From aaefa640b076dcd30652edf1285e3eeac559234b Mon Sep 17 00:00:00 2001
From: James Nairn <jwrn3@cam.ac.uk>
Date: Wed, 18 Nov 2020 12:42:23 +0000
Subject: [PATCH] Imported changes from vitor_testing1
Too difficult to merge the branch so I've pulled in various files by hand.
---
FBbt-GO_routine/FBbt-GO_routine.sh | 4 +-
canto_deploy.yaml | 820 +++++++++++++++++-
.../list-to-extension_config.R | 26 +-
starting-pack.sh | 38 +-
4 files changed, 854 insertions(+), 34 deletions(-)
mode change 100755 => 100644 FBbt-GO_routine/FBbt-GO_routine.sh
mode change 100755 => 100644 starting-pack.sh
diff --git a/FBbt-GO_routine/FBbt-GO_routine.sh b/FBbt-GO_routine/FBbt-GO_routine.sh
old mode 100755
new mode 100644
index bb5cb55..6d5438e
--- a/FBbt-GO_routine/FBbt-GO_routine.sh
+++ b/FBbt-GO_routine/FBbt-GO_routine.sh
@@ -4,8 +4,8 @@
#You must have ROBOT installed - see http://robot.obolibrary.org/
## Copy the two ontologies to merge from ./import_export/ to ./FBbt-GO_routine/
-cp ./import_export/go-basic.obo ./FBbt-GO_routine/
-cp ./import_export/fly_anatomy.obo ./FBbt-GO_routine/
+cp ./import_export/go-basic.obo ./FBbt-GO_routine
+cp ./import_export/fly_anatomy.obo ./FBbt-GO_routine
cd ./FBbt-GO_routine
## Extract everything that is a subclass of 'GO: cellular component'
diff --git a/canto_deploy.yaml b/canto_deploy.yaml
index 41e2291..c604bf6 100644
--- a/canto_deploy.yaml
+++ b/canto_deploy.yaml
@@ -9,6 +9,11 @@ instance_organism:
flybase_mode: 1
+annotation_figure_field: 0
+
+# disable deletion buttons on allele creation table on genotype management page
+show_quick_deletion_buttons: 0
+
Model::TrackModel:
connect_info:
# filepath plus track.sqlite3
@@ -41,7 +46,8 @@ implementation_classes:
alleles_have_expression: 0
strains_mode: 0
split_genotypes_by_organism: 0
-show_genotype_management_genes_list: 0
+##this enables/disables the allele creation table on the genotype management page (0 - disabled; 1 - enabled)
+show_genotype_management_genes_list: 1
diploid_mode: 1
## allow internal notes on single alleles and config:
@@ -68,8 +74,8 @@ allele_type_list:
show_description: true
description_required: false
allele_name_required: false
- allow_expression_change: true
- expression_required: true
+ allow_expression_change: false
+ expression_required: false
hide_type_name: true
placeholder: Please provide a description
- name: accessory
@@ -77,8 +83,8 @@ allele_type_list:
show_description: true
description_required: false
allele_name_required: false
- allow_expression_change: true
- expression_required: true
+ allow_expression_change: false
+ expression_required: false
do_not_annotate: 1
placeholder: Please provide a description
- name: aberration
@@ -88,6 +94,7 @@ allele_type_list:
allele_name_required: false
allow_expression_change: false
expression_required: false
+ do_not_annotate: 1
# the name of the organisation running this Canto - shown in various places in the user interface
@@ -109,6 +116,8 @@ available_annotation_type_list:
- exact
feature_type: 'genotype'
can_have_conditions: 0
+ #allow_annotation_transfer - use true/false
+ allow_annotation_transfer: true
broad_term_suggestions: >
lethal, sterile, visible, cell number defective, locomotor behavior defective
specific_term_examples: >
@@ -123,7 +132,7 @@ 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 +141,8 @@ available_annotation_type_list:
- exact
feature_type: 'genotype'
can_have_conditions: 0
+ #allow_annotation_transfer - use true/false
+ allow_annotation_transfer: true
broad_term_suggestions: >
embryo, wing, eye, ovary, wing disc, neuromuscular junction
specific_term_examples: >
@@ -149,6 +160,8 @@ available_annotation_type_list:
namespace: phenotypic_class
term_suggestions_annotation_type: phenotypic_class
interaction_term_required: 1
+ #allow_annotation_transfer - use true/false
+ allow_annotation_transfer: true
hide_extension_relations: [qual,dv_qual]
display_name: 'phenotype class interaction'
very_short_display_name: 'phen-class interaction'
@@ -165,9 +178,11 @@ 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 - use true/false
+ allow_annotation_transfer: true
hide_extension_relations: [qual,dv_qual]
display_name: 'phenotype anatomy interaction'
very_short_display_name: 'anatomy interaction'
@@ -184,8 +199,13 @@ available_annotation_type_list:
detailed_help_path: /docs/genetic_interaction_annotation
- name: complementation
can_have_conditions: 0
- single_allele_only: 1
- interaction_same_locus: 1
+ #single_allele_only - use true/false
+ single_allele_only: true
+ #interaction_same_locus - use true/false
+ 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'
@@ -196,8 +216,11 @@ available_annotation_type_list:
- Fails to complement
- name: rescue
can_have_conditions: 0
- single_locus_only: 1
- interaction_same_locus: 1
+ allow_annotation_transfer: 1
+ #single_locus_only: true
+ single_locus_only: true
+ #interaction_same_locus - use true/false
+ interaction_same_locus: true
category: interaction
display_name: 'rescue'
feature_type: 'metagenotype'
@@ -342,3 +365,778 @@ 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
diff --git a/extension_config-Rscript/list-to-extension_config.R b/extension_config-Rscript/list-to-extension_config.R
index b8e7800..a4beb28 100644
--- a/extension_config-Rscript/list-to-extension_config.R
+++ b/extension_config-Rscript/list-to-extension_config.R
@@ -7,6 +7,7 @@
# GO CC - GO:0005575.
# extension_config.tsv only uses IDs and, therefore, qualifier namespaces must be converted into their topterm IDs, whcih requires screening the FBcv obo file.
+rm(list=ls())
#set work directory as canto-space
setwd("./")
getwd()
@@ -101,25 +102,31 @@ colnames(Df1)<-c("domain ID", "subset relation", "extension relation", "range ID
#read file with list of allowed qualifiers (on "allowed_qualifiers.tsv")
quallist<-read.table("./extension_config-Rscript/allowed_qualifiers.tsv", sep="\t", header=TRUE, stringsAsFactors=FALSE)
-count<-1
#for each type of allowed qualifier, replace the namespace with corresponding top term with that namespace
+count<-1
+phenpos<-c()
for(m in 1:nrow(quallist)){
phen<-unlist(strsplit(quallist[m,3],","))
+ phenqual1<-c()
for(l in 1:length(phen)){
- phen[l]<-Df[which(Df[,3]==phen[l]&Df[,5]==phen[l]&is.na(Df[,6])==TRUE),1]
+ phenpos<-which(Df[,3]==phen[l]&Df[,5]==phen[l]&is.na(Df[,6])==TRUE)
+ phenqual<-c()
+ for(l1 in 1:length(phenpos)){
+ phenqual[l1]<-Df[phenpos[l1],1]
+ }
+ phenqual1[l]<-paste(phenqual,collapse = "|")
}
-
if(quallist[m,2]=='phenotype'){
#if the annotations are for 'phenotypic class' (FBcv:0000347) then:
# a) the single term 'progressive' shoud be allowed
if(quallist[m,1]==Df[which(Df[,2]=="phenotypic class"),1]){
Df1[count,1]<-quallist[m,1]
- phen<-append(phen, Df[which(Df[,2]=="progressive"), 1])
- Df1[count,4]<-paste(phen,collapse = '|')
+ phenqual1<-append(phenqual1, Df[which(Df[,2]=="progressive"), 1])
+ Df1[count,4]<-paste(phenqual1,collapse = '|')
count<-count+1
# b) and 'the 'fertility/sterility terms must not allow developmental stage terms
##once the ontology file is updated so that all viability/mortality/life-span terms are under a common parent term, this next bit should be updated
- viable<-c("viable","increased mortality","long lived")
+ viable<-c("viable","increased mortality during development","short lived","long lived")
for (n in 1:length(viable)){
viable[n]<-Df[which(Df[,2]==viable[n]),1]
}
@@ -138,7 +145,7 @@ for(m in 1:nrow(quallist)){
}
else{
Df1[count,1]<-quallist[m,1]
- Df1[count,4]<-paste(phen, collapse = '|')
+ Df1[count,4]<-paste(phenqual1, collapse = '|')
count<-count+1
Df1[count,1]<-quallist[m,1]
Df1[count,4]<-"FBdv:00007008"
@@ -150,7 +157,7 @@ for(m in 1:nrow(quallist)){
}
if(quallist[m,2]=='genetic interaction'){
Df1[count,1]<-quallist[m,1]
- Df1[count,4]<-paste(phen, collapse = '|')
+ Df1[count,4]<-paste(phenqual1, collapse = '|')
Df1[count,3]<-"int_qual"
Df1[count,5]<-"Interaction qualifier - ONLY USE FOR INTERACTIONS"
count<-count+1
@@ -173,4 +180,5 @@ if (is.na(Df1[j,8])==TRUE){Df1[j,8]<-as.character("user")}
else{}
}
-write.table(Df1, file = "./canto/extension_config.tsv", sep='\t', quote= FALSE, row.names = FALSE)
\ No newline at end of file
+write.table(Df1, file = "./canto/extension_config.tsv", sep='\t', quote= FALSE, row.names = FALSE)
+#for each type of allowed qualifier, replace the namespace with corresponding top term with that namespace
diff --git a/starting-pack.sh b/starting-pack.sh
old mode 100755
new mode 100644
index 85c9eda..6d7e076
--- a/starting-pack.sh
+++ b/starting-pack.sh
@@ -1,4 +1,5 @@
-#!/bin/sh
+#!/bin/bash
+#This must be run in sudo mode, by typing 'sudo -i' and then typing your sudo password
#before start, add the content of the folder 'starting-pack' to ./canto-space/
#run this @ /canto-space/
@@ -17,7 +18,7 @@ cp canto-docker-initd /sbin/
chmod a+x /sbin/canto-docker-initd
cp canto-docker-initd ./canto/etc/
chmod a+x ./canto/etc/canto-docker-initd
-#rm canto-docker-initd
+rm canto-docker-initd
##create a 'canto' file @ /etc/init.d
##and make it executable
@@ -27,27 +28,40 @@ chmod a+x /etc/init.d/canto
#enable memcached - for caching of the servers
##comment for vitor: not sure it needs more stuff - ask Kim??
-sudo apt-get install memcached
-
-
-#start canto
-/etc/init.d/canto start
+apt-get install memcached
#this loop creates cv terms for all the range of values for the 'priority curation score' within the internal canto database: 0-36
for i in {0..36}; do
- ./canto/script/canto_docker ./script/canto_add.pl --cvterm "Canto curation priorities" "${i}" "FB:cantoscore${i}"
+score="./canto/script/canto_docker ./script/canto_add.pl --cvterm \"Canto curation priorities\" "$i" FB:cantoscore"$i;
+$score
done
+this section will create CV terms for triage statuses, so that the publication list can be sub-divifed into more specific lists. This list is the current in use for phenotype curation (e.g. disease, pheno, training, etc).
+./canto/script/canto_docker ./script/canto_add.pl --cvterm "Canto publication triage status" "DISEASE"
+./canto/script/canto_docker ./script/canto_add.pl --cvterm "Canto publication triage status" "PHENO"
+./canto/script/canto_docker ./script/canto_add.pl --cvterm "Canto publication triage status" "PHENO_ANAT"
+./canto/script/canto_docker ./script/canto_add.pl --cvterm "Canto publication triage status" "PHENO_CHEM"
+./canto/script/canto_docker ./script/canto_add.pl --cvterm "Canto publication triage status" "PHENO_DATASET"
+./canto/script/canto_docker ./script/canto_add.pl --cvterm "Canto publication triage status" "LOW_PRIORITY"
+./canto/script/canto_docker ./script/canto_add.pl --cvterm "Canto publication triage status" "TRAINING"
+./canto/script/canto_docker ./script/canto_add.pl --cvterm "Canto publication triage status" "HIGH_PRIORITY"
+
+
#configure the taxon (Drosophila melanogaster)
-./canto/script/canto_docker ./script/canto_add.pl --organism "Drosophila melanogaster" 7227 "[fruit fly]"
+./canto/script/canto_docker ./script/canto_add.pl --organism "Drosophila melanogaster" 7227 [fruit fly]
-# Create a user
-./canto/script/canto_docker ./script/canto_add.pl --person "Firstname Lastname" spqr1@cam.ac.uk <password> 0000-0002-8728-0281 admin
+
+#add the 'mock' user "FlyBase Curator" (email address ignore@flybase.org), which will be used for publication data import
+./canto/script/canto_docker ./script/canto_add.pl --person "FlyBase Curator" ignore@flybase.org pass admin
+
+
+#start canto
+/etc/init.d/canto start
#run the weekly routine script which executes all configuration steps
-# sh weekly_routine.sh
+bash weekly_routine.sh
--
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