EnaReceiptToMarsTest, validInput & invalidInput

elixir-europe · Nov 19, 2024 · 225f4dc · 225f4dc
1 parent d9aa6ab
commit 225f4dc
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diff --git a/...vices/isajson-ena/src/test/java/com/elixir/biohackaton/ISAToSRA/EnaReceiptToMarsTest.java b/...vices/isajson-ena/src/test/java/com/elixir/biohackaton/ISAToSRA/EnaReceiptToMarsTest.java
@@ -1,8 +1,8 @@
 /** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA;
 
+import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
 import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
-import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.*;
 import com.elixir.biohackaton.ISAToSRA.sra.model.Receipt;
 import com.elixir.biohackaton.ISAToSRA.sra.service.MarsReceiptService;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -15,29 +15,47 @@
 class EnaReceiptToMarsTest {
 
   @Test
-  void convertToMars() {
-    try {
+  void convertToMars_validInput() {
+    String enaReceiptFilePath = "../../test-data/ena-receipt.json";
+    String marsReceiptPath = "../../test-data/mars-ena-receipt.json";
+    convertToMars(enaReceiptFilePath, marsReceiptPath);
+  }
+
+  @Test
+  void convertToMars_invalidInput() {
+    String enaReceiptFilePath = "../../test-data/ena-receipt-invalid.json";
+    String marsReceiptPath = "../../test-data/mars-ena-receipt-invalid.json";
+    convertToMars(enaReceiptFilePath, marsReceiptPath);
+  }
 
-      // Reading Inputs
-      String enaReceiptFilePath = "../../test-data/ena-receipt.json";
-      String isaJsonFilePath = "../../test-data/biosamples-input-isa.json";
-      String receiptFile = Files.readString(new File(enaReceiptFilePath).toPath());
-      String isaJsonFile = Files.readString(new File(isaJsonFilePath).toPath());
+  void convertToMars(final String enaReceiptFilePath, final String marsReceiptPath) {
+    ObjectMapper jsonMapper = new ObjectMapper();
+    MarsReceiptService marsReceiptService = new MarsReceiptService();
+    try {
+      try {
+        // Reading Inputs
+        String receiptFile = Files.readString(new File(enaReceiptFilePath).toPath());
+        String isaJsonFilePath = "../../test-data/biosamples-modified-isa.json";
+        String isaJsonFile = Files.readString(new File(isaJsonFilePath).toPath());
 
-      // Mapping inputs to the proper objects
-      ObjectMapper jsonMapper = new ObjectMapper();
-      Receipt receipt = jsonMapper.readValue(receiptFile, Receipt.class);
-      IsaJson isaJson = jsonMapper.readValue(isaJsonFile, IsaJson.class);
+        // Mapping inputs to the proper objects
+        Receipt receipt = jsonMapper.readValue(receiptFile, Receipt.class);
+        IsaJson isaJson = jsonMapper.readValue(isaJsonFile, IsaJson.class);
 
-      // Converting ENA receipt to MARS receipt
-      MarsReceiptService marsReceiptService = new MarsReceiptService();
-      MarsReceipt marsReceipt = marsReceiptService.convertReceiptToMars(receipt, isaJson);
+        // Converting ENA receipt to MARS receipt
+        marsReceiptService.convertReceiptToMars(receipt, isaJson);
+      } catch (MarsReceiptException e) {
+        marsReceiptService.setMarsReceiptErrors(e.getError());
+      } catch (Exception e) {
+        marsReceiptService.setMarsReceiptErrors(e.getMessage());
+      }
 
       // Saving the result as a Json file
-      String marsReceiptPath = "../../test-data/mars-ena-receipt.json";
-      Files.write(new File(marsReceiptPath).toPath(), jsonMapper.writeValueAsBytes(marsReceipt));
-    } catch (Exception ex) {
-      System.console().printf("%s", ex);
+      Files.write(
+          new File(marsReceiptPath).toPath(),
+          jsonMapper.writeValueAsBytes(marsReceiptService.getMarsReceipt()));
+    } catch (Exception e) {
+      e.printStackTrace();
     }
   }
 }
diff --git a/test-data/ena-receipt-invalid.json b/test-data/ena-receipt-invalid.json
@@ -0,0 +1,58 @@
+{
+    "success": true,
+    "receiptDate": "2023-11-16T10:44:41.618Z",
+    "experiments": [
+        {
+            "alias": "#other_material/332-0.5578006304577448",
+            "accession": "ERX13332762",
+            "status": "PRIVATE"
+        },
+        {
+            "alias": "#other_material/333-0.5578006304577448",
+            "accession": "ERX13332763",
+            "status": "PRIVATE"
+        }
+    ],
+    "runs": [
+        {
+            "alias": "#assay/18_20_21-0.5578006304577448",
+            "accession": "ERR13930853",
+            "status": "PRIVATE"
+        }
+    ],
+    "studies":[
+        {
+            "alias":"Arabidopsis thaliana-0.5578006304577448",
+            "status":"PRIVATE",
+            "holdUntilDate": "2023-01-01Z",
+            "externalAccession": {
+                "id": "PRJEB82366",
+                "db": "Project"
+            }
+        }
+    ],
+    "projects": [
+        {
+            "alias": "Bob's investigation-0.5578006304577448",
+            "accession": "PRJEB82365",
+            "status": "PRIVATE",
+            "holdUntilDate": "2023-01-01Z",
+            "externalAccession": {
+                "id": "ERP166076",
+                "db": "study"
+            }
+        }
+    ],
+    "submission": {
+        "alias": "SUBMISSION-07-11-2024-17:00:52:797",
+        "accession": "ERA30928821"
+    },
+    "messages": {
+        "info": [
+            "All objects in this submission are set to private status (HOLD)."
+        ]
+    },
+    "actions": [
+        "ADD"
+    ]
+}
diff --git a/test-data/mars-ena-receipt-invalid.json b/test-data/mars-ena-receipt-invalid.json
@@ -0,0 +1,80 @@
+{
+    "targetRepository": "ena",
+    "errors": [
+        {
+            "type": "INVALID_METADATA",
+            "message": "ENA receipt: Accession number of Arabidopsis thaliana-0.5578006304577448 is NULL"
+        }
+    ],
+    "info": [
+        {
+            "message": "All objects in this submission are set to private status (HOLD)."
+        }
+    ],
+    "accessions": [
+        {
+            "value": "ERX13332762",
+            "path": [
+                {
+                    "key": "investigation"
+                },
+                {
+                    "key": "studies",
+                    "where": {
+                        "key": "title",
+                        "value": "Arabidopsis thaliana"
+                    }
+                },
+                {
+                    "key": "assays",
+                    "where": {
+                        "key": "@id",
+                        "value": "#assay/18_20_21"
+                    }
+                },
+                {
+                    "key": "materials"
+                },
+                {
+                    "key": "otherMaterials",
+                    "where": {
+                        "key": "@id",
+                        "value": "#other_material/332"
+                    }
+                }
+            ]
+        },
+        {
+            "value": "ERX13332763",
+            "path": [
+                {
+                    "key": "investigation"
+                },
+                {
+                    "key": "studies",
+                    "where": {
+                        "key": "title",
+                        "value": "Arabidopsis thaliana"
+                    }
+                },
+                {
+                    "key": "assays",
+                    "where": {
+                        "key": "@id",
+                        "value": "#assay/18_20_21"
+                    }
+                },
+                {
+                    "key": "materials"
+                },
+                {
+                    "key": "otherMaterials",
+                    "where": {
+                        "key": "@id",
+                        "value": "#other_material/333"
+                    }
+                }
+            ]
+        }
+    ]
+}
diff --git a/test-data/mars-ena-receipt.json b/test-data/mars-ena-receipt.json
@@ -1,5 +1,5 @@
 {
-    "targetRepository": "ena.embl",
+    "targetRepository": "ena",
     "errors": [],
     "info": [
         {
@@ -22,31 +22,6 @@
                 }
             ]
         },
-        {
-            "value": "ERS27605861",
-            "path": [
-                {
-                    "key": "investigation"
-                },
-                {
-                    "key": "studies",
-                    "where": {
-                        "key": "title",
-                        "value": "Arabidopsis thaliana"
-                    }
-                },
-                {
-                    "key": "materials"
-                },
-                {
-                    "key": "samples",
-                    "where": {
-                        "key": "@id",
-                        "value": "#sample/331"
-                    }
-                }
-            ]
-        },
         {
             "value": "ERX9223136",
             "path": [