Update canto_deploy.yaml - better commenting and a few tweaks to match the...

Update canto_deploy.yaml - better commenting and a few tweaks to match the configuration for the Pombase instance

canto_deploy.yaml

 ---
 # Canto config file  -*- conf -*-
 name: Fly-Canto
-long_name: FlyBase-pheno-test-local
+long_name: Fly-Canto: FlyBase phenotype curation @ flybase-vm
 
 
 instance_organism:
-  taxonid: 7227                                                                       
+  taxonid: 7227
 
 flybase_mode: 1
 
 annotation_figure_field: 0
 
-# disable deletion buttons on allele creation table on genotype management page
-show_quick_deletion_buttons: 0
+# enable deletion buttons on allele creation table on genotype management page
+show_quick_deletion_buttons: 1
 
 Model::TrackModel:
   connect_info:
@@ -30,11 +30,11 @@ Model::ChadoModel:
     - PASSWORD
   schema_class: Canto::ChadoDB
 
-#This is required to enable the Chado database connection 
+#This is required to enable connection to Chado database
 chado:
   taxon_id_lookup_strategy: dbxref
   ignore_case_in_gene_query: 0
-#This is also required to enable the Chado database connection 
+#This is also required to enable connection to Chado database
 implementation_classes:
   gene_adaptor: Canto::Chado::GeneLookup
   go_adaptor: Canto::Track::OntologyLookup
@@ -42,15 +42,14 @@ implementation_classes:
 
 
 # configuration of alleles
-## trying to remove fields for strain and allele expression - did not seem to work on initial test
 alleles_have_expression: 0
 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 configures whether the allele creation table on the genotype management page is enabled or not (0 - disabled; 1 - enabled)
 show_genotype_management_genes_list: 1
+##this configures whether diploids are allowed or not
 diploid_mode: 1
-
-## allow internal notes on single alleles and config:
+# configuration of internal notes on single alleles and config:
 notes_on_single_allele_genotypes_only: 1
 allele_note_types:
   - name: phenotype
@@ -64,10 +63,24 @@ 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 '+'
+# Publication-level private notes configuration (i.e. FlyBase's internal notes)
+## Imported pre-existent publication-level internal notes
+### The heading for the pre-existing publication-level internal notes section on the front page (if any); please note that these notes are 'external' to Canto (made upstream of pheno curation), which is why the filed is labelled 'external_notes'
+external_notes_label: Internal notes from JSON
+### if there are no notes we show "[none]" instead of hiding the section
+always_show_external_notes_section: 1
+## publication-level internal notes created by the curator within the session
+### if 1, show the internal notes on the front page
+show_message_for_curators_on_front_page: 1
+### header for the message to curators section on the front page (if enabled)
+message_to_curators_label: Internal notes from session
+
+
+# put the genotype lists in the same order as the allele_type_list
+sort_genotype_management_page_by_allele_type: 1
+
+## display wildtype 'alleles' simply as '+', e.g. w[+]
 wildtype_name_template: '@@gene_display_name@@[+]'
 
 ## configuration of allele types
@@ -101,11 +114,11 @@ allele_type_list:
 
 
 # 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 - Canto for FlyBase Phenotype Curation
 
 available_annotation_type_list:
   - name: phenotypic_class
@@ -121,6 +134,7 @@ available_annotation_type_list:
     can_have_conditions: 0
     #allow_annotation_transfer - use true/false
     allow_annotation_transfer: true
+    annotation_table_columns_to_hide: [term_ontid]
     broad_term_suggestions: >
       lethal, sterile, visible, cell number defective, locomotor behavior defective
     specific_term_examples: >
@@ -146,6 +160,7 @@ available_annotation_type_list:
     can_have_conditions: 0
     #allow_annotation_transfer - use true/false
     allow_annotation_transfer: true
+    annotation_table_columns_to_hide: [term_ontid]
     broad_term_suggestions: >
       embryo, wing, eye, ovary, wing disc, neuromuscular junction
     specific_term_examples: >
@@ -165,6 +180,7 @@ available_annotation_type_list:
     interaction_term_required: 1
     #allow_annotation_transfer - use true/false
     allow_annotation_transfer: true
+    annotation_table_columns_to_hide: [term_ontid]
     hide_extension_relations: [qual,dv_qual]
     display_name: 'phenotype class interaction'
     very_short_display_name: 'phen-class interaction'
@@ -186,6 +202,7 @@ available_annotation_type_list:
     interaction_term_required: 1
     #allow_annotation_transfer - use true/false
     allow_annotation_transfer: true
+    annotation_table_columns_to_hide: [term_ontid]
     hide_extension_relations: [qual,dv_qual]
     display_name: 'phenotype anatomy interaction'
     very_short_display_name: 'anatomy interaction'
@@ -208,7 +225,7 @@ available_annotation_type_list:
     interaction_same_locus: false
     #allow_annotation_transfer - use true/false
     allow_annotation_transfer: true
-    show_quick_deletion_buttons: 0
+    annotation_table_columns_to_hide: [term_ontid]
     category: interaction
     display_name: 'complementation'
     feature_type: 'metagenotype'
@@ -219,11 +236,13 @@ available_annotation_type_list:
       - Fails to complement
   - name: rescue
     can_have_conditions: 0
-    allow_annotation_transfer: 1
     #single_locus_only -  use true/false
     single_locus_only: true
     #interaction_same_locus -  use true/false
     interaction_same_locus: true
+    #allow_annotation_transfer - use true/false
+    allow_annotation_transfer: true
+    annotation_table_columns_to_hide: [term_ontid]
     category: interaction
     display_name: 'rescue'
     feature_type: 'metagenotype'
@@ -234,7 +253,7 @@ available_annotation_type_list:
       - Fails to rescue
 
 
-# restrict the list of annotation types
+# define which annotation types are enabled
 enabled_annotation_type_list:
   - phenotypic_class
   - anatomy
@@ -244,41 +263,7 @@ enabled_annotation_type_list:
   - rescue
 
 
-ontology_namespace_config:
-  subsets_to_ignore:
-    primary_autocomplete:
-      - "is_a(Grouping_terms)"
-    primary_select:
-      - "is_a(Grouping_terms)"
-      - "is_a(qc_do_not_annotate)"
-    extension:
-# - add the ash to allow top/root terms (while still disallowing 'do not annotate' terms):
-      # - "is_a(canto_root_subset)"
-      - "is_a(qc_do_not_annotate)"
-  do_not_annotate_subsets:
-    - "is_a(canto_root_subset)"
-    - "is_a(qc_do_not_annotate)"
-
-
-# configuration for annotation extensions in the user interface
-# See: https://github.com/pombase/canto/wiki/AnnotationExtensionConfig
-extension_conf_files:
-   - extension_config.tsv
-
-
-# to show the gene list on the genotype management gene list, un-comment the next three lines - i.e. remove the #. The spaces before "taxonid:" are needed
-#show_genotype_management_genes_list: 1
-#instance_organism:
-#   taxonid: 7227
-
-
-cache:
-  memcached:
-    servers:
-      - 127.0.0.1:11211
-
-
-#which interaction evidence codes can be used with which phenotype classes
+#configure which interaction evidence codes can be used with which phenotype classes
 namespace_term_evidence_codes:
   phenotypic_class:
     # viable (minus partially lethal - majority live)
@@ -369,6 +354,41 @@ namespace_term_evidence_codes:
        - suppressible
        - non-suppressible
 
+
+ontology_namespace_config:
+  subsets_to_ignore:
+    primary_autocomplete:
+      - "is_a(Grouping_terms)"
+    primary_select:
+      - "is_a(Grouping_terms)"
+      - "is_a(qc_do_not_annotate)"
+    extension:
+# - add the ash to allow top/root terms (while still disallowing 'do not annotate' terms):
+      # - "is_a(canto_root_subset)"
+      - "is_a(qc_do_not_annotate)"
+  do_not_annotate_subsets:
+    - "is_a(canto_root_subset)"
+    - "is_a(qc_do_not_annotate)"
+
+
+# configuration for annotation extensions in the user interface
+# See: https://github.com/pombase/canto/wiki/AnnotationExtensionConfig
+extension_conf_files:
+   - extension_config.tsv
+
+
+# to show the gene list on the genotype management gene list, un-comment the next three lines - i.e. remove the #. The spaces before "taxonid:" are needed
+#show_genotype_management_genes_list: 1
+#instance_organism:
+#   taxonid: 7227
+
+
+cache:
+  memcached:
+    servers:
+      - 127.0.0.1:11211
+
+
 class_info:
   track:
     cv:
@@ -1137,8 +1157,7 @@ reports:
 
 
 curs_config:
-  # Possible reasons for a paper to have no phenotype annotation in the case
-  # where genes are mentioned.
+  # List of possible reasons for a paper to have no phenotype annotation in the case although there are associated genes
   no_annotation_reasons:
     - No phenotypic data
     - Only pheno_chem data