIVE,
                     KEY_INSTITUTE:"",
+                    KEY_NOTES:"",
                     KEY_THREADS:1,
                     KEY_VERBOSE:False,
-
+                    
                     KEY_CONFIGURATION_TABLE_FIELDS: VALUE_CONFIGURATION_TABLE_FIELDS,
                     KEY_COLOUR_MAP: VALUE_COLOUR_MAP,
                     KEY_COLOUR_THEME: VALUE_COLOUR_THEME
@@ -200,12 +201,13 @@ def setup_config_dict(cwd,config_arg):
         config[KEY_INPUT_PATH] = cwd
     return config
 
-def misc_args_to_config(verbose,threads,username,institute,run_name,config):
+def misc_args_to_config(verbose,threads,username,institute,run_name,notes,config):
     misc.add_arg_to_config(KEY_VERBOSE,verbose,config)
     misc.add_arg_to_config(KEY_THREADS,threads,config)
     misc.add_arg_to_config(KEY_USERNAME,username,config)
     misc.add_arg_to_config(KEY_INSTITUTE,institute,config)
     misc.add_arg_to_config(KEY_RUNNAME,run_name,config)
+    misc.add_arg_to_config(KEY_NOTES,notes,config)
 
 def set_up_verbosity(config):
     if config[KEY_VERBOSE]:

diff --git a/piranha/utils/config.py b/piranha/utils/config.py
@@ -108,6 +108,7 @@
 KEY_USERNAME="username"
 KEY_INSTITUTE="institute"
 KEY_RUNNAME="runname"
+KEY_NOTES="notes"
 KEY_VERBOSE="verbose"
 KEY_THREADS="threads"
 KEY_LOG_API="log_api"