From 54818e009f19363687dcf169bbeeff14cf64971c Mon Sep 17 00:00:00 2001
From: Aakash Aanegola <aakash.aanegola@gmail.com>
Date: Fri, 18 Apr 2025 15:53:22 -0400
Subject: [PATCH 1/3] loaded cxr table; buggy dicom

---
 inst/extdata/config/concept-dict.R    | 32 ++++++++++++++
 inst/extdata/config/concept-dict.json | 28 ++++++++++++
 inst/extdata/config/data-sources.R    | 27 ++++++++++--
 inst/extdata/config/data-sources.json | 63 +++++++++++++++++++++++++++
 4 files changed, 147 insertions(+), 3 deletions(-)

diff --git a/inst/extdata/config/concept-dict.R b/inst/extdata/config/concept-dict.R
index c8d15cb6..4820f8e3 100644
--- a/inst/extdata/config/concept-dict.R
+++ b/inst/extdata/config/concept-dict.R
@@ -3322,6 +3322,38 @@ cfg <- list(
       )
     ),
     class = c("unt_cncpt", "num_cncpt")
+  ),
+  viewposition = list(
+    levels = c("frontal", "lateral", "decubitus", "oblique", "special", "unknown"),
+    class = "fct_cncpt",
+    description = "Grouped X-ray view positions",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(
+          table = "cxrmetadata",
+          val_var = "viewposition",
+          callback = "apply_map(
+            c(
+              'PA' = 'frontal', 'AP' = 'frontal', 'AP AXIAL' = 'frontal',
+              'LATERAL' = 'lateral', 'LL' = 'lateral', 'XTABLE LATERAL' = 'lateral',
+              'PA LLD' = 'decubitus', 'AP LLD' = 'decubitus', 'AP RLD' = 'decubitus', 'PA RLD' = 'decubitus',
+              'LAO' = 'oblique', 'RAO' = 'oblique', 'LPO' = 'oblique',
+              'SWIMMERS' = 'special'
+            )
+          )",
+          class = "col_itm"
+        )
+      )
+    )
+  ),
+  study_id = list(
+    description = "unique identifier for the subject",
+    sources = list(
+      miiv = list(
+        list(table = "cxrmetadata", val_var = "study_id", class = "col_itm")
+      )
+    )
   )
 )
 
diff --git a/inst/extdata/config/concept-dict.json b/inst/extdata/config/concept-dict.json
index 1c8ea243..e1b215cc 100644
--- a/inst/extdata/config/concept-dict.json
+++ b/inst/extdata/config/concept-dict.json
@@ -5999,6 +5999,18 @@
       ]
     }
   },
+  "study_id": {
+    "description": "unique identifier for the subject",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrmetadata",
+          "val_var": "study_id",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "supp_o2": {
     "concepts": ["vent_ind", "fio2"],
     "description": "supplemental oxygen",
@@ -6624,6 +6636,22 @@
       ]
     }
   },
+  "viewposition": {
+    "levels": ["frontal", "lateral", "decubitus", "oblique", "special", "unknown"],
+    "class": "fct_cncpt",
+    "description": "Grouped X-ray view positions",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrmetadata",
+          "val_var": "viewposition",
+          "callback": "apply_map(\n            c(\n              'PA' = 'frontal', 'AP' = 'frontal', 'AP AXIAL' = 'frontal',\n              'LATERAL' = 'lateral', 'LL' = 'lateral', 'XTABLE LATERAL' = 'lateral',\n              'PA LLD' = 'decubitus', 'AP LLD' = 'decubitus', 'AP RLD' = 'decubitus', 'PA RLD' = 'decubitus',\n              'LAO' = 'oblique', 'RAO' = 'oblique', 'LPO' = 'oblique',\n              'SWIMMERS' = 'special'\n            )\n          )",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "wbc": {
     "unit": ["K/uL", "G/l"],
     "min": 0,
diff --git a/inst/extdata/config/data-sources.R b/inst/extdata/config/data-sources.R
index fcf5963d..7ff483c2 100644
--- a/inst/extdata/config/data-sources.R
+++ b/inst/extdata/config/data-sources.R
@@ -1226,6 +1226,19 @@ miiv_tbl_cfg <- function() {
       statusdescription = list(spec = "col_character"),
       originalamount = list(spec = "col_double"),
       originalrate = list(spec = "col_double")
+    ),
+    cxrmetadata = list(
+      dicom_id = list(spec = "col_character"),
+      subject_id = list(spec = "col_integer"),
+      study_id = list(spec = "col_integer"),
+      performedprocedurestepdescription = list(spec = "col_character"),
+      viewposition = list(spec = "col_character"),
+      rows = list(spec = "col_integer"),
+      columns = list(spec = "col_integer"),
+      studytime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
+      procedurecodesequence_codemeaning = list(spec = "col_character"),
+      viewcodesequence_codemeaning = list(spec = "col_character"),
+      patientorientationcodesequence_codemeaning = list(spec = "col_character")
     )
   )
 
@@ -1346,6 +1359,10 @@ miiv_tbl_cfg <- function() {
       index_var = "starttime",
       val_var = "rate",
       unit_var = "rateuom"
+    ),
+    cxrmetadata = list(
+      id_var = "dicom_id",
+      index_var = "studytime"
     )
   )
 
@@ -1387,7 +1404,8 @@ miiv_tbl_cfg <- function() {
     omr = 6439169L,
     caregiver = 15468L,
     provider = 40508L,
-    ingredientevents = 11627821L
+    ingredientevents = 11627821L,
+    cxrmetadata = 377110L
   )
 
   files <- c(
@@ -1421,7 +1439,8 @@ miiv_tbl_cfg <- function() {
     omr = "hosp/omr.csv.gz",
     caregiver = "icu/caregiver.csv.gz",
     provider = "hosp/provider.csv.gz",
-    ingredientevents = "icu/ingredientevents.csv.gz"
+    ingredientevents = "icu/ingredientevents.csv.gz",
+    cxrmetadata = "cxr/cxrmetadata.csv.gz"
   )
 
   part <- list(
@@ -1739,7 +1758,9 @@ cfg <- list(
       hadm = list(id = "hadm_id", position = 2L, start = "admittime",
                   end = "dischtime", table = "admissions"),
       icustay = list(id = "stay_id", position = 3L, start = "intime",
-                     end = "outtime", table = "icustays")
+                     end = "outtime", table = "icustays"),
+      dicom_id = list(id = "dicom_id", position = 4L, start = "studytime", 
+                      end = "studytime", table = "cxrmetadata")
     ),
     tables = miiv_tbl_cfg()
   ),
diff --git a/inst/extdata/config/data-sources.json b/inst/extdata/config/data-sources.json
index e31b3232..66267d9d 100644
--- a/inst/extdata/config/data-sources.json
+++ b/inst/extdata/config/data-sources.json
@@ -7061,6 +7061,13 @@
         "start": "intime",
         "end": "outtime",
         "table": "icustays"
+      },
+      "dicom_id": {
+        "id": "dicom_id",
+        "position": 4,
+        "start": "studytime",
+        "end": "studytime",
+        "table": "cxrmetadata"
       }
     },
     "tables": {
@@ -8832,6 +8839,62 @@
             "spec": "col_double"
           }
         }
+      },
+      "cxrmetadata": {
+        "files": "cxr/cxrmetadata.csv.gz",
+        "defaults": {
+          "id_var": "dicom_id",
+          "index_var": "studytime",
+          "time_vars": "studytime"
+        },
+        "num_rows": 377110,
+        "cols": {
+          "dicom_id": {
+            "name": "dicom_id",
+            "spec": "col_character"
+          },
+          "subject_id": {
+            "name": "subject_id",
+            "spec": "col_integer"
+          },
+          "study_id": {
+            "name": "study_id",
+            "spec": "col_integer"
+          },
+          "performedprocedurestepdescription": {
+            "name": "performedprocedurestepdescription",
+            "spec": "col_character"
+          },
+          "viewposition": {
+            "name": "viewposition",
+            "spec": "col_character"
+          },
+          "rows": {
+            "name": "rows",
+            "spec": "col_integer"
+          },
+          "columns": {
+            "name": "columns",
+            "spec": "col_integer"
+          },
+          "studytime": {
+            "name": "studytime",
+            "spec": "col_datetime",
+            "format": "%Y-%m-%d %H:%M:%S"
+          },
+          "procedurecodesequence_codemeaning": {
+            "name": "procedurecodesequence_codemeaning",
+            "spec": "col_character"
+          },
+          "viewcodesequence_codemeaning": {
+            "name": "viewcodesequence_codemeaning",
+            "spec": "col_character"
+          },
+          "patientorientationcodesequence_codemeaning": {
+            "name": "patientorientationcodesequence_codemeaning",
+            "spec": "col_character"
+          }
+        }
       }
     }
   },

From e03e75050d6a506edcaba341aaa2926c5471106d Mon Sep 17 00:00:00 2001
From: Aakash Aanegola <aakash.aanegola@gmail.com>
Date: Fri, 18 Apr 2025 17:01:11 -0400
Subject: [PATCH 2/3] chexpert concepts

---
 inst/extdata/config/concept-dict.R    | 127 ++++++++++++++++++
 inst/extdata/config/concept-dict.json | 183 ++++++++++++++++++++++++++
 inst/extdata/config/data-sources.R    |  29 +++-
 inst/extdata/config/data-sources.json |  80 +++++++++++
 4 files changed, 417 insertions(+), 2 deletions(-)

diff --git a/inst/extdata/config/concept-dict.R b/inst/extdata/config/concept-dict.R
index 4820f8e3..685050b6 100644
--- a/inst/extdata/config/concept-dict.R
+++ b/inst/extdata/config/concept-dict.R
@@ -3349,11 +3349,138 @@ cfg <- list(
   ),
   study_id = list(
     description = "unique identifier for the subject",
+    category = "imaging",
     sources = list(
       miiv = list(
         list(table = "cxrmetadata", val_var = "study_id", class = "col_itm")
       )
     )
+  ),
+  atelectasis = list(
+    description = "Atelectasis",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "atelectasis", class = "col_itm")
+      )
+    )
+  ),
+  cardiomegaly = list(
+    description = "Cardiomegaly",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "cardiomegaly", class = "col_itm")
+      )
+    )
+  ),
+  consolidation = list(
+    description = "Consolidation",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "consolidation", class = "col_itm")
+      )
+    )
+  ),
+  edema = list(
+    description = "Edema",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "edema", class = "col_itm")
+      )
+    )
+  ),
+  enlarged_cardiomediastinum = list(
+    description = "Enlarged Cardiomediastinum",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "enlarged_cardiomediastinum", class = "col_itm")
+      )
+    )
+  ),
+  fracture = list(
+    description = "Fracture",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "fracture", class = "col_itm")
+      )
+    )
+  ),
+  lung_lesion = list(
+    description = "Lung Lesion",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "lung_lesion", class = "col_itm")
+      )
+    )
+  ),
+  lung_opacity = list(
+    description = "Lung Opacity",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "lung_opacity", class = "col_itm")
+      )
+    )
+  ),
+  no_finding = list(
+    description = "If all other chexpert labels are 0 or -1, no finding is 1",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "no_finding", class = "col_itm")
+      )
+    )
+  ),
+  pleural_effusion = list(
+    description = "Pleural Effusion",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "pleural_effusion", class = "col_itm")
+      )
+    )
+  ),
+  pleural_other = list(
+    description = "Pleural Other",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "pleural_other", class = "col_itm")
+      )
+    )
+  ),
+  pneumonia = list(
+    description = "Pneumonia",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "pneumonia", class = "col_itm")
+      )
+    )
+  ),
+  pneumothorax = list(
+    description = "Pneumothorax",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "pneumothorax", class = "col_itm")
+      )
+    )
+  ),
+  support_devices = list(
+    description = "Support Devices",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "support_devices", class = "col_itm")
+      )
+    )
   )
 )
 
diff --git a/inst/extdata/config/concept-dict.json b/inst/extdata/config/concept-dict.json
index e1b215cc..d4d11d00 100644
--- a/inst/extdata/config/concept-dict.json
+++ b/inst/extdata/config/concept-dict.json
@@ -592,6 +592,19 @@
       ]
     }
   },
+  "atelectasis": {
+    "description": "Atelectasis",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "atelectasis",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "avpu": {
     "concepts": "gcs",
     "description": "AVPU scale",
@@ -1215,6 +1228,19 @@
       ]
     }
   },
+  "cardiomegaly": {
+    "description": "Cardiomegaly",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "cardiomegaly",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "ck": {
     "unit": ["IU/L", "U/l"],
     "min": 0,
@@ -1414,6 +1440,19 @@
       ]
     }
   },
+  "consolidation": {
+    "description": "Consolidation",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "consolidation",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "cort": {
     "class": "lgl_cncpt",
     "description": "corticosteroids",
@@ -2228,6 +2267,19 @@
     "callback": "vaso60",
     "class": "rec_cncpt"
   },
+  "edema": {
+    "description": "Edema",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "edema",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "egcs": {
     "min": 1,
     "max": 4,
@@ -2294,6 +2346,19 @@
       ]
     }
   },
+  "enlarged_cardiomediastinum": {
+    "description": "Enlarged Cardiomediastinum",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "enlarged_cardiomediastinum",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "eos": {
     "unit": "%",
     "min": 0,
@@ -2888,6 +2953,19 @@
       ]
     }
   },
+  "fracture": {
+    "description": "Fracture",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "fracture",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "gcs": {
     "concepts": ["egcs", "mgcs", "vgcs", "tgcs", "ett_gcs"],
     "description": "Glasgow coma scale (non-sedated)",
@@ -3690,6 +3768,32 @@
       ]
     }
   },
+  "lung_lesion": {
+    "description": "Lung Lesion",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "lung_lesion",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
+  "lung_opacity": {
+    "description": "Lung Opacity",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "lung_opacity",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "lymph": {
     "unit": "%",
     "min": 0,
@@ -4437,6 +4541,19 @@
     "callback": "news_score",
     "class": "rec_cncpt"
   },
+  "no_finding": {
+    "description": "If all other chexpert labels are 0 or -1, no finding is 1",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "no_finding",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "norepi_dur": {
     "description": "norepinephrine duration",
     "category": "medications",
@@ -5052,6 +5169,32 @@
       ]
     }
   },
+  "pleural_effusion": {
+    "description": "Pleural Effusion",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "pleural_effusion",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
+  "pleural_other": {
+    "description": "Pleural Other",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "pleural_other",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "plt": {
     "unit": ["K/uL", "G/l"],
     "min": 5,
@@ -5119,6 +5262,32 @@
       ]
     }
   },
+  "pneumonia": {
+    "description": "Pneumonia",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "pneumonia",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
+  "pneumothorax": {
+    "description": "Pneumothorax",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "pneumothorax",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "po2": {
     "unit": ["mmHg", "mm Hg"],
     "min": 40,
@@ -6001,6 +6170,7 @@
   },
   "study_id": {
     "description": "unique identifier for the subject",
+    "category": "imaging",
     "sources": {
       "miiv": [
         {
@@ -6019,6 +6189,19 @@
     "callback": "supp_o2",
     "class": "rec_cncpt"
   },
+  "support_devices": {
+    "description": "Support Devices",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrchexpert",
+          "val_var": "support_devices",
+          "class": "col_itm"
+        }
+      ]
+    }
+  },
   "susp_inf": {
     "concepts": ["abx", "samp"],
     "description": "suspected infection",
diff --git a/inst/extdata/config/data-sources.R b/inst/extdata/config/data-sources.R
index 7ff483c2..f097d023 100644
--- a/inst/extdata/config/data-sources.R
+++ b/inst/extdata/config/data-sources.R
@@ -1239,6 +1239,25 @@ miiv_tbl_cfg <- function() {
       procedurecodesequence_codemeaning = list(spec = "col_character"),
       viewcodesequence_codemeaning = list(spec = "col_character"),
       patientorientationcodesequence_codemeaning = list(spec = "col_character")
+    ),
+    cxrchexpert = list(
+      subject_id = list(spec = "col_integer"),
+      study_id = list(spec = "col_integer"),
+      atelectasis = list(spec = "col_double"),
+      cardiomegaly = list(spec = "col_double"),
+      consolidation = list(spec = "col_double"),
+      edema = list(spec = "col_double"),
+      enlarged_cardiomediastinum = list(spec = "col_double"),
+      fracture = list(spec = "col_double"),
+      lung_lesion = list(spec = "col_double"),
+      lung_opacity = list(spec = "col_double"),
+      no_finding = list(spec = "col_double"),
+      pleural_effusion = list(spec = "col_double"),
+      pleural_other = list(spec = "col_double"),
+      pneumonia = list(spec = "col_double"),
+      pneumothorax = list(spec = "col_double"),
+      support_devices = list(spec = "col_double"),
+      studytime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S")
     )
   )
 
@@ -1363,6 +1382,10 @@ miiv_tbl_cfg <- function() {
     cxrmetadata = list(
       id_var = "dicom_id",
       index_var = "studytime"
+    ),
+    cxrchexpert = list(
+      id_var = "subject_id",
+      index_var = "studytime"
     )
   )
 
@@ -1405,7 +1428,8 @@ miiv_tbl_cfg <- function() {
     caregiver = 15468L,
     provider = 40508L,
     ingredientevents = 11627821L,
-    cxrmetadata = 377110L
+    cxrmetadata = 377110L,
+    cxrchexpert = 227827L
   )
 
   files <- c(
@@ -1440,7 +1464,8 @@ miiv_tbl_cfg <- function() {
     caregiver = "icu/caregiver.csv.gz",
     provider = "hosp/provider.csv.gz",
     ingredientevents = "icu/ingredientevents.csv.gz",
-    cxrmetadata = "cxr/cxrmetadata.csv.gz"
+    cxrmetadata = "cxr/cxrmetadata.csv.gz",
+    cxrchexpert = "cxr/cxrchexpert.csv.gz"
   )
 
   part <- list(
diff --git a/inst/extdata/config/data-sources.json b/inst/extdata/config/data-sources.json
index 66267d9d..f43d86fe 100644
--- a/inst/extdata/config/data-sources.json
+++ b/inst/extdata/config/data-sources.json
@@ -8895,6 +8895,86 @@
             "spec": "col_character"
           }
         }
+      },
+      "cxrchexpert": {
+        "files": "cxr/cxrchexpert.csv.gz",
+        "defaults": {
+          "id_var": "subject_id",
+          "index_var": "studytime",
+          "time_vars": "studytime"
+        },
+        "num_rows": 227827,
+        "cols": {
+          "subject_id": {
+            "name": "subject_id",
+            "spec": "col_integer"
+          },
+          "study_id": {
+            "name": "study_id",
+            "spec": "col_integer"
+          },
+          "atelectasis": {
+            "name": "atelectasis",
+            "spec": "col_double"
+          },
+          "cardiomegaly": {
+            "name": "cardiomegaly",
+            "spec": "col_double"
+          },
+          "consolidation": {
+            "name": "consolidation",
+            "spec": "col_double"
+          },
+          "edema": {
+            "name": "edema",
+            "spec": "col_double"
+          },
+          "enlarged_cardiomediastinum": {
+            "name": "enlarged_cardiomediastinum",
+            "spec": "col_double"
+          },
+          "fracture": {
+            "name": "fracture",
+            "spec": "col_double"
+          },
+          "lung_lesion": {
+            "name": "lung_lesion",
+            "spec": "col_double"
+          },
+          "lung_opacity": {
+            "name": "lung_opacity",
+            "spec": "col_double"
+          },
+          "no_finding": {
+            "name": "no_finding",
+            "spec": "col_double"
+          },
+          "pleural_effusion": {
+            "name": "pleural_effusion",
+            "spec": "col_double"
+          },
+          "pleural_other": {
+            "name": "pleural_other",
+            "spec": "col_double"
+          },
+          "pneumonia": {
+            "name": "pneumonia",
+            "spec": "col_double"
+          },
+          "pneumothorax": {
+            "name": "pneumothorax",
+            "spec": "col_double"
+          },
+          "support_devices": {
+            "name": "support_devices",
+            "spec": "col_double"
+          },
+          "studytime": {
+            "name": "studytime",
+            "spec": "col_datetime",
+            "format": "%Y-%m-%d %H:%M:%S"
+          }
+        }
       }
     }
   },

From fe9e07a91ebb906caca291fd514f22983cef9b55 Mon Sep 17 00:00:00 2001
From: Aakash Aanegola <aakash.aanegola@gmail.com>
Date: Sun, 20 Apr 2025 14:28:37 -0400
Subject: [PATCH 3/3] removing dicom ID

---
 inst/extdata/config/concept-dict.R    | 10 ++++++++++
 inst/extdata/config/concept-dict.json | 14 ++++++++++++++
 inst/extdata/config/data-sources.R    |  6 ++----
 inst/extdata/config/data-sources.json |  9 +--------
 4 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/inst/extdata/config/concept-dict.R b/inst/extdata/config/concept-dict.R
index 685050b6..f56d6f4c 100644
--- a/inst/extdata/config/concept-dict.R
+++ b/inst/extdata/config/concept-dict.R
@@ -3356,6 +3356,16 @@ cfg <- list(
       )
     )
   ),
+  dicom_id = list(
+    description = "unique identifier for the image",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrmetadata", sub_var = "dicom_id", regex = "^.*$",
+          class = "rgx_itm")
+      )
+    )
+  ),
   atelectasis = list(
     description = "Atelectasis",
     category = "imaging",
diff --git a/inst/extdata/config/concept-dict.json b/inst/extdata/config/concept-dict.json
index d4d11d00..ffe02d9c 100644
--- a/inst/extdata/config/concept-dict.json
+++ b/inst/extdata/config/concept-dict.json
@@ -1871,6 +1871,20 @@
     },
     "class": ["unt_cncpt", "num_cncpt"]
   },
+  "dicom_id": {
+    "description": "unique identifier for the image",
+    "category": "imaging",
+    "sources": {
+      "miiv": [
+        {
+          "table": "cxrmetadata",
+          "sub_var": "dicom_id",
+          "regex": "^.*$",
+          "class": "rgx_itm"
+        }
+      ]
+    }
+  },
   "dobu_dur": {
     "description": "dobutamine duration",
     "category": "medications",
diff --git a/inst/extdata/config/data-sources.R b/inst/extdata/config/data-sources.R
index f097d023..bfaff167 100644
--- a/inst/extdata/config/data-sources.R
+++ b/inst/extdata/config/data-sources.R
@@ -1380,7 +1380,7 @@ miiv_tbl_cfg <- function() {
       unit_var = "rateuom"
     ),
     cxrmetadata = list(
-      id_var = "dicom_id",
+      id_var = "subject_id",
       index_var = "studytime"
     ),
     cxrchexpert = list(
@@ -1783,9 +1783,7 @@ cfg <- list(
       hadm = list(id = "hadm_id", position = 2L, start = "admittime",
                   end = "dischtime", table = "admissions"),
       icustay = list(id = "stay_id", position = 3L, start = "intime",
-                     end = "outtime", table = "icustays"),
-      dicom_id = list(id = "dicom_id", position = 4L, start = "studytime", 
-                      end = "studytime", table = "cxrmetadata")
+                     end = "outtime", table = "icustays")
     ),
     tables = miiv_tbl_cfg()
   ),
diff --git a/inst/extdata/config/data-sources.json b/inst/extdata/config/data-sources.json
index f43d86fe..07d645dd 100644
--- a/inst/extdata/config/data-sources.json
+++ b/inst/extdata/config/data-sources.json
@@ -7061,13 +7061,6 @@
         "start": "intime",
         "end": "outtime",
         "table": "icustays"
-      },
-      "dicom_id": {
-        "id": "dicom_id",
-        "position": 4,
-        "start": "studytime",
-        "end": "studytime",
-        "table": "cxrmetadata"
       }
     },
     "tables": {
@@ -8843,7 +8836,7 @@
       "cxrmetadata": {
         "files": "cxr/cxrmetadata.csv.gz",
         "defaults": {
-          "id_var": "dicom_id",
+          "id_var": "subject_id",
           "index_var": "studytime",
           "time_vars": "studytime"
         },