Fix bugs in relationships and rebuild schema_meta.xml

.github/workflows/pkgdown.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [results-data-model, main, master]
   pull_request:
     branches: [main, master]
   release:
@@ -81,7 +81,7 @@ jobs:
 
     - name: Execute SchemaSpy
       run: |
-        java -jar extras/rdms/schemaspy-6.2.4.jar -vizjs -dp $HOME -configFile extras/rdms/schemaspy-config.properties -meta extras/rdms/schema_meta.xml -debug -desc "Results data model" -noTablePaging
+        java -jar extras/rdms/schemaspy-6.2.4.jar -vizjs -dp $HOME -configFile extras/rdms/schemaspy-config.properties -meta extras/rdms/schema_meta.xml -debug -desc "Results data model" -noTablePaging -noimplied
 
     - name: Upload artifact
       uses: actions/upload-artifact@v4

extras/DocumentResultsDataModel.R

@@ -110,7 +110,12 @@ schemaMeta <- xml_new_root("schemaMeta",
                            "xsi:noNamespaceSchemaLocation" = "http://schemaspy.org/xsd/6/schemameta.xsd")
 
 # Add comments node
-xml_add_child(schemaMeta, "comments", "This is where we'll describe the Strategus results data model.")
+xml_add_child(
+  schemaMeta,
+  "comments",
+  "The tables in the results data model are grouped using a unique prefix for
+  each Strategus module. For example, the CharacterizationModule results tables
+  all start with \"c_\".")
 
 # Create tables node
 tables <- xml_add_child(schemaMeta, "tables")
@@ -127,7 +132,7 @@ resultsTableRelationships <-CohortGenerator::readCsv(
 for (i in seq_along(uniqueTableNames)) {
   # Add table node with attributes
   currentTableName <- uniqueTableNames[i]
-  print(currentTableName)
+  #print(currentTableName)
   # Get the table description, if it exists
   currentTableDescriptionInfo <- tableDescriptions %>%
     filter(.data$tableName == currentTableName)
@@ -144,14 +149,14 @@ for (i in seq_along(uniqueTableNames)) {
   for (j in 1:nrow(columnsForCurrentTable)) {
     curColumnName <- columnsForCurrentTable$columnName[j]
     description <- columnsForCurrentTable$description[j]
-    print(paste0("  -- ", curColumnName))
+    #print(paste0("  -- ", curColumnName))
     # Add column node with attributes
     columnNode <- xml_add_child(table, "column", name = curColumnName, comments = description)
     # Determine if this table + column has a FK relationship to any other tables
     curColumnFk <- resultsTableRelationships %>%
       filter(.data$tableName == currentTableName & .data$columnName == curColumnName)
     if (nrow(curColumnFk) > 0) {
-      print(paste0("-- FK FOUND FOR: ", currentTableName, ".", curColumnName))
+      #print(paste0("-- FK FOUND FOR: ", currentTableName, ".", curColumnName))
       for (k in 1:nrow(curColumnFk)) {
         fkTable <- curColumnFk$fkTableName[k]
         fkColumn <- curColumnFk$fkColumnName[k]

extras/rdms/results_table_relationships.csv

@@ -18,35 +18,35 @@ c_covariates_continuous,covariate_id,c_covariate_ref,covariate_id
 c_covariates_continuous,database_id,c_settings,database_id
 c_covariates_continuous,database_id,database_meta_data,database_id
 database_meta_data,database_id,c_cohort_details,database_id
-c_DECHALLENGE_RECHALLENGE,target_cohort_definition_id,cg_cohort_definition,cohort_definition_id
-c_DECHALLENGE_RECHALLENGE,outcome_cohort_definition_id,cg_cohort_definition,cohort_definition_id
-c_DECHALLENGE_RECHALLENGE,database_id,database_meta_data,database_id
-ci_incidence_SUMMARY,outcome_id,ci_outcome_def,outcome_id
-ci_incidence_SUMMARY,ref_id,ci_outcome_def,ref_id
-ci_incidence_SUMMARY,ref_id,ci_tar_def,ref_id
-ci_incidence_SUMMARY,tar_id,ci_tar_def,ref_id
-ci_incidence_SUMMARY,subgroup_id,ci_subgroup_def,subgroup_id
-ci_incidence_SUMMARY,ref_id,ci_subgroup_def,ref_id
-ci_incidence_SUMMARY,age_group_id,ci_age_group_def,age_group_id
-ci_incidence_SUMMARY,ref_id,ci_age_group_def,ref_id
-ci_incidence_SUMMARY,database_id,database_meta_data,database_id
-ci_incidence_SUMMARY,target_cohort_definition_id,cg_cohort_definition,cohort_definition_id
-ci_incidence_SUMMARY,outcome_cohort_definition_id,cg_cohort_definition,cohort_definition_id
-c_TIME_TO_EVENT,database_id,database_meta_data,database_id
+c_dechallenge_rechallenge,target_cohort_definition_id,cg_cohort_definition,cohort_definition_id
+c_dechallenge_rechallenge,outcome_cohort_definition_id,cg_cohort_definition,cohort_definition_id
+c_dechallenge_rechallenge,database_id,database_meta_data,database_id
+ci_incidence_summary,outcome_id,ci_outcome_def,outcome_id
+ci_incidence_summary,ref_id,ci_outcome_def,ref_id
+ci_incidence_summary,ref_id,ci_tar_def,ref_id
+ci_incidence_summary,tar_id,ci_tar_def,ref_id
+ci_incidence_summary,subgroup_id,ci_subgroup_def,subgroup_id
+ci_incidence_summary,ref_id,ci_subgroup_def,ref_id
+ci_incidence_summary,age_group_id,ci_age_group_def,age_group_id
+ci_incidence_summary,ref_id,ci_age_group_def,ref_id
+ci_incidence_summary,database_id,database_meta_data,database_id
+ci_incidence_summary,target_cohort_definition_id,cg_cohort_definition,cohort_definition_id
+ci_incidence_summary,outcome_cohort_definition_id,cg_cohort_definition,cohort_definition_id
+c_time_to_event,database_id,database_meta_data,database_id
 cd_temporal_covariate_ref,analysis_id,cd_temporal_analysis_ref,analysis_id
 cd_temporal_covariate_ref,covariate_id,cd_temporal_covariate_value,covariate_id
 cd_temporal_covariate_ref,time_id,cd_temporal_time_ref,time_id
 cd_included_source_concept,concept_id,cd_concept,concept_id
 cd_incidence_rate,database_id,cd_cohort_count,database_id
 cd_incidence_rate,cohort_id,cd_cohort_count,cohort_id
 cd_index_event_breakdown,concept_id,cd_concept,concept_id
-cd_orphan_concept,cohort_id,cd_concept_set,cohort_id
-cd_orphan_concept,concept_set_id,cd_concept_set,concept_set_id
+cd_orphan_concept,cohort_id,cd_concept_sets,cohort_id
+cd_orphan_concept,concept_set_id,cd_concept_sets,concept_set_id
 cd_orphan_concept,concept_id,cd_concept,concept_id
 cd_cohort_count,database_id,database_meta_data,database_id
 cd_visit_context,concept_id,cd_concept,concept_id
 cg_cohort_count,database_id,database_meta_data,database_id
-cg_cohort_count,cohort_id,cg_cohort_definition,cohort_id
+cg_cohort_count,cohort_id,cg_cohort_definition,cohort_definition_id
 cg_cohort_generation,database_id,database_meta_data,database_id
 cg_cohort_summary_stats,database_id,database_meta_data,database_id
 cg_cohort_summary_stats,cohort_definition_id,cg_cohort_definition,cohort_definition_id
@@ -68,11 +68,11 @@ cm_covariate_balance,database_id,cm_covariate,database_id
 cm_covariate,covariate_id,cm_propensity_model,covariate_id
 cm_analysis,analysis_id,cm_result,analysis_id
 cm_analysis,database_id,database_meta_data,database_id
-cm_analysis,analysis_id,cm_diagnostic_summary,analysis_id
-cm_analysis,target_id,cm_diagnostic_summary,target_id
-cm_analysis,comparator_id,cm_diagnostic_summary,comparator_id
-cm_analysis,outcome_id,cm_diagnostic_summary,outcome_id
-cm_analysis,database_id,cm_diagnostic_summary,database_id
+cm_analysis,analysis_id,cm_diagnostics_summary,analysis_id
+cm_analysis,target_id,cm_diagnostics_summary,target_id
+cm_analysis,comparator_id,cm_diagnostics_summary,comparator_id
+cm_analysis,outcome_id,cm_diagnostics_summary,outcome_id
+cm_analysis,database_id,cm_diagnostics_summary,database_id
 cm_analysis,target_id,cg_cohort_definition,cohort_definition_id
 cm_analysis,outcome_id,cg_cohort_definition,cohort_definition_id
 cm_analysis,comparator_id,cg_cohort_definition,cohort_definition_id
@@ -100,12 +100,12 @@ sccs_result,exposures_outcome_set_id,sccs_covariate,exposures_outcome_set_id
 sccs_result,database_id,sccs_covariate,database_id
 sccs_result,covariate_id,sccs_covariate,covariate_id
 sccs_result,database_id,database_meta_data,database_id
-sccs_result,exposures_outcome_set_id,sccs_diagnostics_sumary,exposures_outcome_set_id
-sccs_result,database_id,sccs_diagnostics_sumary,database_id
-sccs_result,analysis_id,sccs_diagnostics_sumary,analysis_id
-sccs_result,covariate_id,sccs_diagnostics_sumary,covariate_id
+sccs_result,exposures_outcome_set_id,sccs_diagnostics_summary,exposures_outcome_set_id
+sccs_result,database_id,sccs_diagnostics_summary,database_id
+sccs_result,analysis_id,sccs_diagnostics_summary,analysis_id
+sccs_result,covariate_id,sccs_diagnostics_summary,covariate_id
 sccs_result,analysis_id,sccs_covariate,analysis_id
-sccs_result,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
+sccs_result,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
 sccs_result,analysis_id,sccs_analysis,analysis_id
 sccs_result,outcome_id,cg_cohort_definition,cohort_definition_id
 sccs_exposures_outcome_set,nesting_cohort_id,cg_cohort_definition,cohort_definition_id
@@ -114,15 +114,15 @@ sccs_exposures_outcome_set,exposures_outcome_set_id,sccs_exposure,exposures_outc
 sccs_exposures_outcome_set,era_id,sccs_exposure,era_id
 sccs_exposures_outcome_set,era_id,cg_cohort_definition,era_id
 sccs_result,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
-sccs_covariate_result,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
-sccs_time_trend,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
-sccs_diagnostics_summary,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
-sccs_time_to_event,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
-sccs_attrition,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
-sccs_event_dep_observation,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
-sccs_age_spanning,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
-sccs_calendar_time_spanning,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
-sccs_spline,exposures_outcome_set_id,sccs_exposure_outcome_set,exposures_outcome_set_id
+sccs_covariate_result,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
+sccs_time_trend,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
+sccs_diagnostics_summary,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
+sccs_time_to_event,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
+sccs_attrition,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
+sccs_event_dep_observation,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
+sccs_age_spanning,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
+sccs_calendar_time_spanning,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
+sccs_spline,exposures_outcome_set_id,sccs_exposures_outcome_set,exposures_outcome_set_id
 sccs_diagnostics_summary,analysis_id,sccs_covariate,analysis_id
 plp_model_designs,target_id,cg_cohort_definition,cohort_definition_id
 plp_model_designs,outcome_id,cg_cohort_definition,cohort_definition_id
@@ -137,4 +137,4 @@ plp_performances,development_database_id,database_meta_data,database_id
 plp_performances,validation_database_id,database_meta_data,database_id
 plp_performances,database_id,database_meta_data,database_id
 plp_cohorts,cohort_definition_id,cg_cohort_definition,cohort_definition_id
-c_cohort_details,target_id,cg_cohort_definition,cohort_id
+c_cohort_details,target_id,cg_cohort_definition,cohort_definition_id

extras/rdms/run-local.txt

@@ -1 +1 @@
-"E:\Program Files\Amazon Corretto\jdk17.0.12_7\bin\java.exe" -jar schemaspy-6.2.4.jar -vizjs -dp E:\jdbcDrivers -configFile schemaspy-config.properties -meta schema_meta.xml -desc "Results data model" -noTablePaging
+"E:\Program Files\Amazon Corretto\jdk17.0.12_7\bin\java.exe" -jar schemaspy-6.2.4.jar -vizjs -dp E:\jdbcDrivers -configFile schemaspy-config.properties -meta schema_meta.xml -desc "Results data model" -noTablePaging -noimplied