Merge branch 'master' into DB-959

Dockerfile

@@ -3,7 +3,7 @@
 #
 
 FROM ubuntu:18.04
-RUN apt-get update && apt-get install -y gnupg curl ca-certificates 
+RUN apt-get update && apt-get install -y gnupg curl ca-certificates
 RUN curl https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -
 # Add the PostgreSQL PGP key to verify their Debian packages.
 # It should be the same key as https://www.postgresql.org/media/keys/ACCC4CF8.asc
@@ -16,7 +16,7 @@ ARG SOURCE_BRANCH=master
 
 # Add PostgreSQL's repository. Idocker-boomt contains the most recent stable release
 #     of PostgreSQL, ``9.3``.
-RUN echo "deb http://apt.postgresql.org/pub/repos/apt/ bionic-pgdg main" > /etc/apt/sources.list.d/pgdg.list
+RUN echo "deb http://apt-archive.postgresql.org/pub/repos/apt/ bionic-pgdg main" > /etc/apt/sources.list.d/pgdg.list
 
 # Install ``python-software-properties``, ``software-properties-common`` and PostgreSQL 9.3
 #  There are some warnings (in red) that show up during the build. You can hide

Load/gene_alleles.py

@@ -732,6 +732,19 @@ def create_allele_GA90(cursor, org_dict, feature_id, cvterm_id, db_id, pub_id):
             cursor.execute(fpp_sql, (fp_id, pub_id))
 
 
+def create_bracket_gene(cursor, org_dict, feature_id, cvterm_id, db_id, pub_id):
+    """
+    Create genes/allels with '(' and [}' in them.
+    This will be used for testing formats allowed etc.
+    """
+    create_gene_alleles(cursor, org_dict, feature_id, cvterm_id, db_id, pub_id,
+                        num_genes=6,
+                        num_alleles=1,
+                        gene_prefix='a(1)48',
+                        tool_prefix=''
+                        )
+
+
 def create_G1f_gene(cursor, org_dict, feature_id, cvterm_id, db_id, pub_id, dbxref_id):
     """Create gene data for G1f to test merging.
 
@@ -997,3 +1010,5 @@ def add_genes_and_alleles(cursor, organism_id, feature_id, cvterm_id, dbxref_id,
     create_G1f_gene(cursor, organism_id, feature_id, cvterm_id, db_id, feature_id['Nature_3'], dbxref_id)
 
     create_allele_PDEV_184(cursor, organism_id, feature_id, cvterm_id, db_id, pub_id)
+
+    create_bracket_gene(cursor, organism_id, feature_id, cvterm_id, db_id, pub_id)

data/cv_cvterm.yaml

@@ -10,11 +10,13 @@ SO: ['chromosome_arm', 'chromosome', 'gene', 'mRNA', 'DNA', 'golden_path', 'ncRN
      'natural_transposable_element', 'gene_group', 'polypeptide', 'chromosome_breakpoint', 'engineered_plasmid', 'sgRNA',
      'oligo', 'engineered_foreign_gene', 'point_mutation', 'cDNA_clone', 'TSS', 'rescue_region', 'insertion_site', 'synthetic_sequence', 'RNA']
 molecular_function: ['mRNA binding']
-cellular_component: ['nucleolus', 'something' ,'extracellular space', 'endoplasmic reticulum']
+cellular_component: ['nucleolus', 'something' ,'extracellular space', 'endoplasmic reticulum',
+                     'mitochondrial crista', 'mitochondrion']
 biological_process: ['activation of immune response', 'defense response to other organism', 'rRNA processing']
 FlyBase anatomy CV: ['embryo','dopaminergic PAM neuron 1', 'dopaminergic PAM neuron 5', 'dissociated larval fat cell',
                      'embryonic/larval hemolymph',
-                     'anatomy 1', 'anatomy 2', 'anatomy 3', 'mesoderm']
+                     'anatomy 1', 'anatomy 2', 'anatomy 3', 'mesoderm',
+                     'indirect flight muscle', 'macrochaeta', 'scutellar bristle']
 ####### End of order matters cv/cvterms
 
 cell_line_cvtermprop type: ['basis']
@@ -35,7 +37,8 @@ feature_cvtermprop type: [
     'common_tool_uses', 'webcv', 'date']
 feature_expression property type: ['curated_as', 'comment']
 feature_pubprop type: ['abstract_languages']
-feature_relationshipprop type: ['fly_disease-implication_change', 'comment', 'relative_position', 'score', 'start_location', 'end_location']
+feature_relationshipprop type: ['fly_disease-implication_change', 'comment', 'relative_position', 'score',
+                                'start_location', 'end_location', 'is_subset_expression', 'is_relative_wildtype']
 
 FlyBase: ['FlyBase analysis']
 FlyBase_internal: ['pubprop type:curated_by']

schema.sql

@@ -3,7 +3,7 @@
 --
 
 -- Dumped from database version 13.3
--- Dumped by pg_dump version 13.3
+-- Dumped by pg_dump version 14.7 (Homebrew)
 
 SET statement_timeout = 0;
 SET lock_timeout = 0;
@@ -12730,7 +12730,8 @@ CREATE TABLE public.analysis (
     sourcename character varying(255),
     sourceversion character varying(255),
     sourceuri text,
-    timeexecuted timestamp without time zone DEFAULT ('now'::text)::timestamp(6) with time zone NOT NULL
+    timeexecuted timestamp without time zone DEFAULT ('now'::text)::timestamp(6) with time zone NOT NULL,
+    is_obsolete boolean DEFAULT false NOT NULL
 );
 
 
@@ -19049,6 +19050,44 @@ CREATE TABLE public.pub (
 
 ALTER TABLE public.pub OWNER TO go;
 
+--
+-- Name: pub_analysis_feature; Type: TABLE; Schema: public; Owner: postgres
+--
+
+CREATE TABLE public.pub_analysis_feature (
+    pub_analysis_feature_id integer NOT NULL,
+    pub_id integer NOT NULL,
+    analysis_id integer NOT NULL,
+    feature_id integer NOT NULL,
+    score double precision,
+    status character varying(30)
+);
+
+
+ALTER TABLE public.pub_analysis_feature OWNER TO go;
+
+--
+-- Name: pub_analysis_feature_pub_analysis_feature_id_seq; Type: SEQUENCE; Schema: public; Owner: postgres
+--
+
+CREATE SEQUENCE public.pub_analysis_feature_pub_analysis_feature_id_seq
+    AS integer
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
+
+
+ALTER TABLE public.pub_analysis_feature_pub_analysis_feature_id_seq OWNER TO go;
+
+--
+-- Name: pub_analysis_feature_pub_analysis_feature_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: postgres
+--
+
+ALTER SEQUENCE public.pub_analysis_feature_pub_analysis_feature_id_seq OWNED BY public.pub_analysis_feature.pub_analysis_feature_id;
+
+
 --
 -- Name: pub_dbxref; Type: TABLE; Schema: public; Owner: postgres
 --
@@ -21066,6 +21105,13 @@ ALTER TABLE ONLY public.project ALTER COLUMN project_id SET DEFAULT nextval('pub
 ALTER TABLE ONLY public.pub ALTER COLUMN pub_id SET DEFAULT nextval('public.pub_pub_id_seq'::regclass);
 
 
+--
+-- Name: pub_analysis_feature pub_analysis_feature_id; Type: DEFAULT; Schema: public; Owner: postgres
+--
+
+ALTER TABLE ONLY public.pub_analysis_feature ALTER COLUMN pub_analysis_feature_id SET DEFAULT nextval('public.pub_analysis_feature_pub_analysis_feature_id_seq'::regclass);
+
+
 --
 -- Name: pub_dbxref pub_dbxref_id; Type: DEFAULT; Schema: public; Owner: postgres
 --
@@ -23733,6 +23779,22 @@ ALTER TABLE ONLY public.project
     ADD CONSTRAINT project_pkey PRIMARY KEY (project_id);
 
 
+--
+-- Name: pub_analysis_feature pub_analysis_feature_pkey; Type: CONSTRAINT; Schema: public; Owner: postgres
+--
+
+ALTER TABLE ONLY public.pub_analysis_feature
+    ADD CONSTRAINT pub_analysis_feature_pkey PRIMARY KEY (pub_analysis_feature_id);
+
+
+--
+-- Name: pub_analysis_feature pub_analysis_feature_pub_id_analysis_id_feature_id_key; Type: CONSTRAINT; Schema: public; Owner: postgres
+--
+
+ALTER TABLE ONLY public.pub_analysis_feature
+    ADD CONSTRAINT pub_analysis_feature_pub_id_analysis_id_feature_id_key UNIQUE (pub_id, analysis_id, feature_id);
+
+
 --
 -- Name: pub_dbxref pub_dbxref_pkey; Type: CONSTRAINT; Schema: public; Owner: postgres
 --
@@ -30497,6 +30559,30 @@ ALTER TABLE ONLY public.organismprop
     ADD CONSTRAINT organismprop_type_id_fkey FOREIGN KEY (type_id) REFERENCES public.cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED;
 
 
+--
+-- Name: pub_analysis_feature paf_fk_analysis; Type: FK CONSTRAINT; Schema: public; Owner: postgres
+--
+
+ALTER TABLE ONLY public.pub_analysis_feature
+    ADD CONSTRAINT paf_fk_analysis FOREIGN KEY (analysis_id) REFERENCES public.analysis(analysis_id);
+
+
+--
+-- Name: pub_analysis_feature paf_fk_feature; Type: FK CONSTRAINT; Schema: public; Owner: postgres
+--
+
+ALTER TABLE ONLY public.pub_analysis_feature
+    ADD CONSTRAINT paf_fk_feature FOREIGN KEY (feature_id) REFERENCES public.feature(feature_id);
+
+
+--
+-- Name: pub_analysis_feature paf_fk_pub; Type: FK CONSTRAINT; Schema: public; Owner: postgres
+--
+
+ALTER TABLE ONLY public.pub_analysis_feature
+    ADD CONSTRAINT paf_fk_pub FOREIGN KEY (pub_id) REFERENCES public.pub(pub_id);
+
+
 --
 -- Name: phendesc phendesc_environment_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: postgres
 --