Merge pull request #962 from ctti-clinicaltrials/dev

Release 6.2.5

Author: micronix

README.md

@@ -36,6 +36,16 @@ You can find information about the ClinicalTrials.gov beta API here: https://cli
 
 <br>
 
+## Requireqments
+
+- Install zip  
+    - For mac `brew install zip`
+    - For windows `gem install rubyzip` 
+    - For linux `sudo apt install ruby-zip`
+- Install [graphviz](https://graphviz.org/download/)
+
+<br>
+
 ## Getting Started
 
 1.  Install PostgreSQL 13. If you have a Mac you can use brew to install PostgreSQL.  

app/models/study_json_record.rb

@@ -541,7 +541,10 @@ def eligibility_data
       gender_based: get_boolean(eligibility['GenderBased']),
       gender_description: eligibility['GenderDescription'],
       healthy_volunteers: eligibility['HealthyVolunteers'],
-      criteria: eligibility['EligibilityCriteria']
+      criteria: eligibility['EligibilityCriteria'],
+      adult: eligibility.dig('StdAgeList', 'StdAge')&.include?('Adult'),
+      child: eligibility.dig('StdAgeList', 'StdAge')&.include?('Child'),
+      older_adult: eligibility.dig('StdAgeList', 'StdAge')&.include?('Older Adult')
     }
   end
 
@@ -820,14 +823,30 @@ def id_information_data
     secondary_info = identification_module.dig('SecondaryIdInfoList', 'SecondaryIdInfo') || []
     org_study_info = identification_module['OrgStudyIdInfo']
     collection = []
-    collection << { nct_id: nct_id, id_type: 'org_study_id', id_value: org_study_info['OrgStudyId'] } if org_study_info
+    collection << {
+      nct_id: nct_id,
+      id_source: 'org_study_id',
+      id_type: identification_module.dig('OrgStudyIdInfo', "OrgStudyIdType"),
+      id_type_description = identification_module.dig('OrgStudyIdInfo', "OrgStudyIdDomain"),
+      id_link = identification_module.dig('OrgStudyIdInfo', "OrgStudyIdLink"),
+      id_value: org_study_info['OrgStudyId'] 
+      } if org_study_info
 
+    .Study.ProtocolSection.id.OrgStudyIdInfo.OrgStudyIdType && 
+    .Study.ProtocolSection.IdentificationModule.SecondaryIdInfoList.SecondaryIdInfo.SecondaryIdType
 
     nct_id_alias.each do |nct_alias|
-      collection << { nct_id: nct_id, id_type: 'nct_alias', id_value: nct_alias }
+      collection << { nct_id: nct_id, id_source: 'nct_alias', id_value: nct_alias }
     end
     secondary_info.each do |info|
-      collection << { nct_id: nct_id, id_type: 'secondary_id', id_value: info['SecondaryId'] }
+      collection << { 
+        nct_id: nct_id,
+        id_source: 'secondary_id',
+        id_type: info['SecondaryIdType'],
+        id_type_description: info['SecondaryIdDomain'],
+        id_value: info['SecondaryId'],
+        id_link: info['SecondaryIdLink'] 
+      }
     end
     collection
   end
@@ -1292,7 +1311,8 @@ def responsible_party_data
       name: responsible_party['ResponsiblePartyInvestigatorFullName'],
       title: responsible_party['ResponsiblePartyInvestigatorTitle'],
       organization: responsible_party['ResponsiblePartyOldOrganization'],
-      affiliation: responsible_party['ResponsiblePartyInvestigatorAffiliation']
+      affiliation: responsible_party['ResponsiblePartyInvestigatorAffiliation'],
+      old_name_title: responsible_party['ResponsiblePartyOldNameTitle']
     }
   end
 

app/models/util/db_manager.rb

@@ -41,7 +41,7 @@ def dump_database
       run_command_line(cmd)
 
       filename = File.basename(dump_file_location)
-      record = FileRecord.create(file_type: "snapshot", filename: filename ) 
+      record = FileRecord.create(file_type: "snapshot", filename: filename )
       record.file.attach(io: File.open(dump_file_location), filename: filename)
       record.update(url: record.file.service_url(filename: filename))
 
@@ -109,7 +109,7 @@ def refresh_public_db(schema='ctgov')
       restore_database(schema, public_connection, fm.pg_dump_file)
     end
 
-      
+
     def clear_out_data_for(nct_ids)
       ids=nct_ids.map { |i| "'" + i.to_s + "'" }.join(",")
       Util::DbManager.loadable_tables.each { |table|
@@ -427,7 +427,7 @@ def schema_image
     }
 
     END
-  
+
     File.write("./public/static/documentation/schema.dot", graph)
     `dot -Tpng ./public/static/documentation/schema.dot -o ./public/static/documentation/aact_schema.png`
     end
@@ -528,11 +528,6 @@ def super_username
       AACT::Application::AACT_DB_SUPER_USERNAME
     end
 
-    def static_file_dir
-      AACT::Application::AACT_STATIC_FILE_DIR
-    end
-
-
     def public_connection
       db = @config[:public]
       return unless db
@@ -556,12 +551,12 @@ def restore_from_file(path_to_file: "#{Rails.root}/tmp/postgres_data.dmp", datab
       restore_database('normal', ActiveRecord::Base.connection, path_to_file)
       puts 'done'
     end
-    
+
     def restore_from_url(params={})
       url = params[:url]
       database_name = params[:database_name] || 'aact'
       return unless url
-      
+
       tries ||= 5
       file_path = "#{Rails.root}/tmp/snapshots"
       FileUtils.rm_rf(file_path)
@@ -593,7 +588,7 @@ def restore_from_url(params={})
       puts 'done'
 
       restore_from_file({path_to_file: "#{file_path}/postgres_data.dmp", database: database_name})
-      
+
       print 'removing temp folder...'
       FileUtils.rm_rf(file_path)
       puts 'done'

config/application.rb

@@ -31,10 +31,7 @@ class Application < Rails::Application
     AACT_DB_SUPER_USERNAME = ENV['AACT_DB_SUPER_USERNAME'] || 'aact'   # Name of postgres superuser that has permission to create a database.
     AACT_OWNER_EMAIL       = ENV['AACT_OWNER_EMAIL']                   # Don't define this if your email service is not setup
     AACT_ADMIN_EMAILS      = ENV['AACT_ADMIN_EMAILS'] || "aact@your-org.org,admin@your-org.org" # Identifes who will receive load notifications
-    AACT_STATIC_FILE_DIR   = ENV['AACT_STATIC_FILE_DIR'] || '~/aact-files'  # directory containing AACT static files such as the downloadable db snapshots
-    RACK_TIMEOUT           = ENV['RACK_TIMEOUT'] || 10
 
-    APPLICATION_HOST          = 'localhost'
     AACT_HOST = ENV['AACT_HOST'] || 'localhost'
     if Rails.env != 'test'
       AACT_PUBLIC_HOSTNAME      =  ENV['AACT_PUBLIC_HOSTNAME'] || 'localhost'#Server on which the publicly accessible database resides

config/deploy.rb

@@ -51,7 +51,6 @@
 set :default_env, {
   'PATH' => ENV['AACT_PATH'] || "<server-path>/shared/bundle/ruby/2.4.5/bin:/opt/rh/rh-ruby24/root/usr/lib64",
   'LD_LIBRARY_PATH' => ENV['LD_LIBRARY_PATH'] || "/opt/rh/rh-ruby24/root/usr/lib64",
-  'APPLICATION_HOST' => ENV['APPLICATION_HOST'] || 'localhost',
   'AACT_STATIC_FILE_DIR' => ENV['AACT_STATIC_FILE_DIR'] || '~/aact-files',
   'RUBY_VERSION' =>  ENV['RUBY_VERSION'] || 'ruby 2.4.5',
   'GEM_HOME' => ENV['GEM_HOME'] || '~/.gem/ruby',

db/migrate/20220520124716_fix_id_information_table.rb

@@ -0,0 +1,8 @@
+class FixIdInformationTable < ActiveRecord::Migration[6.0]
+  def change
+    rename_column :id_information, :id_type, :id_source
+    add_column :id_information, :id_type, :string
+    add_column :id_information, :id_type_description, :string
+    add_column :id_information, :id_link, :string
+  end
+end

db/migrate/20220520133313_add_old_name_title_to_responsible_parties.rb

@@ -0,0 +1,5 @@
+class AddOldNameTitleToResponsibleParties < ActiveRecord::Migration[6.0]
+  def change
+    add_column :responsible_parties, :old_name_title, :string
+  end
+end

db/migrate/20220523123928_add_adult_child_older_adult_to_eligibilities.rb

@@ -0,0 +1,7 @@
+class AddAdultChildOlderAdultToEligibilities < ActiveRecord::Migration[6.0]
+  def change
+    add_column :eligibilities, :adult, :boolean
+    add_column :eligibilities, :child, :boolean
+    add_column :eligibilities, :older_adult, :boolean
+  end
+end

db/structure.sql

@@ -540,8 +540,11 @@ CREATE VIEW ctgov.all_group_types AS
 CREATE TABLE ctgov.id_information (
     id integer NOT NULL,
     nct_id character varying,
+    id_source character varying,
+    id_value character varying,
     id_type character varying,
-    id_value character varying
+    id_type_description character varying,
+    id_link character varying
 );
 
 
@@ -1085,7 +1088,10 @@ CREATE TABLE ctgov.eligibilities (
     population text,
     criteria text,
     gender_description text,
-    gender_based boolean
+    gender_based boolean,
+    adult boolean,
+    child boolean,
+    older_adult boolean
 );
 
 
@@ -2236,7 +2242,8 @@ CREATE TABLE ctgov.responsible_parties (
     name character varying,
     title character varying,
     organization character varying,
-    affiliation text
+    affiliation text,
+    old_name_title character varying
 );
 
 
@@ -3815,10 +3822,10 @@ CREATE INDEX index_facility_contacts_on_contact_type ON ctgov.facility_contacts
 
 
 --
--- Name: index_id_information_on_id_type; Type: INDEX; Schema: ctgov; Owner: -
+-- Name: index_id_information_on_id_source; Type: INDEX; Schema: ctgov; Owner: -
 --
 
-CREATE INDEX index_id_information_on_id_type ON ctgov.id_information USING btree (id_type);
+CREATE INDEX index_id_information_on_id_source ON ctgov.id_information USING btree (id_source);
 
 
 --
@@ -4220,62 +4227,6 @@ CREATE INDEX "index_support.study_xml_records_on_nct_id" ON support.study_xml_re
 CREATE TRIGGER category_insert_trigger INSTEAD OF INSERT ON ctgov.categories FOR EACH ROW EXECUTE FUNCTION ctgov.category_insert_function();
 
 
---
--- Name: baseline_counts baseline_counts_result_group_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.baseline_counts
-    ADD CONSTRAINT baseline_counts_result_group_id_fkey FOREIGN KEY (result_group_id) REFERENCES ctgov.result_groups(id);
-
-
---
--- Name: baseline_measurements baseline_measurements_result_group_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.baseline_measurements
-    ADD CONSTRAINT baseline_measurements_result_group_id_fkey FOREIGN KEY (result_group_id) REFERENCES ctgov.result_groups(id);
-
-
---
--- Name: design_group_interventions design_group_interventions_design_group_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.design_group_interventions
-    ADD CONSTRAINT design_group_interventions_design_group_id_fkey FOREIGN KEY (design_group_id) REFERENCES ctgov.design_groups(id);
-
-
---
--- Name: design_group_interventions design_group_interventions_intervention_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.design_group_interventions
-    ADD CONSTRAINT design_group_interventions_intervention_id_fkey FOREIGN KEY (intervention_id) REFERENCES ctgov.interventions(id);
-
-
---
--- Name: drop_withdrawals drop_withdrawals_result_group_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.drop_withdrawals
-    ADD CONSTRAINT drop_withdrawals_result_group_id_fkey FOREIGN KEY (result_group_id) REFERENCES ctgov.result_groups(id);
-
-
---
--- Name: facility_contacts facility_contacts_facility_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.facility_contacts
-    ADD CONSTRAINT facility_contacts_facility_id_fkey FOREIGN KEY (facility_id) REFERENCES ctgov.facilities(id);
-
-
---
--- Name: facility_investigators facility_investigators_facility_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.facility_investigators
-    ADD CONSTRAINT facility_investigators_facility_id_fkey FOREIGN KEY (facility_id) REFERENCES ctgov.facilities(id);
-
-
 --
 -- Name: active_storage_attachments fk_rails_c3b3935057; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
 --
@@ -4284,86 +4235,6 @@ ALTER TABLE ONLY ctgov.active_storage_attachments
     ADD CONSTRAINT fk_rails_c3b3935057 FOREIGN KEY (blob_id) REFERENCES ctgov.active_storage_blobs(id);
 
 
---
--- Name: intervention_other_names intervention_other_names_intervention_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.intervention_other_names
-    ADD CONSTRAINT intervention_other_names_intervention_id_fkey FOREIGN KEY (intervention_id) REFERENCES ctgov.interventions(id);
-
-
---
--- Name: milestones milestones_result_group_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.milestones
-    ADD CONSTRAINT milestones_result_group_id_fkey FOREIGN KEY (result_group_id) REFERENCES ctgov.result_groups(id);
-
-
---
--- Name: outcome_analyses outcome_analyses_outcome_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.outcome_analyses
-    ADD CONSTRAINT outcome_analyses_outcome_id_fkey FOREIGN KEY (outcome_id) REFERENCES ctgov.outcomes(id);
-
-
---
--- Name: outcome_analysis_groups outcome_analysis_groups_outcome_analysis_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.outcome_analysis_groups
-    ADD CONSTRAINT outcome_analysis_groups_outcome_analysis_id_fkey FOREIGN KEY (outcome_analysis_id) REFERENCES ctgov.outcome_analyses(id);
-
-
---
--- Name: outcome_analysis_groups outcome_analysis_groups_result_group_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.outcome_analysis_groups
-    ADD CONSTRAINT outcome_analysis_groups_result_group_id_fkey FOREIGN KEY (result_group_id) REFERENCES ctgov.result_groups(id);
-
-
---
--- Name: outcome_counts outcome_counts_outcome_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.outcome_counts
-    ADD CONSTRAINT outcome_counts_outcome_id_fkey FOREIGN KEY (outcome_id) REFERENCES ctgov.outcomes(id);
-
-
---
--- Name: outcome_counts outcome_counts_result_group_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.outcome_counts
-    ADD CONSTRAINT outcome_counts_result_group_id_fkey FOREIGN KEY (result_group_id) REFERENCES ctgov.result_groups(id);
-
-
---
--- Name: outcome_measurements outcome_measurements_outcome_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.outcome_measurements
-    ADD CONSTRAINT outcome_measurements_outcome_id_fkey FOREIGN KEY (outcome_id) REFERENCES ctgov.outcomes(id);
-
-
---
--- Name: outcome_measurements outcome_measurements_result_group_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.outcome_measurements
-    ADD CONSTRAINT outcome_measurements_result_group_id_fkey FOREIGN KEY (result_group_id) REFERENCES ctgov.result_groups(id);
-
-
---
--- Name: reported_events reported_events_result_group_id_fkey; Type: FK CONSTRAINT; Schema: ctgov; Owner: -
---
-
-ALTER TABLE ONLY ctgov.reported_events
-    ADD CONSTRAINT reported_events_result_group_id_fkey FOREIGN KEY (result_group_id) REFERENCES ctgov.result_groups(id);
-
-
 --
 -- Name: sanity_checks fk_rails_9d86ec7e91; Type: FK CONSTRAINT; Schema: support; Owner: -
 --
@@ -4414,6 +4285,7 @@ INSERT INTO "schema_migrations" (version) VALUES
 ('20220429175157'),
 ('20220512025646'),
 ('20220512030503'),
-('20220512030831');
-
-
+('20220512030831'),
+('20220520124716'),
+('20220520133313'),
+('20220523123928');