KPMP-6545: load biopsy tracking long table

data_management/main.py

@@ -43,6 +43,9 @@ def upsert_new_spectrack_specimens(self):
     def load_biopsy_tracking(self):
         return self.tableau.load_biopsy_tracking()
 
+    def load_biopsy_tracking_long(self):
+        return self.tableau.load_biopsy_tracking_long()
+
     def load_data_manager_data(self):
         return self.tableau.load_data_manager_data()
 
@@ -88,6 +91,7 @@ def update_biomarker_tracking_redcap_ids(self):
         if args.action == "insert" or args.action == "update":
             records_modified = main.load_biopsy_tracking()
             records_modified = records_modified + main.load_data_manager_data()
+            records_modified = records_modified + main.load_biopsy_tracking_long()
 
     if "records_modified" in locals():
         logger.info(f"{records_modified} records modified")

data_management/services/dlu_management.py

@@ -191,6 +191,12 @@ def get_biopsy_tracking(self):
         )
         return result
 
+    def get_biopsy_tracking_long(self):
+        result = self.db.get_data(
+            "select * from biopsy_tracking_long_v"
+        )
+        return result
+
     def get_data_manager_data(self):
         result = self.db.get_data(
             """

data_management/services/tableau.py

@@ -27,7 +27,17 @@ def load_biopsy_tracking(self):
         query = "INSERT INTO biopsy_tracking (redcap_record_id, `Whole Slide Images`, `Single-nucleus RNA-Seq Status`, `Single-nucleus RNA-Seq Specimen ID`, `ATAC RNA-seq Status`, `ATAC RNA-seq Specimen ID`, `Single-cell RNA-Seq Status`, `Single-cell RNA-Seq Specimen ID`, `Regional Transcriptomics Status`, `Regional Transcriptomics Specimen ID`, `Bulk total/mRNA Experiment Status`, `Bulk total/mRNA Experiment Specimen ID`, `3D Tissue Imaging and Cytometry Experiment Status`, `3D Tissue Imaging and Cytometry Experiment Specimen ID`, `Regional Proteomics Experiment Status`, `Regional Proteomics Specimen ID`, `Spatial Metabolomics Experiment Status`, `Spatial Metabolomics Specimen ID`, `Spatial Lipidomics Experiment Status`, `Spatial Lipidomics Specimen ID`, `Spatial N-glycomics Experiment Status`, `Spatial N-glycomics Specimen ID`, `Spatial Transcriptomics Experiment Status`, `Spatial Transcriptomics Specimen ID`, `CODEX (IU) Experiment Status`, `CODEX (IU) Specimen ID`, `CODEX (UCSF) Experiment Status`, `CODEX (UCSF) Specimen ID`, `IMC Experiment Status`, `IMC Specimen ID`, `DNA Methyl-seq Experiment Status`, `DNA Methyl-seq Specimen ID`, `CUT & RUN Experiment Status`, `CUT & RUN Specimen ID`, `Metabolon Timed Urine - UHPLC MS-MS Experiment Status`, `Metabolon Timed Urine - UHPLC MS-MS Specimen ID`, `Metabolon Plasma EDTA - UHPLC MS-MS Experiment Status`, `Metabolon Plasma EDTA - UHPLC MS-MS Specimen ID`, `MSDQ120 Spot Urine Biomarker Status`, `MSDQ120 Spot Urine Biomarker Specimen ID`, `MSDQ120 Plasma EDTA Biomarker Status`, `MSDQ120 Plasma EDTA Biomarker Specimen ID`, `Litholink Timed Urine - BCAU680 - Status`, `Litholink Timed Urine - BCAU680 - Specimen ID`, `Stool Microbiome - Qaigen NextEra Status`, `Stool Microbiome - Qaigen NextEra Specimen ID`, `Clinical Chemistry Spot/Timed Urine - BCAU5812 Status`, `Clinical Chemistry Spot/Timed Urine - BCAU5812 Specimen ID`, `Clinical Chemistry Serum - BCAU5812 Status`, `Clinical Chemistry Serum - BCAU5812 Specimen ID`, `SomaScan Plasma EDTA - Status`, `SomaScan Plasma EDTA - Specimen ID`, `SomaScan Spot Urine - Status`, `SomaScan Spot Urine - Specimen ID`, `Descriptor Scoring (TIV)`, `Segmentation/Features Data - Status`, `fMRI - Status`, `Retinal - Status`) VALUES(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)"
         records_modified = 0
         for result in bt_results:
-            insert_result = self.db_tableau.insert_data(query, tuple(result.values()))
+            self.db_tableau.insert_data(query, tuple(result.values()))
+            records_modified = records_modified + 1
+        return records_modified
+
+    def load_biopsy_tracking_long(self):
+        self.truncate_biopsy_tracking_long()
+        bt_results = self.dlu_management.get_biopsy_tracking_long()
+        query = "INSERT INTO biopsy_tracking_long(redcap_id, specimen_id, dlu_packageType, status) VALUES(%s, %s, %s, %s)"
+        records_modified = 0
+        for result in bt_results:
+            self.db_tableau.insert_data(query, tuple(result.values()))
             records_modified = records_modified + 1
         return records_modified
 
@@ -39,7 +49,7 @@ def load_data_manager_data(self):
         records_modified = 0
         for result in results:
             result["dlu_created"] = result["dlu_created"].strftime('%Y-%m-%d %H:%M:%S')
-            insert_result = self.db_tableau.insert_data(query, tuple(result.values()))
+            self.db_tableau.insert_data(query, tuple(result.values()))
             records_modified = records_modified + 1
         return records_modified
 

data_management/sql/biopsy_tracking_long.sql

@@ -0,0 +1,9 @@
+CREATE TABLE biopsy_tracking_long
+(
+    redcap_id       varchar(100) NULL,
+    specimen_id     varchar(100) NULL,
+    dlu_packageType varchar(100) NULL,
+    status          varchar(100) NULL
+) ENGINE=InnoDB
+DEFAULT CHARSET=latin1
+COLLATE=latin1_swedish_ci;