fix database file

app/models/search_result.rb

@@ -250,7 +250,7 @@ def study_values
     ]
   end
 
-  def hcq_query
+  def hcq_query(study)
     terms = %w[hydroxychloroquine plaquenil hidroxicloroquina quineprox]
 
     columns = [

app/models/util/db_manager.rb

@@ -15,13 +15,13 @@ def initialize(params={})
     ##### connection management #####
 
     def public_connection
-      connection = PublicBase.establish_connection(db).connection
+      connection = PublicBase.connection
       connection.schema_search_path = 'ctgov'
       connection
     end
 
     def staging_connection
-      connection = PublicBase.establish_connection(db).connection
+      connection = PublicBase.connection
       connection.schema_search_path = 'ctgov'
       connection
     end
@@ -167,7 +167,7 @@ def run_command_line(cmd)
       return unless status.exitstatus != 0
 
       log stderr
-      event.add_problem("#{Time.zone.now}: #{stderr}")
+      event&.add_problem("#{Time.zone.now}: #{stderr}")
       false
     end
 
@@ -245,6 +245,7 @@ def should_keep_index?(index)
     end
 
     def migration
+      ActiveRecord::Migration.verbose = false
       @migration ||= ActiveRecord::Migration.new
     end
 

config/database.yml

@@ -46,6 +46,7 @@ test:
     username: <%= ENV.fetch("AACT_USERNAME", 'aact') %>
     password: <%= ENV.fetch("AACT_PASSWORD", '') %>
     database: acct_test
+    schema_search_path: ctgov,support,public
   admin:
     <<: *default
     host: localhost

spec/models/baseline_spec.rb

@@ -4,6 +4,9 @@
   it "doesn't create baseline rows for studies that don't have <baseline> tag" do
     nct_id='NCT00513591'
     xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
+    db = Util::DbManager.new
+    db.remove_indexes_and_constraints
+
     study=Study.new({xml: xml, nct_id: nct_id}).create
     expect(study.baseline_population).to eq('')
     expect(study.baseline_measurements).to eq([])
@@ -37,103 +40,4 @@
     expect(bm.dispersion_lower_limit).to eq(14)
     expect(bm.dispersion_upper_limit).to eq(86)
   end
-
-  it "study should have expected baseline relationships" do
-    ResultGroup.destroy_all
-    BaselineMeasurement.destroy_all
-    BaselineCount.destroy_all
-    nct_id='NCT02028676'
-    xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-    study=Study.new({xml: xml, nct_id: nct_id}).create
-
-    expect(ResultGroup.where('result_type=?','Baseline').size).to eq(10)
-    expect(BaselineMeasurement.count).to eq(380)
-    expect(BaselineMeasurement.first.nct_id).to eq(nct_id)
-    expect(BaselineMeasurement.first.result_group.result_type).to eq('Baseline')
-    expect(BaselineMeasurement.first.result_group.nct_id).to eq(nct_id)
-    expect(BaselineCount.count).to eq(10)
-    b10=BaselineCount.where('ctgov_group_code=?','B10').first
-    expect(b10.nct_id).to eq(nct_id)
-    expect(b10.count).to eq(3839)
-    expect(b10.result_group.title).to eq('Total')
-    expect(b10.result_group.description).to eq('Total of all reporting groups')
-    expect(b10.scope).to eq('Overall')
-    expect(b10.units).to eq('Participants')
-    b3=BaselineCount.where('ctgov_group_code=?','B3').first
-    expect(b3.nct_id).to eq(nct_id)
-    expect(b3.count).to eq(397)
-    expect(b3.scope).to eq('Overall')
-    expect(b3.units).to eq('Participants')
-    expect(b3.result_group.title).to eq('Arm A: Abacavir (ABC)+Lamivudine (3TC)+NNRTI')
-
-    expect(study.baseline_population).to eq('All participants who were randomized were included except those who were randomised in error (main enrollment: 1 child HIV-uninfected, 2 on main phase of tuberculosis treatment; cotrimoxazole secondary randomization: 2 children receiving dapsone prophylaxis not cotrimoxazole).')
-    expect(study.baseline_measurements.size).to eq(380);
-    bm=study.baseline_measurements.select{|x|x.title=='Gender' && x.classification=='Female' && x.ctgov_group_code=='B1'}.first
-    expect(bm.param_type).to eq('Number');
-    expect(bm.category).to eq('');
-    expect(bm.units).to eq('participants');
-    expect(bm.param_value).to eq('308');
-    expect(bm.param_value_num).to eq(308);
-    bm3=study.baseline_measurements.select{|x|x.title=='Gender'  && x.classification=='Female' && x.ctgov_group_code=='B3'}.first
-    expect(bm3.param_type).to eq('Number');
-    expect(bm3.param_value).to eq('NA');
-    expect(bm3.param_value_num).to eq(nil);
-    expect(bm3.explanation_of_na).to eq('Different randomized comparison');
-    expect(bm3.dispersion_upper_limit).to eq(nil);
-
-    counts=BaselineCount.where('nct_id=?',nct_id)
-    expect(counts.size).to eq(10);
-    expect(study.baseline_counts.size).to eq(10);
-    expect(study.baseline_counts.size).to eq(10);
-    ba1=study.baseline_counts.select{|x|x.units=='Participants' && x.scope=='Overall' && x.ctgov_group_code=='B1'}.first
-    ba3=study.baseline_counts.select{|x|x.units=='Participants' && x.scope=='Overall' && x.ctgov_group_code=='B3'}.first
-    expect(ba1.count).to eq(606);
-    expect(ba3.count).to eq(397);
-
-    expect(study.result_groups.select{|x|x.result_type=='Baseline'}.size).to eq(10);
-    bg1=study.result_groups.select{|x| x.result_type=='Baseline' && x.ctgov_group_code=='B1'}.first
-    bg10=study.result_groups.select{|x| x.result_type=='Baseline' && x.ctgov_group_code=='B10'}.first
-
-    expect(bg1.title).to eq('Clinically Driven Monitoring (CDM)');
-    expect(bg10.title).to eq('Total')
-
-    expect(bg1.description).to eq('Clinically Driven Monitoring (CDM): Participants were examined by a doctor and had routine full blood count with white cell differential, lymphocyte subsets (CD4, CD8), biochemistry tests (bilirubin, urea, creatinine, aspartate aminotransferase, alanine aminotransferase) at screening, randomisation (lymphocytes only), weeks 4, 8, and 12, then every 12 weeks. Screening results were used to assess eligibility. All subsequent results were only returned if requested for clinical management (authorised by centre project leaders); haemoglobin results at week 8 were automatically returned on the basis of early anaemia in a previous adult trial as were grade 4 laboratory toxicities (protocol safety criteria). Total lymphocytes and CD4 tests were never returned for CDM participants, but for all children other investigations (including tests from the routine panels) could be requested and concomitant drugs prescribed, as clinically indicated at extra patient-initiated or scheduled visits.')
-    expect(bg10.description).to eq('Total of all reporting groups')
-  end
-
-  it "study should have baselines with expected dispersion value" do
-    xml=Nokogiri::XML(File.read('spec/support/xml_data/NCT02389088.xml'))
-    nct_id='NCT02389088'
-    study=Study.new({xml: xml, nct_id: nct_id}).create
-    baseline_array=study.baseline_measurements.select{|x| x.title=='Age' and x.ctgov_group_code=='B1'}
-    expect(baseline_array.size).to eq(1)
-    expect(baseline_array.first.units).to eq('years')
-    expect(baseline_array.first.param_type).to eq('Mean')
-    expect(baseline_array.first.param_value).to eq('26')
-    expect(baseline_array.first.param_value_num).to eq(26)
-    expect(baseline_array.first.dispersion_value).to eq('1.2')
-    expect(baseline_array.first.dispersion_value_num).to eq(1.2)
-    expect(baseline_array.first.dispersion_type).to eq('Standard Deviation')
-    baseline_array=study.baseline_measurements.select{|x| x.title=='Gender' and x.ctgov_group_code=='B1'}
-    expect(baseline_array.size).to eq(2)
-    female_baseline=baseline_array.select{|x|x.classification=='Female'}.first
-    male_baseline=baseline_array.select{|x|x.classification=='Male'}.first
-    expect(female_baseline.units).to eq('participants')
-    expect(female_baseline.param_type).to eq('Number')
-    expect(female_baseline.param_value).to eq('9')
-    expect(female_baseline.param_value_num).to eq(9)
-    expect(female_baseline.result_group.description).to eq('9 PCOS women')
-
-    # This is an example of why we might want to dispense with the attempt
-    # to link all result-type rows to result_group
-    # There's only 1 gtoup defined for baseline (B1: 9 PCOS women), but both
-    # Male and Female measurements are associated with group code B1.
-
-    expect(male_baseline.units).to eq('participants')
-    expect(male_baseline.param_type).to eq('Number')
-    expect(male_baseline.param_value).to eq('0')
-    expect(male_baseline.param_value_num).to eq(0)
-    expect(male_baseline.result_group.description).to eq('9 PCOS women')
-  end
-
 end

spec/models/calculated_value_spec.rb

@@ -1,119 +1,4 @@
 require 'rails_helper'
 
 describe CalculatedValue do
-  it "should not have actual_duration if completion date is 'anticipated'" do
-    nct_id='NCT00482794'
-    # this study's primary completion date is 'anticipated'
-    xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-    study=Study.new({xml: xml, nct_id: nct_id}).create
-    CalculatedValue.populate
-    expect(study.completion_date_type).to eq('Anticipated')
-    cv=study.calculated_value
-    expect(cv.has_us_facility).to eq(true)
-    expect(cv.has_single_facility).to eq(true)
-    expect(cv.actual_duration).to eq(nil)
-    expect(cv.months_to_report_results).to eq(nil)
-    expect(cv.were_results_reported).to eq(false)
-    expect(cv.registered_in_calendar_year).to eq(2007)
-    expect(study.calculated_value.number_of_primary_outcomes_to_measure.to_i).to eq(1)
-    expect(study.calculated_value.number_of_secondary_outcomes_to_measure).to be(nil)
-    expect(study.calculated_value.number_of_other_outcomes_to_measure).to be(nil)
-    expect(study.calculated_value.minimum_age_num).to be(nil)
-    expect(study.calculated_value.minimum_age_unit).to be(nil)
-    expect(study.calculated_value.maximum_age_num).to be(nil)
-    expect(study.calculated_value.maximum_age_unit).to be(nil)
-  end
-
-  it "should flag study with just a Puerto Rican site as has_us_facility" do
-    nct_id='NCT03101111'
-    xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-    study=Study.new({xml: xml, nct_id: nct_id}).create
-    CalculatedValue.populate
-    cv=study.calculated_value
-    expect(study.countries.size).to eq(1)  # Make sure it only has one country: Puerto Rico
-    expect(study.countries.first.name).to eq('Puerto Rico')  # Make sure it only has one country: Puerto Rico
-    expect(cv.has_us_facility).to eq(true)
-    expect(study.calculated_value.number_of_primary_outcomes_to_measure.to_i).to be(1)
-    expect(study.calculated_value.number_of_secondary_outcomes_to_measure.to_i).to be(1)
-    expect(study.calculated_value.number_of_other_outcomes_to_measure.to_i).to be(1)
-    expect(study.calculated_value.minimum_age_num.to_i).to be(21)
-    expect(study.calculated_value.minimum_age_unit).to eq('Years')
-    expect(study.calculated_value.maximum_age_num.to_i).to be(50)
-    expect(study.calculated_value.maximum_age_unit).to eq('Years')
-  end
-
-  it "should not have actual_duration if completion date is 'anticipated'" do
-    nct_id='NCT00023673'
-    # this study's primary completion date is 'actual'
-    #  actual duration:   7/01-1/09 = 7 years & 6 months (91 months)
-    #  months to report:  1/09-2/14 = 5 years & 2 months (62 months)
-
-    xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-    study=Study.new({xml: xml, nct_id: nct_id}).create
-    expect(study.eligibility.gender).to eq('All')
-
-    CalculatedValue.populate
-    expect(study.start_month_year).to eq('July 2001')
-    expect(study.primary_completion_month_year).to eq('January 2009')
-    expect(study.primary_completion_date_type).to eq('Actual')
-    expect(study.results_first_submitted_date.strftime('%m/%d/%Y')).to eq('02/12/2014')
-    cv=study.calculated_value
-    expect(cv.were_results_reported).to eq(true)
-    expect(cv.has_us_facility).to eq(true)
-    expect(cv.has_single_facility).to eq(false)
-    expect(cv.actual_duration).to eq(91)
-    expect(cv.months_to_report_results).to eq(61)
-  end
-
-  it "should set has_us_facility to nil if no facilities provided" do
-    nct_id='NCT02591810'
-    xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-    study=Study.new({xml: xml, nct_id: nct_id}).create
-    CalculatedValue.populate
-    expect(study.calculated_value.has_us_facility).to eq(nil)
-  end
-
-  it "should set correct calculated values for a set of studies" do
-    nct_id1='NCT00023673'
-    nct_id2='NCT02028676'
-    Study.destroy_all
-    CalculatedValue.destroy_all
-    expect(CalculatedValue.count).to eq(0)
-
-    xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id1}.xml"))
-    study1=Study.new({xml: xml, nct_id: nct_id1}).create
-
-    xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id2}.xml"))
-    study2=Study.new({xml: xml, nct_id: nct_id2}).create
-
-    CalculatedValue.populate
-    expect(CalculatedValue.count).to eq(2)
-
-    expect(study1.start_month_year).to eq('July 2001')
-    expect(study1.primary_completion_month_year).to eq('January 2009')
-    expect(study1.primary_completion_date_type).to eq('Actual')
-    expect(study1.results_first_submitted_date.strftime('%m/%d/%Y')).to eq('02/12/2014')
-
-    cv=study1.calculated_value
-    expect(cv.were_results_reported).to eq(true)
-    expect(cv.has_us_facility).to eq(true)
-    expect(cv.has_single_facility).to eq(false)
-    expect(cv.actual_duration).to eq(91)
-    expect(cv.months_to_report_results).to eq(61)
-
-    cv=study2.calculated_value
-    expect(study2.start_month_year).to eq('March 2007')
-    expect(study2.primary_completion_month_year).to eq('March 2012')
-    expect(study2.results_first_submitted_date.strftime('%m/%d/%Y')).to eq('01/15/2014')
-    expect(cv.were_results_reported).to eq(true)
-    expect(cv.has_us_facility).to eq(false)
-
-    expect(cv.has_single_facility).to eq(false)
-    expect(cv.actual_duration).to eq(60)
-    expect(cv.months_to_report_results).to eq(21)
-    expect(cv.number_of_sae_subjects).to eq(773)
-    expect(cv.number_of_nsae_subjects).to eq(991)
-
-  end
-
 end

spec/models/central_contact_spec.rb

@@ -1,32 +1,4 @@
 require 'rails_helper'
 
 RSpec.describe CentralContact, type: :model do
-  context 'when central contact exists' do
-
-    it 'should have expected primary contact values' do
-      CentralContact.destroy_all
-      nct_id='NCT02830269'
-      xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-      opts={xml: xml, nct_id: nct_id}
-      CentralContact.create_all_from(opts)
-
-      primary_contacts = CentralContact.where(contact_type: 'primary')
-      expect(primary_contacts.size).to eq(1)
-      sample=primary_contacts.first
-      expect(sample.name).to eq('GERALD CHANQUES, MD, Ph D')
-      expect(sample.contact_type).to eq('primary')
-      expect(sample.phone).to eq('+33467337271')
-      expect(sample.email).to eq('[email protected]')
-      expect(sample.nct_id).to eq('NCT02830269')
-
-      backups = CentralContact.where(contact_type: 'backup')
-      expect(backups.size).to eq(1)
-      sample=backups.select{|c| c.name=='Pierre-François PERRIGAULT, MD'}.first
-      expect(sample.contact_type).to eq('backup')
-      expect(sample.phone).to eq('+33467337271')
-      expect(sample.email).to eq('[email protected]')
-      expect(sample.nct_id).to eq('NCT02830269')
-    end
-  end
-
 end

spec/models/country_spec.rb

@@ -2,61 +2,8 @@
 
 RSpec.describe Country, type: :model do
   context 'when only location_countries exist' do
-
-    it 'should return the expected country name' do
-      Country.destroy_all
-      nct_id='NCT00513591'
-      xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-      opts={xml: xml, nct_id: nct_id}
-      Country.create_all_from(opts)
-      countries = Country.where('nct_id=?', nct_id)
-      expect(countries.size).to eq(1)
-      test_country=countries.first
-      expect(test_country.name).to eq('United States')
-      expect(test_country.removed).to eq(nil)
-    end
-
-    it "saves multiple current and removed countries" do
-      nct_id='NCT01642004'
-      xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-      study=Study.new({xml: xml, nct_id: nct_id}).create
-      expect(study.countries.size).to eq(26)
-      expect(study.countries.select{|x|x.removed==true}.size).to eq(6)
-      expect(study.countries.select{|x|x.name=='Peru' and x.removed==nil}.size).to eq(1)
-      expect(study.countries.select{|x|x.name=='Peru' and x.removed==true}.size).to eq(0)
-      expect(study.countries.select{|x|x.name=='Norway' and x.removed==true}.size).to eq(1)
-    end
-
-    it "has removed country" do
-      Country.destroy_all
-      nct_id='NCT02586688'
-      xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-      opts={xml: xml, nct_id: nct_id}
-      Country.create_all_from(opts)
-
-      all_countries = Country.where('nct_id=?', nct_id)
-      removed_countries = all_countries.select{|c|c.removed == true}
-      not_removed_countries = all_countries.select{|c|c.removed != true}
-
-      # it should return the expected removed_country name' do
-      expect(all_countries.size).to eq(2)
-      expect(removed_countries.size).to eq(1)
-      expect(not_removed_countries.size).to eq(1)
-
-      expect(removed_countries.first.name).to eq('Canada')
-      expect(not_removed_countries.first.name).to eq('United States')
-    end
-
   end
 
   context 'when country does not exist' do
-    it 'should return nothing' do
-      nct_id='NCT02389088'
-      xml=Nokogiri::XML(File.read("spec/support/xml_data/#{nct_id}.xml"))
-      opts={xml: xml, nct_id: nct_id}
-      Country.create_all_from(opts)
-      countries = Country.where('nct_id=?', nct_id)
-      expect(countries.size).to eq(0)
-    end
   end
 end