Update canto_deploy.yaml - edits to better match configuration at PomBase's...

Update canto_deploy.yaml - edits to better match configuration at PomBase's instance; small edits to improve comments and order of configuration fields

canto_deploy.yaml

 ---
 # Canto config file  -*- conf -*-
 name: Fly-Canto
-long_name: FlyBase-pheno-test-local
+long_name: FlyBase's phenotype curation tool @ flybase-vm
+database_name: FlyBase
 
 
 instance_organism:
-  taxonid: 7227                                                                       
+  taxonid: 7227                    
 
 flybase_mode: 1
 
 annotation_figure_field: 0
 
-# disable deletion buttons on allele creation table on genotype management page
+# disable deletion buttons on genotype management page?
 show_quick_deletion_buttons: 0
 
 Model::TrackModel:
@@ -30,28 +31,43 @@ Model::ChadoModel:
     - PASSWORD
   schema_class: Canto::ChadoDB
 
-#This is required to enable the Chado database connection 
+#This is required to enable connection to main Chado
 chado:
   taxon_id_lookup_strategy: dbxref
   ignore_case_in_gene_query: 0
+  
 #This is also required to enable the Chado database connection 
 implementation_classes:
   gene_adaptor: Canto::Chado::GeneLookup
   go_adaptor: Canto::Track::OntologyLookup
   ontology_adaptor: Canto::Track::OntologyLookup
 
+# Configuration of private notes (internal notes in FlyBase lingo)
+## the heading above the external_notes section on the front page of the publication session, if any (this notes are external to Canto but internal for FlyBase, hence the difference in labels)
+external_notes_label: Internal notes from JSON
+## header for 'message to curators' section on the front page (if enabled); for FlyBase, these are the publication-level internal notes created by the curator within the session
+message_to_curators_label: Internal notes from session
+# if 1 (if yes), show the internal notes on the front page
+show_message_for_curators_on_front_page: 1
+
 
 # configuration of alleles
 ## trying to remove fields for strain and allele expression - did not seem to work on initial test
 alleles_have_expression: 0
+#disable strains
 strains_mode: 0
 split_genotypes_by_organism: 0
-##this enables/disables the allele creation table on the genotype management page (0 - disabled; 1 - enabled)
+##this enables the allele creation table on the genotype management page
 show_genotype_management_genes_list: 1
+#this allows annotation of diploid genotypes 
 diploid_mode: 1
 
+## display wildtype 'alleles' simply as '+'
+wildtype_name_template: '@@gene_display_name@@[+]'
+
 ## allow internal notes on single alleles and config:
 notes_on_single_allele_genotypes_only: 1
+
 allele_note_types:
   - name: phenotype
     display_name: Phenotype
@@ -64,11 +80,6 @@ allele_note_types:
   - name: internal_note
     display_name: Internal note
 
-# The heading above the external_notes section on the front page of the publication session, if any (tis notes are external to canto but internal for FlyBase, hence the difference in labels)
-external_notes_label: Internal notes
-
-## display wildtype 'alleles' simply as '+'
-wildtype_name_template: '@@gene_display_name@@[+]'
 
 ## configuration of allele types
 allele_type_list:
@@ -99,13 +110,16 @@ allele_type_list:
     expression_required: false
     do_not_annotate: 1
 
+# put the genotype lists in the same order as the allele_type_list
+sort_genotype_management_page_by_allele_type: 1
+
 
 # the name of the organisation running this Canto - shown in various places in the user interface
-database_name: Fly-Canto
+database_name: FlyBase
 
 database_url: www.flybase.org
 
-instance_front_subtitle: Canto for FlyBase
+instance_front_subtitle: Fly-Canto for FlyBase
 
 available_annotation_type_list:
   - name: phenotypic_class
@@ -208,7 +222,6 @@ available_annotation_type_list:
     interaction_same_locus: false
     #allow_annotation_transfer - use true/false
     allow_annotation_transfer: true
-    show_quick_deletion_buttons: 0
     category: interaction
     display_name: 'complementation'
     feature_type: 'metagenotype'
@@ -224,6 +237,8 @@ available_annotation_type_list:
     single_locus_only: true
     #interaction_same_locus -  use true/false
     interaction_same_locus: true
+    #allow_annotation_transfer - use true/false
+    allow_annotation_transfer: true
     category: interaction
     display_name: 'rescue'
     feature_type: 'metagenotype'
@@ -234,7 +249,7 @@ available_annotation_type_list:
       - Fails to rescue
 
 
-# restrict the list of annotation types
+# Which of the annotation types listed above (under 'available_annotation_type_list:') to display and enable.
 enabled_annotation_type_list:
   - phenotypic_class
   - anatomy
@@ -1137,8 +1152,7 @@ reports:
 
 
 curs_config:
-  # Possible reasons for a paper to have no phenotype annotation in the case
-  # where genes are mentioned.
+  # Possible reasons for a paper to have no phenotype annotation in the case where genes/alleles are mentioned
   no_annotation_reasons:
     - No phenotypic data
     - Only pheno_chem data