Merge pull request #140 from darwin-eu/tidying

license statements and dbms tests
darwin-eu · May 8, 2024 · ca9c76d · ca9c76d
2 parents d288146 + 1c017e9
commit ca9c76d
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diff --git a/R/checks.R b/R/checks.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU (C)
+# Copyright 2024 DARWIN EU (C)
 #
 # This file is part of CodelistGenerator
 #

diff --git a/R/codesFromConceptSet.R b/R/codesFromConceptSet.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU (C)
+# Copyright 2024 DARWIN EU (C)
 #
 # This file is part of CodelistGenerator
 #
@@ -299,7 +299,13 @@ addDetails <- function(conceptList, cdm){
    conceptList <- split(
     x = conceptList %>% dplyr::select(!"concept_set"),
     f = as.factor(conceptList$concept_set)
-  )}
+   )
+   }
+
+  for(i in seq_along(conceptList)){
+    conceptList[[i]] <- conceptList[[i]] %>%
+      dplyr::arrange(.data$concept_name)
+  }
 
    return(conceptList)
 

diff --git a/R/codesInUse.R b/R/codesInUse.R
@@ -1,3 +1,19 @@
+# Copyright 2024 DARWIN EU (C)
+#
+# This file is part of CodelistGenerator
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Filter a codelist to keep only the codes used in the database
 #'
 #' @param x A codelist

diff --git a/R/compareCodelists.R b/R/compareCodelists.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU®
+# Copyright 2024 DARWIN EU®
 #
 # This file is part of IncidencePrevalence
 #

diff --git a/R/drugCodes.R b/R/drugCodes.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU®
+# Copyright 2024 DARWIN EU®
 #
 # This file is part of IncidencePrevalence
 #

diff --git a/R/getCandidateCodes.R b/R/getCandidateCodes.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU®
+# Copyright 2024 DARWIN EU (C)
 #
 # This file is part of IncidencePrevalence
 #
@@ -14,8 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-
 #' Generate candidate codelist for the OMOP CDM
 #'
 #' @description

diff --git a/R/getICD10StandardCodes.R b/R/getICD10StandardCodes.R
@@ -1,3 +1,19 @@
+# Copyright 2024 DARWIN EU (C)
+#
+# This file is part of IncidencePrevalence
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Get corresponding standard codes for ICD-10 chapters and sub-chapters
 #'
 #' @param cdm cdm_reference via CDMConnector

diff --git a/R/getMappings.R b/R/getMappings.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU®
+# Copyright 2024 DARWIN EU®
 #
 # This file is part of IncidencePrevalence
 #

diff --git a/R/inputValidation.R b/R/inputValidation.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU®
+# Copyright 2024 DARWIN EU (C)
 #
 # This file is part of IncidencePrevalence
 #

diff --git a/R/mockVocabRef.R b/R/mockVocabRef.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU®
+# Copyright 2024 DARWIN EU (C)
 #
 # This file is part of IncidencePrevalence
 #

diff --git a/R/runSearch.R b/R/runSearch.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU®
+# Copyright 2024 DARWIN EU®
 #
 # This file is part of IncidencePrevalence
 #
@@ -421,16 +421,9 @@ getMatches <- function(words,
     for (j in seq_along(workingExclude)) {
       if (nchar(workingExclude[j]) >= 1) {
 
-        if(inherits(workingConcepts, "tbl_sql")){
-          workingConcepts <- workingConcepts %>%
-            dplyr::filter(dplyr::sql(paste0("concept_name LIKE '%", .env$workingExclude[j], "%'")))
-        } else {
-          workingConcepts <- workingConcepts %>%
-            dplyr::filter(stringr::str_detect(
-              .data$concept_name,
-              .env$workingExclude[j]
-            ))
-        }
+      cToSearch <-  paste0("%", workingExclude[j], "%")
+      workingConcepts <- workingConcepts %>%
+        dplyr::filter(stringr::str_like(.data$concept_name, .env$cToSearch))
 
       }
     }

diff --git a/R/summariseCodeUse.R b/R/summariseCodeUse.R
@@ -1,3 +1,19 @@
+# Copyright 2024 DARWIN EU (C)
+#
+# This file is part of IncidencePrevalence
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Summarise code use in patient-level data
 #'
 #' @param x List of concept IDs

diff --git a/R/vocabUtilities.R b/R/vocabUtilities.R
@@ -1,4 +1,4 @@
-# Copyright 2023 DARWIN EU®
+# Copyright 2024 DARWIN EU (C)
 #
 # This file is part of IncidencePrevalence
 #
@@ -390,14 +390,20 @@ getDescendantsOnly <- function(cdm, conceptId, ingredientRange, doseForm) {
 }
 
 getDescendantsAndAncestor <- function(cdm, conceptId, ingredientRange, doseForm) {
+  conceptIdDbTable <- omopgenerics::uniqueTableName()
+  cdm <- omopgenerics::insertTable(cdm = cdm,
+                            name = conceptIdDbTable,
+                            table = dplyr::tibble(ancestor_concept_id = as.integer(conceptId)),
+                            overwrite = TRUE)
 
   descendants <- cdm$concept_ancestor %>%
-    dplyr::inner_join(dplyr::tibble(ancestor_concept_id = as.integer(conceptId)),
-                      by = "ancestor_concept_id",
-                      copy = TRUE) %>%
+    dplyr::inner_join(cdm[[conceptIdDbTable]],
+                      by = "ancestor_concept_id") %>%
     dplyr::rename("concept_id" = "descendant_concept_id") %>%
     dplyr::left_join(cdm$concept,
-                     by = "concept_id")
+                     by = "concept_id") %>%
+    dplyr::compute()
+  CDMConnector::dropTable(cdm, conceptIdDbTable)
 
   descendants <- addIngredientCount(cdm = cdm, concepts = descendants) %>%
     dplyr::filter(.data$ingredient_count >= !!ingredientRange[1],

diff --git a/inst/cohorts2/GIBleed_male.json b/inst/cohorts2/GIBleed_male.json
@@ -0,0 +1,120 @@
+{
+  "ConceptSets": [
+    {
+      "id": 0,
+      "name": "Gastrointestinal hemorrhage",
+      "expression": {
+        "items": [
+          {
+            "concept": {
+              "CONCEPT_CLASS_ID": "Clinical Finding",
+              "CONCEPT_CODE": "74474003",
+              "CONCEPT_ID": 192671,
+              "CONCEPT_NAME": "Gastrointestinal hemorrhage",
+              "DOMAIN_ID": "Condition",
+              "INVALID_REASON": "V",
+              "INVALID_REASON_CAPTION": "Valid",
+              "STANDARD_CONCEPT": "S",
+              "STANDARD_CONCEPT_CAPTION": "Standard",
+              "VOCABULARY_ID": "SNOMED"
+            },
+            "includeDescendants": true
+          }
+        ]
+      }
+    }
+  ],
+  "PrimaryCriteria": {
+    "CriteriaList": [
+      {
+        "ConditionOccurrence": {
+          "CodesetId": 0
+        }
+      }
+    ],
+    "ObservationWindow": {
+      "PriorDays": 0,
+      "PostDays": 0
+    },
+    "PrimaryCriteriaLimit": {
+      "Type": "All"
+    }
+  },
+  "QualifiedLimit": {
+    "Type": "First"
+  },
+  "ExpressionLimit": {
+    "Type": "First"
+  },
+  "InclusionRules": [
+    {
+      "name": "Male",
+      "expression": {
+        "Type": "ALL",
+        "CriteriaList": [],
+        "DemographicCriteriaList": [
+          {
+            "Gender": [
+              {
+                "CONCEPT_CODE": "M",
+                "CONCEPT_ID": 8507,
+                "CONCEPT_NAME": "MALE",
+                "DOMAIN_ID": "Gender",
+                "INVALID_REASON_CAPTION": "Unknown",
+                "STANDARD_CONCEPT_CAPTION": "Unknown",
+                "VOCABULARY_ID": "Gender"
+              }
+            ]
+          }
+        ],
+        "Groups": []
+      }
+    },
+    {
+      "name": "30 days prior observation",
+      "expression": {
+        "Type": "ALL",
+        "CriteriaList": [
+          {
+            "Criteria": {
+              "ObservationPeriod": {}
+            },
+            "StartWindow": {
+              "Start": {
+                "Coeff": -1
+              },
+              "End": {
+                "Days": 30,
+                "Coeff": -1
+              },
+              "UseEventEnd": false
+            },
+            "EndWindow": {
+              "Start": {
+                "Days": 0,
+                "Coeff": 1
+              },
+              "End": {
+                "Coeff": 1
+              },
+              "UseEventEnd": true
+            },
+            "Occurrence": {
+              "Type": 2,
+              "Count": 1
+            }
+          }
+        ],
+        "DemographicCriteriaList": [],
+        "Groups": []
+      }
+    }
+  ],
+  "CensoringCriteria": [],
+  "CollapseSettings": {
+    "CollapseType": "ERA",
+    "EraPad": 0
+  },
+  "CensorWindow": {},
+  "cdmVersionRange": ">=5.0.0"
+}