From d483c2002e2ccd23d9a2e32edff71fb2e91e015d Mon Sep 17 00:00:00 2001
From: Vitor Trovisco <vmt25@cam.ac.uk>
Date: Fri, 24 Sep 2021 15:06:52 +0000
Subject: [PATCH] Update canto_deploy.yaml - better commenting and small edits
to better match the configuration of the instance @ PomBase
---
canto_deploy.yaml | 127 ++++++++++++++++++++++++++--------------------
1 file changed, 73 insertions(+), 54 deletions(-)
diff --git a/canto_deploy.yaml b/canto_deploy.yaml
index 6fb504f..9bc8250 100644
--- a/canto_deploy.yaml
+++ b/canto_deploy.yaml
@@ -1,18 +1,18 @@
---
# 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
@@ -105,7 +118,7 @@ database_name: Fly-Canto
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
--
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