Merge pull request #1261 from research-software-directory/database-pe…

…rformance

Database performance

data-generation/main.js

@@ -26,7 +26,7 @@ function generateUniqueCaseInsensitiveString(randomStringGenerator) {
 	throw 'Tried to generate a unique (ignoring case) string for 10000 times but failed to do so';
 }
 
-function generateMentions(amountExtra = 100) {
+function generateMentions(amountExtra = 1000) {
 	const mentionTypes = [
 		'blogPost',
 		'book',
@@ -91,7 +91,7 @@ function generateMentions(amountExtra = 100) {
 	return result;
 }
 
-function generateSoftware(amount = 500) {
+function generateSoftware(amount = 1000) {
 	// real software has a real concept DOI
 	const amountRealSoftware = Math.min(conceptDois.length, amount);
 	const brandNames = [];
@@ -399,7 +399,7 @@ function generateSoftwareHighlights(ids) {
 	return result;
 }
 
-function generateProjects(amount = 500) {
+function generateProjects(amount = 1000) {
 	const result = [];
 
 	const projectStatuses = ['finished', 'running', 'starting'];

database/009-create-keyword-and-category.sql

@@ -42,12 +42,16 @@ CREATE TABLE keyword_for_software (
 	PRIMARY KEY (software, keyword)
 );
 
+CREATE INDEX keyword_for_software_keyword_idx ON keyword_for_software(keyword);
+
 CREATE TABLE keyword_for_project (
 	project UUID references project (id),
 	keyword UUID references keyword (id),
 	PRIMARY KEY (project, keyword)
 );
 
+CREATE INDEX keyword_for_project_keyword_idx ON keyword_for_project(keyword);
+
 -- ADD basic keywords from topics and tags
 INSERT into keyword (value)
 VALUES
@@ -72,6 +76,8 @@ CREATE TABLE keyword_for_community (
 	PRIMARY KEY (community, keyword)
 );
 
+CREATE INDEX keyword_for_community_keyword_idx ON keyword_for_community(keyword);
+
 
 ----------------
 -- Categories --
@@ -92,8 +98,8 @@ CREATE TABLE category (
 	CONSTRAINT highlight_must_be_top_level_category CHECK (NOT ((properties->>'is_highlight')::boolean AND parent IS NOT NULL))
 );
 
-CREATE INDEX category_parent_idx ON category (parent);
-CREATE INDEX category_community_idx ON category (community);
+CREATE INDEX category_parent_idx ON category(parent);
+CREATE INDEX category_community_idx ON category(community);
 
 
 CREATE TABLE category_for_software (
@@ -102,6 +108,8 @@ CREATE TABLE category_for_software (
 	PRIMARY KEY (software_id, category_id)
 );
 
+CREATE INDEX category_for_software_category_id_idx ON category_for_software(category_id);
+
 
 -- sanitize categories
 

database/010-create-research-domain.sql

@@ -64,6 +64,8 @@ CREATE TABLE research_domain_for_project (
 	PRIMARY KEY (project, research_domain)
 );
 
+CREATE INDEX research_domain_for_project_research_domain_idx ON research_domain_for_project(research_domain);
+
 
 -- insert RSE list of research domains
 

database/011-create-mention-table.sql

@@ -83,20 +83,26 @@ CREATE TABLE mention_for_software (
 	PRIMARY KEY (mention, software)
 );
 
+CREATE INDEX mention_for_software_software_idx ON mention_for_software(software);
+
 
 CREATE TABLE reference_paper_for_software (
 	mention UUID REFERENCES mention (id),
 	software UUID REFERENCES software (id),
 	PRIMARY KEY (mention, software)
 );
 
+CREATE INDEX reference_paper_for_software_software_idx ON reference_paper_for_software(software);
+
 
 CREATE TABLE citation_for_mention (
 	mention UUID REFERENCES mention (id),
 	citation UUID REFERENCES mention (id),
 	PRIMARY KEY (mention, citation)
 );
 
+CREATE INDEX citation_for_mention_citation_idx ON citation_for_mention(citation);
+
 
 CREATE FUNCTION search_mentions_for_software(software_id UUID, search_text VARCHAR) RETURNS SETOF mention STABLE LANGUAGE plpgsql AS
 $$
@@ -120,6 +126,7 @@ CREATE TABLE output_for_project (
 	PRIMARY KEY (mention, project)
 );
 
+CREATE INDEX output_for_project_project_idx ON output_for_project(project);
 
 
 CREATE TABLE impact_for_project (
@@ -128,6 +135,8 @@ CREATE TABLE impact_for_project (
 	PRIMARY KEY (mention, project)
 );
 
+CREATE INDEX impact_for_project_project_idx ON impact_for_project(project);
+
 
 CREATE FUNCTION search_impact_for_project(project_id UUID, search_text VARCHAR) RETURNS SETOF mention STABLE LANGUAGE plpgsql AS
 $$

database/012-create-release-table.sql

@@ -17,6 +17,8 @@ CREATE TABLE release_version (
 	PRIMARY KEY (release_id, mention_id)
 );
 
+CREATE INDEX release_version_mention_id_idx ON release_version(mention_id);
+
 
 CREATE FUNCTION z_delete_old_releases() RETURNS TRIGGER LANGUAGE plpgsql SECURITY DEFINER AS
 $$

database/014-create-organisation-table.sql

@@ -29,8 +29,9 @@ CREATE TABLE organisation (
 	UNIQUE (slug, parent)
 );
 
-CREATE UNIQUE INDEX unique_slug_for_top_level_org_idx ON organisation (slug, (parent IS NULL)) WHERE parent IS NULL;
-CREATE UNIQUE INDEX unique_name_and_parent_idx ON organisation (name, parent);
+CREATE INDEX organisation_parent_idx ON organisation(parent);
+CREATE UNIQUE INDEX unique_slug_for_top_level_org_idx ON organisation(slug, (parent IS NULL)) WHERE parent IS NULL;
+CREATE UNIQUE INDEX unique_name_and_parent_idx ON organisation(name, parent);
 
 CREATE FUNCTION check_cycle_organisations() RETURNS TRIGGER STABLE LANGUAGE plpgsql SECURITY DEFINER AS
 $$

database/015-inter-relation-tables.sql

@@ -106,6 +106,8 @@ CREATE TABLE software_for_organisation (
 	PRIMARY KEY (software, organisation)
 );
 
+CREATE INDEX software_for_organisation_organisation_idx ON software_for_organisation(organisation);
+
 CREATE FUNCTION sanitise_update_software_for_organisation() RETURNS TRIGGER LANGUAGE plpgsql AS
 $$
 BEGIN
@@ -143,6 +145,8 @@ CREATE TABLE project_for_organisation (
 	PRIMARY KEY (project, organisation, role)
 );
 
+CREATE INDEX project_for_organisation_organisation_idx ON project_for_organisation(organisation);
+
 CREATE FUNCTION sanitise_update_project_for_organisation() RETURNS TRIGGER LANGUAGE plpgsql AS
 $$
 BEGIN

database/100-create-api-views.sql

@@ -264,7 +264,7 @@ CREATE FUNCTION releases_by_organisation() RETURNS TABLE (
 	release_authors VARCHAR
 ) LANGUAGE sql STABLE AS
 $$
-SELECT DISTINCT
+SELECT DISTINCT ON (organisation_id, software_id, mention.id)
 	organisation.id AS organisation_id,
 	software.id AS software_id,
 	software.slug AS software_slug,

database/104-software-views.sql

@@ -83,18 +83,7 @@ WHERE
 	)
 GROUP BY
 	reference_paper_for_software.software,
-	mention.id,
-	mention.doi,
-	mention.url,
-	mention.title,
-	mention.authors,
-	mention.publisher,
-	mention.publication_year,
-	mention.journal,
-	mention.page,
-	mention.image_url,
-	mention.mention_type,
-	mention.source
+	mention.id
 ;
 $$;
 
@@ -116,46 +105,48 @@ CREATE FUNCTION mentions_by_software() RETURNS TABLE (
 	source VARCHAR
 ) LANGUAGE sql STABLE AS
 $$
--- mentions for software
-SELECT
-	mention_for_software.software,
-	mention.id,
-	mention.doi,
-	mention.url,
-	mention.title,
-	mention.authors,
-	mention.publisher,
-	mention.publication_year,
-	mention.journal,
-	mention.page,
-	mention.image_url,
-	mention.mention_type,
-	mention.source
-FROM
-	mention
-INNER JOIN
-	mention_for_software ON mention_for_software.mention = mention.id
--- will deduplicate identical entries
--- from scraped citations
-UNION
--- scraped citations from reference papers
-SELECT
-	software,
-	id,
-	doi,
-	url,
-	title,
-	authors,
-	publisher,
-	publication_year,
-	journal,
-	page,
-	image_url,
-	mention_type,
-	source
-FROM
-	citation_by_software()
-;
+WITH mentions_and_citations AS (
+	-- mentions for software
+	SELECT
+		mention_for_software.software,
+		mention.id,
+		mention.doi,
+		mention.url,
+		mention.title,
+		mention.authors,
+		mention.publisher,
+		mention.publication_year,
+		mention.journal,
+		mention.page,
+		mention.image_url,
+		mention.mention_type,
+		mention.source
+	FROM
+		mention
+	INNER JOIN
+		mention_for_software ON mention_for_software.mention = mention.id
+	-- does not deduplicate identical entries, but we will do so below with DISTINCT
+	-- from scraped citations
+	UNION ALL
+	-- scraped citations from reference papers
+	SELECT
+		software,
+		id,
+		doi,
+		url,
+		title,
+		authors,
+		publisher,
+		publication_year,
+		journal,
+		page,
+		image_url,
+		mention_type,
+		source
+	FROM
+		citation_by_software()
+)
+SELECT DISTINCT ON (mentions_and_citations.software, mentions_and_citations.id) * FROM mentions_and_citations;
 $$;
 
 -- COUNT mentions per software

database/106-project-views.sql

@@ -55,18 +55,7 @@ WHERE
 	)
 GROUP BY
 	output_for_project.project,
-	mention.id,
-	mention.doi,
-	mention.url,
-	mention.title,
-	mention.authors,
-	mention.publisher,
-	mention.publication_year,
-	mention.journal,
-	mention.page,
-	mention.image_url,
-	mention.mention_type,
-	mention.source
+	mention.id
 ;
 $$;
 
@@ -90,49 +79,51 @@ CREATE FUNCTION impact_by_project() RETURNS TABLE (
 	note VARCHAR
 ) LANGUAGE sql STABLE AS
 $$
--- impact for project
-SELECT
-	impact_for_project.project,
-	mention.id,
-	mention.doi,
-	mention.url,
-	mention.title,
-	mention.authors,
-	mention.publisher,
-	mention.publication_year,
-	mention.journal,
-	mention.page,
-	mention.image_url,
-	mention.mention_type,
-	mention.source,
-	mention.note
-FROM
-	mention
-INNER JOIN
-	impact_for_project ON impact_for_project.mention = mention.id
--- will deduplicate identical entries
--- from scraped citations
-UNION
--- scraped citations from reference papers
-SELECT
-	project,
-	id,
-	doi,
-	url,
-	title,
-	authors,
-	publisher,
-	publication_year,
-	journal,
-	page,
-	image_url,
-	mention_type,
-	source,
-	-- scraped citations have no note prop
-	-- we need this prop in the edit impact section
-	NULL as note
-FROM
-	citation_by_project()
+WITH impact_and_citations AS (
+	-- impact for project
+	SELECT
+		impact_for_project.project,
+		mention.id,
+		mention.doi,
+		mention.url,
+		mention.title,
+		mention.authors,
+		mention.publisher,
+		mention.publication_year,
+		mention.journal,
+		mention.page,
+		mention.image_url,
+		mention.mention_type,
+		mention.source,
+		mention.note
+	FROM
+		mention
+	INNER JOIN
+		impact_for_project ON impact_for_project.mention = mention.id
+	-- does not deduplicate identical entries, but we will do so below with DISTINCT
+	-- from scraped citations
+	UNION ALL
+	-- scraped citations from reference papers
+	SELECT
+		project,
+		id,
+		doi,
+		url,
+		title,
+		authors,
+		publisher,
+		publication_year,
+		journal,
+		page,
+		image_url,
+		mention_type,
+		source,
+		-- scraped citations have no note prop
+		-- we need this prop in the edit impact section
+		NULL as note
+	FROM
+		citation_by_project()
+) SELECT DISTINCT ON (impact_and_citations.project, impact_and_citations.id) * FROM impact_and_citations;
 ;
 $$;