From ea3bb51566509a5ed26a1a886d66aca44529ac68 Mon Sep 17 00:00:00 2001
From: Vitor Trovisco <vmt25@cam.ac.uk>
Date: Thu, 8 Oct 2020 15:15:10 +0000
Subject: [PATCH] Update canto_deploy.yaml. Corrects fly anatomy ontology
namespace. Allows transfer of annotations. Configures publication categories
as well as the corresponding track reports.
---
canto_deploy.yaml | 787 +++++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 785 insertions(+), 2 deletions(-)
diff --git a/canto_deploy.yaml b/canto_deploy.yaml
index 41e2291..a15a052 100644
--- a/canto_deploy.yaml
+++ b/canto_deploy.yaml
@@ -9,6 +9,8 @@ instance_organism:
flybase_mode: 1
+annotation_figure_field: 0
+
Model::TrackModel:
connect_info:
# filepath plus track.sqlite3
@@ -109,6 +111,7 @@ available_annotation_type_list:
- exact
feature_type: 'genotype'
can_have_conditions: 0
+ allow_annotation_transfer: 1
broad_term_suggestions: >
lethal, sterile, visible, cell number defective, locomotor behavior defective
specific_term_examples: >
@@ -123,7 +126,7 @@ available_annotation_type_list:
detailed_help_path: /docs/fypo_annotation
- name: anatomy
category: ontology
- namespace: fly_anatomy.ontology
+ namespace: FlyBase_anatomy_CV
hide_extension_relations: [qual,dv_qual]
very_short_display_name: 'anatomy'
short_display_name: 'anatomy'
@@ -132,6 +135,7 @@ available_annotation_type_list:
- exact
feature_type: 'genotype'
can_have_conditions: 0
+ allow_annotation_transfer: 1
broad_term_suggestions: >
embryo, wing, eye, ovary, wing disc, neuromuscular junction
specific_term_examples: >
@@ -149,6 +153,7 @@ available_annotation_type_list:
namespace: phenotypic_class
term_suggestions_annotation_type: phenotypic_class
interaction_term_required: 1
+ allow_annotation_transfer: 1
hide_extension_relations: [qual,dv_qual]
display_name: 'phenotype class interaction'
very_short_display_name: 'phen-class interaction'
@@ -165,9 +170,10 @@ available_annotation_type_list:
detailed_help_path: /docs/genetic_interaction_annotation
- name: anatomy_interaction
category: interaction
- namespace: fly_anatomy.ontology
+ namespace: FlyBase_anatomy_CV
term_suggestions_annotation_type: anatomy
interaction_term_required: 1
+ allow_annotation_transfer: 1
hide_extension_relations: [qual,dv_qual]
display_name: 'phenotype anatomy interaction'
very_short_display_name: 'anatomy interaction'
@@ -184,6 +190,7 @@ available_annotation_type_list:
detailed_help_path: /docs/genetic_interaction_annotation
- name: complementation
can_have_conditions: 0
+ allow_annotation_transfer: 1
single_allele_only: 1
interaction_same_locus: 1
category: interaction
@@ -196,6 +203,7 @@ available_annotation_type_list:
- Fails to complement
- name: rescue
can_have_conditions: 0
+ allow_annotation_transfer: 1
single_locus_only: 1
interaction_same_locus: 1
category: interaction
@@ -342,3 +350,778 @@ namespace_term_evidence_codes:
evidence_codes:
- suppressible
- non-suppressible
+
+class_info:
+ track:
+ cv:
+ class_display_name: controlled vocabulary
+ editable: 1
+ display_field: name
+ field_info_list:
+ - name: name
+ editable: 1
+ - name: definition
+ editable: 1
+ - name: "term count"
+ source:
+ sql: 'select count(*) from cvterm where cvterm.cv_id = me.cv_id'
+ - name: "load date"
+ source:
+ sql: "select value from cvprop p join cvterm pt on p.type_id = pt.cvterm_id where p.cv_id = me.cv_id and pt.name = 'cv_date'"
+ cvprop:
+ class_display_name: controlled vocabulary properties
+ display_field: value
+ field_info_list:
+ - name: type
+ source: type_id
+ referenced_class: Cvterm
+ - name: value
+ editable: 1
+ cvterm:
+ class_display_name: controlled vocabulary term
+ editable: 1
+ display_field: name
+ field_info_list:
+ - name: name
+ editable: 1
+ - name: definition
+ editable: 1
+ - name: cv_id
+ editable: 1
+ db:
+ editable: 1
+ display_field: name
+ field_info_list:
+ - name: name
+ editable: 1
+ - name: description
+ editable: 1
+ - name: url
+ editable: 1
+ - name: "accessions stored"
+ source:
+ sql: 'select count(*) from dbxref where dbxref.db_id = me.db_id'
+ dbxref:
+ editable: 1
+ display_field: accession
+ field_info_list:
+ - name: db_id
+ editable: 1
+ - name: accession
+ editable: 1
+ - name: description
+ editable: 1
+ - name: cvterm_id
+ editable: 1
+ organism:
+ editable: 1
+ display_field: full_name
+ order_by:
+ - scientific_name
+ field_info_list:
+ - name: scientific_name
+ editable: 1
+ organism_report:
+ extends: organism
+ '+field_info_list':
+ - name: Number of genes
+ source:
+ sql: 'select count(*) from gene where gene.organism = me.organism_id'
+ person:
+ object_title_format: 'Details for @@DISPLAY_FIELD@@'
+ editable: 1
+ display_field: name
+ order_by: name
+ search_fields:
+ - email_address
+ - name
+ - orcid
+ field_info_list:
+ - name: name
+ source: name
+ editable: 1
+ - name: orcid
+ editable: 1
+ - name: known_as
+ editable: 1
+ - name: email_address
+ editable: 1
+ - name: role
+ default_value: "'user'"
+ values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "Canto user types")'
+ editable: 1
+ admin_only: 1
+ - name: Sessions
+ source:
+ sql: "select count(curs) from curs_curator cc1 where cc1.curator = person_id and curs_curator_id = (select max(curs_curator_id) from curs_curator cc2 where cc2.curs = cc1.curs)"
+ - name: Approved sessions
+ source:
+ sql: "select count(curs) from curs_curator cc1 where cc1.curator = person_id and curs_curator_id = (select max(curs_curator_id) from curs_curator cc2 where cc2.curs = cc1.curs) and cc1.curs in (select curs_id from curs where curs_id in (select curs from cursprop p join cvterm t on p.type = t.cvterm_id where t.name = 'annotation_status' and p.value = 'APPROVED'))"
+ - name: password
+ editable: 1
+ admin_only: 1
+ lab:
+ editable: 1
+ display_field: name
+ order_by: name
+ field_info_list:
+ - name: name
+ editable: 1
+ - name: lab_head
+ editable: 1
+ - name: people
+ is_collection: 1
+ editable: 1
+ pub:
+ object_title_format: 'Details for publication: @@$object->uniquename()@@'
+ class_display_name: publication
+ display_field: 'Publication ID'
+ search_fields:
+ - uniquename
+ editable: 1
+ # hack to order by pubmed id, or by doi number
+ order_by: "cast((case me.uniquename like 'PMID:%' WHEN 1 THEN substr(me.uniquename, 6) ELSE me.uniquename END) as integer)"
+ field_info_list:
+ - name: 'Publication ID'
+ source: uniquename
+ - name: title
+ - name: authors
+ - name: abstract
+ extra_field_class: non-important-attribute-field
+ hide_context:
+ - list
+ - inline_list
+ - name: citation
+ hide_context:
+ - list
+ - inline_list
+ - name: publication_date
+ hide_context:
+ - list
+ - inline_list
+ - name: affiliation
+ hide_context:
+ - list
+ - inline_list
+ - name: corresponding_author
+ editable: 1
+ - name: current_curator
+ referenced_class: Person
+ source:
+ sql: "select curator from curs_curator where curs_curator_id = (select max(curs_curator_id) from curs_curator cc, curs c where cc.curs = c.curs_id and c.pub = me.pub_id)"
+ - name: session_first_sent
+ source:
+ sql: "select (case when (value is null) THEN 'no' ELSE value END) from curs, cursprop p, cvterm t where me.pub_id = curs.pub and curs.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'link_sent_to_curator_date' order by value"
+ default: no
+ editable: 0
+ - name: session_last_sent
+ source:
+ sql: "select (case when (value is null) THEN 'no' ELSE value END) from curs, cursprop p, cvterm t where me.pub_id = curs.pub and curs.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'link_sent_to_curator_date' order by value DESC"
+ default: no
+ editable: 0
+ - name: session_sent_count
+ source:
+ sql: "cast((select count(value) from curs, cursprop p, cvterm t where me.pub_id = curs.pub and curs.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'link_sent_to_curator_date') as int)"
+ # - name: type
+ # source: type_id
+ # values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "Canto publication type")'
+ # referenced_class: Cvterm
+ # editable: 1
+ - name: session_status
+ source:
+ sql: "select value from curs, cursprop p, cvterm t where me.pub_id = curs.pub and curs.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'annotation_status'"
+ editable: 0
+ - name: approver_name
+ source:
+ sql: "select value from curs, cursprop p, cvterm t where me.pub_id = curs.pub and curs.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'approver_name'"
+ editable: 0
+ - name: load_type
+ source: load_type_id
+ values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "Canto publication load types")'
+ referenced_class: Cvterm
+ editable: 1
+ hide_context:
+ - list
+ - inline_list
+ - name: triage_status
+ source: triage_status_id
+ values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "Canto publication triage status")'
+ referenced_class: Cvterm
+ editable: 1
+ hide_context:
+ - inline_list
+ - name: curation_priority
+ source: curation_priority_id
+ values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "Canto curation priorities")'
+ referenced_class: Cvterm
+ editable: 1
+ pub_curation_status:
+ class_display_name: publication curation status
+ display_field: status_id
+ editable: 1
+ field_info_list:
+ - name: publication
+ source: pub_id
+ editable: 1
+ - name: annotation_type
+ editable: 1
+ - name: status
+ source: status_id
+ values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "Canto publication curation status")'
+ referenced_class: Cvterm
+ editable: 1
+ pubprop:
+ class_display_name: publication properties
+ display_field: value
+ editable: 1
+ field_info_list:
+ - name: publication
+ source: pub_id
+ editable: 1
+ - name: type_id
+ values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "Canto publication experiment types")'
+ referenced_class: Cvterm
+ editable: 1
+ - name: value
+ editable: 1
+ curs:
+ class_display_name: curation session
+ display_field: curs_key
+ editable: 0
+ field_info_list:
+ - name: curs_key
+ editable: 0
+ - name: publication
+ editable: 0
+ source: pub
+ - name: creation_date
+ editable: 0
+ - name: current_curator
+ referenced_class: Person
+ source:
+ sql: "select curator from curs_curator where curs_curator_id = (select max(curs_curator_id) from curs_curator where curs = me.curs_id)"
+ - name: accepted
+ source:
+ sql: "select (case when (accepted_date is null) THEN 'no' ELSE accepted_date END) from curs_curator where curs_curator_id = (select max(curs_curator_id) from curs_curator where curs = me.curs_id)"
+ - name: last_assigned
+ source:
+ sql: "select creation_date from curs_curator where curs_curator_id = (select max(curs_curator_id) from curs_curator where curs = me.curs_id)"
+ - name: last_sent_date
+ source:
+ sql: "select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'link_sent_to_curator_date' order by value DESC"
+ - name: session_sent_count
+ source:
+ sql: "cast((select count(value) from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'link_sent_to_curator_date') as int)"
+ - name: status
+ source:
+ sql: "select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'annotation_status'"
+ - name: approver_name
+ source:
+ sql: "select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'approver_name'"
+ - name: genes_added
+ source:
+ sql: "cast((select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'session_genes_count') as int)"
+ - name: term_suggestions
+ source:
+ sql: "cast((select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'session_term_suggestions_count') as int)"
+# if the hook dies the creation fails
+ pre_create_hook: 'Canto::Track::create_curs_db_hook'
+ cursprop:
+ class_display_name: Session properties
+ editable: 1
+ field_info_list:
+ - name: type
+ values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "Canto cursprop types")'
+ referenced_class: Cvterm
+ editable: 1
+ - name: value
+ editable: 1
+ - name: curs
+ editable: 1
+ curs_curator:
+ class_display_name: Session curator
+ editable: 1
+ field_info_list:
+ - name: curs
+ editable: 1
+ - name: curator
+ editable: 1
+ gene:
+ editable: 1
+ display_field: primary_identifier
+ search_fields:
+ - primary_identifier
+ - primary_name
+ - product
+ field_info_list:
+ - name: primary_identifier
+ editable: 1
+ - name: primary_name
+ editable: 1
+ - name: product
+ editable: 1
+ - name: genesynonyms
+ editable: 1
+ is_collection: 1
+ - name: organism
+ editable: 1
+ genesynonym:
+ editable: 1
+ display_field: identifier
+ field_info_list:
+ - name: identifier
+ editable: 1
+ - name: gene
+ editable: 1
+ named_genes:
+ extends: gene
+ constraint: "primary_name is not null"
+
+ all_publications:
+ extends: pub
+ curated_publications:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'NEEDS_APPROVAL' or p.value = 'APPROVAL_IN_PROGRESS' or p.value ='APPROVED')))"
+ high_priority_publications:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'HIGH_PRIORITY')"
+ high_priority_publications_with_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'HIGH_PRIORITY')"
+ high_priority_publications_with_approved_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')) and triage_status_id in (select cvterm_id from cvterm where name = 'HIGH_PRIORITY')"
+ high_priority_publications_with_multiple_sessions:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'HIGH_PRIORITY') and exists (select * from curs c1, curs c2 where c1.pub = me.pub_id and c2.pub = me.pub_id and c1.curs_id <> c2.curs_id)"
+ high_priority_publications_without_sessions:
+ extends: pub
+ constraint: "pub_id not in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'HIGH_PRIORITY')"
+ high_priority_publications_with_new_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'SESSION_CREATED')) and triage_status_id in (select cvterm_id from cvterm where name = 'HIGH_PRIORITY')"
+ high_priority_publications_with_active_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'SESSION_ACCEPTED' or p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED'))) and triage_status_id in (select cvterm_id from cvterm where name = 'HIGH_PRIORITY')"
+ disease_publications:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'DISEASE')"
+ disease_publications_with_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'DISEASE')"
+ disease_publications_with_approved_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')) and triage_status_id in (select cvterm_id from cvterm where name = 'DISEASE')"
+ disease_publications_with_multiple_sessions:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'DISEASE') and exists (select * from curs c1, curs c2 where c1.pub = me.pub_id and c2.pub = me.pub_id and c1.curs_id <> c2.curs_id)"
+ disease_publications_without_sessions:
+ extends: pub
+ constraint: "pub_id not in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'DISEASE')"
+ disease_publications_with_new_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'SESSION_CREATED')) and triage_status_id in (select cvterm_id from cvterm where name = 'DISEASE')"
+ disease_publications_with_active_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'SESSION_ACCEPTED' or p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED'))) and triage_status_id in (select cvterm_id from cvterm where name = 'DISEASE')"
+ pheno_publications:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'PHENO')"
+ pheno_publications_with_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO')"
+ pheno_publications_with_approved_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO')"
+ pheno_publications_with_multiple_sessions:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'PHENO') and exists (select * from curs c1, curs c2 where c1.pub = me.pub_id and c2.pub = me.pub_id and c1.curs_id <> c2.curs_id)"
+ pheno_publications_without_sessions:
+ extends: pub
+ constraint: "pub_id not in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO')"
+ pheno_publications_with_new_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'SESSION_CREATED')) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO')"
+ pheno_publications_with_active_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'SESSION_ACCEPTED' or p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED'))) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO')"
+ pheno_anat_publications:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_ANAT')"
+ pheno_anat_publications_with_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_ANAT')"
+ pheno_anat_publications_with_approved_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_ANAT')"
+ pheno_anat_publications_with_multiple_sessions:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_ANAT') and exists (select * from curs c1, curs c2 where c1.pub = me.pub_id and c2.pub = me.pub_id and c1.curs_id <> c2.curs_id)"
+ pheno_anat_publications_without_sessions:
+ extends: pub
+ constraint: "pub_id not in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_ANAT')"
+ pheno_anat_publications_with_new_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'SESSION_CREATED')) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_ANAT')"
+ pheno_anat_publications_with_active_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'SESSION_ACCEPTED' or p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED'))) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_ANAT')"
+ pheno_chem_publications:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_CHEM')"
+ pheno_chem_publications_with_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_CHEM')"
+ pheno_chem_publications_with_approved_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_CHEM')"
+ pheno_chem_publications_with_multiple_sessions:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_CHEM') and exists (select * from curs c1, curs c2 where c1.pub = me.pub_id and c2.pub = me.pub_id and c1.curs_id <> c2.curs_id)"
+ pheno_chem_publications_without_sessions:
+ extends: pub
+ constraint: "pub_id not in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_CHEM')"
+ pheno_chem_publications_with_new_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'SESSION_CREATED')) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_CHEM')"
+ pheno_chem_publications_with_active_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'SESSION_ACCEPTED' or p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED'))) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_CHEM')"
+ pheno_dataset_publications:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_DATASET')"
+ pheno_dataset_publications_with_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_DATASET')"
+ pheno_dataset_publications_with_approved_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_DATASET')"
+ pheno_dataset_publications_with_multiple_sessions:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_DATASET') and exists (select * from curs c1, curs c2 where c1.pub = me.pub_id and c2.pub = me.pub_id and c1.curs_id <> c2.curs_id)"
+ pheno_dataset_publications_without_sessions:
+ extends: pub
+ constraint: "pub_id not in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_DATASET')"
+ pheno_dataset_publications_with_new_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'SESSION_CREATED')) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_DATASET')"
+ pheno_dataset_publications_with_active_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'SESSION_ACCEPTED' or p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED'))) and triage_status_id in (select cvterm_id from cvterm where name = 'PHENO_DATASET')"
+ low_priority_publications:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'LOW_PRIORITY')"
+ low_priority_publications_with_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'LOW_PRIORITY')"
+ low_priority_publications_with_approved_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')) and triage_status_id in (select cvterm_id from cvterm where name = 'LOW_PRIORITY')"
+ low_priority_publications_with_multiple_sessions:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'LOW_PRIORITY') and exists (select * from curs c1, curs c2 where c1.pub = me.pub_id and c2.pub = me.pub_id and c1.curs_id <> c2.curs_id)"
+ low_priority_publications_without_sessions:
+ extends: pub
+ constraint: "pub_id not in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'LOW_PRIORITY')"
+ low_priority_publications_with_new_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'SESSION_CREATED')) and triage_status_id in (select cvterm_id from cvterm where name = 'LOW_PRIORITY')"
+ low_priority_publications_with_active_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'SESSION_ACCEPTED' or p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED'))) and triage_status_id in (select cvterm_id from cvterm where name = 'LOW_PRIORITY')"
+ training_publications:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'TRAINING')"
+ training_publications_with_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'TRAINING')"
+ training_publications_with_approved_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')) and triage_status_id in (select cvterm_id from cvterm where name = 'TRAINING')"
+ training_publications_with_multiple_sessions:
+ extends: pub
+ constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'TRAINING') and exists (select * from curs c1, curs c2 where c1.pub = me.pub_id and c2.pub = me.pub_id and c1.curs_id <> c2.curs_id)"
+ training_publications_without_sessions:
+ extends: pub
+ constraint: "pub_id not in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'TRAINING')"
+ training_publications_with_new_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'SESSION_CREATED')) and triage_status_id in (select cvterm_id from cvterm where name = 'TRAINING')"
+ training_publications_with_active_sessions:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'SESSION_ACCEPTED' or p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED'))) and triage_status_id in (select cvterm_id from cvterm where name = 'TRAINING')"
+
+ publications_with_session_needing_approval:
+ extends: pub
+ '+field_info_list':
+ - name: last_status_change
+ source:
+ sql: "select value from curs, cursprop p, cvterm t where me.pub_id = curs.pub and curs.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'annotation_status_datestamp'"
+ editable: 0
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'NEEDS_APPROVAL' or p.value = 'APPROVAL_IN_PROGRESS')))"
+ publications_with_approved_session:
+ extends: pub
+ constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED'))"
+ sessions_needing_approval:
+ extends: curs
+ constraint: "me.curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'NEEDS_APPROVAL' or p.value = 'APPROVAL_IN_PROGRESS'))"
+ sessions_without_a_curator:
+ extends: curs
+ constraint: "me.curs_id not in (select curs from curs_curator)"
+ exported_sessions:
+ extends: curs
+ constraint: "me.curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'EXPORTED')"
+ sessions_with_term_requests:
+ extends: curs
+ constraint: "me.curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED' or p.value = 'NEEDS_APPROVAL' or p.value = 'APPROVAL_IN_PROGRESS')) and me.curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'session_term_suggestions_count' and value > 0)"
+ reactivated_sessions:
+ extends: curs
+ constraint: "me.curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'CURATION_IN_PROGRESS')) and me.curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'session_reactivated_timestamp')"
+ approved_sessions:
+ extends: curs
+ constraint: "me.curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')"
+ all_sessions:
+ extends: curs
+
+ chado:
+ chadoprop:
+ class_display_name: chado properties
+ editable: 0
+ display_field: value
+ field_info_list:
+ - name: type
+ source: type_id
+ referenced_class: Cvterm
+ - name: value
+ editable: 0
+ cv:
+ class_display_name: controlled vocabulary
+ editable: 1
+ display_field: name
+ field_info_list:
+ - name: name
+ editable: 1
+ - name: definition
+ editable: 1
+ - name: "terms in this CV"
+ source:
+ sql: 'select count(*) from cvterm where cvterm.cv_id = me.cv_id'
+ - name: "terms used"
+ source:
+ sql: 'select count(*) from cvterm c where c.cv_id = me.cv_id and c.cvterm_id in (select cvterm_id from feature_cvterm)'
+ - name: "annotation count"
+ source:
+ sql: 'select count(*) from feature_cvterm fc, cvterm c where fc.cvterm_id = c.cvterm_id and c.cv_id = me.cv_id'
+ cvterm:
+ class_display_name: controlled vocabulary term
+ editable: 1
+ display_field: name
+ field_info_list:
+ - name: name
+ editable: 1
+ - name: definition
+ editable: 1
+ - name: cv
+ source: cv_id
+ editable: 1
+ - name: dbxref_id
+ editable: 1
+ - name: "features annotated with this term"
+ source:
+ sql: 'select count(*) from feature_cvterm fc where fc.cvterm_id = me.cvterm_id'
+ organism:
+ editable: 1
+ display_field: full_name
+ order_by:
+ - genus
+ - species
+ field_info_list:
+ - name: genus
+ editable: 1
+ - name: species
+ editable: 1
+ pub:
+ object_title_format: 'Details for publication ID: @@$object->uniquename()@@'
+ class_display_name: publication
+ display_field: title
+ editable: 1
+ field_info_list:
+ - name: title
+ editable: 1
+ - name: uniquename
+ editable: 1
+ - name: type
+ source: type_id
+ values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "genedb_literature")'
+ referenced_class: Cvterm
+ editable: 1
+ feature:
+ editable: 1
+ display_field: uniquename
+ search_fields:
+ - uniquename
+ - name
+ field_info_list:
+ - name: uniquename
+ editable: 1
+ - name: name
+ editable: 1
+ - name: type
+ source: type_id
+ values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "sequence")'
+ referenced_class: Cvterm
+ editable: 1
+ - name: featureprops
+ is_collection: 1
+ editable: 1
+ featureprop:
+ editable: 1
+ display_field: value
+ field_info_list:
+ - name: type
+ source: type_id
+ referenced_class: Cvterm
+ - name: value
+ editable: 1
+ db:
+ editable: 1
+ display_field: name
+ field_info_list:
+ - name: name
+ editable: 1
+ - name: description
+ editable: 1
+ - name: url
+ editable: 1
+ - name: "accessions stored"
+ source:
+ sql: 'select count(*) from dbxref where dbxref.db_id = me.db_id'
+ dbxref:
+ editable: 1
+ display_field: accession
+ field_info_list:
+ - name: db_id
+ editable: 1
+ - name: accession
+ editable: 1
+ - name: description
+ editable: 1
+ genes:
+ extends: feature
+ constraint: "type_id = (select cvterm_id from cvterm, cv where cvterm.name = 'gene' and cvterm.cv_id = cv.cv_id and cv.name = 'sequence')"
+ pombe_genes:
+ class_display_name: S. pombe genes
+ extends: feature
+ constraint: "type_id = (select cvterm_id from cvterm, cv where cvterm.name = 'gene' and cvterm.cv_id = cv.cv_id and cv.name = 'sequence') and organism_id = (select organism_id from organism where genus = 'Schizosaccharomyces' and species = 'pombe')"
+ protein_and_domain_terms:
+ class_display_name: PomBase family or domain terms
+ extends: cvterm
+ constraint: "cv_id = (select cv_id from cv where cv.name = 'PomBase family or domain')"
+ types_and_counts:
+ class_display_name: SO DNA feature types and counts
+ constraint: "(select count(*) from feature where type_id = me.cvterm_id) > 0"
+ display_field: name
+ extends: cvterm
+ field_info_list:
+ - name: name
+ editable: 1
+ - name: cv
+ source: cv_id
+ editable: 1
+ - name: "features of this type"
+ as: count
+ source:
+ sql: 'select count(*) from feature where type_id = me.cvterm_id'
+
+reports:
+ track:
+ - report: all_publications
+ children:
+ - report: high_priority_publications
+ children:
+ - report: high_priority_publications_with_sessions
+ children:
+ - report: high_priority_publications_with_new_sessions
+ - report: high_priority_publications_with_active_sessions
+ - report: high_priority_publications_with_approved_sessions
+ - report: high_priority_publications_with_multiple_sessions
+ - report: high_priority_publications_without_sessions
+ - report: disease_publications
+ children:
+ - report: disease_publications_with_sessions
+ children:
+ - report: disease_publications_with_new_sessions
+ - report: disease_publications_with_active_sessions
+ - report: disease_publications_with_approved_sessions
+ - report: disease_publications_with_multiple_sessions
+ - report: disease_publications_without_sessions
+ - report: pheno_publications
+ children:
+ - report: pheno_publications_with_sessions
+ children:
+ - report: pheno_publications_with_new_sessions
+ - report: pheno_publications_with_active_sessions
+ - report: pheno_publications_with_approved_sessions
+ - report: pheno_publications_with_multiple_sessions
+ - report: pheno_publications_without_sessions
+ - report: pheno_anat_publications
+ children:
+ - report: pheno_anat_publications_with_sessions
+ children:
+ - report: pheno_anat_publications_with_new_sessions
+ - report: pheno_anat_publications_with_active_sessions
+ - report: pheno_anat_publications_with_approved_sessions
+ - report: pheno_anat_publications_with_multiple_sessions
+ - report: pheno_anat_publications_without_sessions
+ - report: pheno_chem_publications
+ children:
+ - report: pheno_chem_publications_with_sessions
+ children:
+ - report: pheno_chem_publications_with_new_sessions
+ - report: pheno_chem_publications_with_active_sessions
+ - report: pheno_chem_publications_with_approved_sessions
+ - report: pheno_chem_publications_with_multiple_sessions
+ - report: pheno_chem_publications_without_sessions
+ - report: pheno_dataset_publications
+ children:
+ - report: pheno_dataset_publications_with_sessions
+ children:
+ - report: pheno_dataset_publications_with_new_sessions
+ - report: pheno_dataset_publications_with_active_sessions
+ - report: pheno_dataset_publications_with_approved_sessions
+ - report: pheno_dataset_publications_with_multiple_sessions
+ - report: pheno_dataset_publications_without_sessions
+ - report: low_priority_publications
+ children:
+ - report: low_priority_publications_with_sessions
+ children:
+ - report: low_priority_publications_with_new_sessions
+ - report: low_priority_publications_with_active_sessions
+ - report: low_priority_publications_with_approved_sessions
+ - report: low_priority_publications_with_multiple_sessions
+ - report: low_priority_publications_without_sessions
+ - report: training_publications
+ children:
+ - report: training_publications_with_sessions
+ children:
+ - report: training_publications_with_new_sessions
+ - report: training_publications_with_active_sessions
+ - report: training_publications_with_approved_sessions
+ - report: training_publications_with_multiple_sessions
+ - report: training_publications_without_sessions
+ - report: all_sessions
+ children:
+ - report: approved_sessions
+ - report: exported_sessions
+ - report: sessions_needing_approval
+ - report: reactivated_sessions
+ - report: sessions_without_a_curator
+
+
+curs_config:
+ # Possible reasons for a paper to have no phenotype annotation in the case
+ # where genes are mentioned.
+ no_annotation_reasons:
+ - No phenotypic data
+ - Only pheno_chem data
+ - Other
--
GitLab