From d211696551d902489876e460ff32299a1473b930 Mon Sep 17 00:00:00 2001
From: Bill Riehl <wjriehl@lbl.gov>
Date: Thu, 19 Dec 2024 12:13:58 -0500
Subject: [PATCH] fix dts manifest / other json mapping

---
 .../conf/supported_apps_w_extensions.json     | 32 ++++++++++---------
 .../autodetect/GenerateMappings.py            |  4 ++-
 staging_service/autodetect/Mappings.py        |  4 +++
 3 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/deployment/conf/supported_apps_w_extensions.json b/deployment/conf/supported_apps_w_extensions.json
index a4649424..47af9b64 100644
--- a/deployment/conf/supported_apps_w_extensions.json
+++ b/deployment/conf/supported_apps_w_extensions.json
@@ -121,8 +121,7 @@
       "csv",
       "tsv",
       "xls",
-      "xlsx",
-      "json"
+      "xlsx"
     ],
     "media": [
       "tsv",
@@ -149,6 +148,9 @@
     ],
     "escher_map": [
       "json"
+    ],
+    "dts_manifest": [
+      "json"
     ]
   },
   "types": {
@@ -1102,31 +1104,31 @@
         }
       ]
     },
-    "json": {
+    "smbl": {
       "file_ext_type": [
-        "JSON"
+        "SBML"
       ],
       "mappings": [
         {
-          "id": "import_specification",
-          "title": "Import Specification",
-          "app_weight": 1
-        },
-        {
-          "id": "escher_map",
-          "title": "EscherMap",
+          "id": "fba_model",
+          "title": "FBA Model",
           "app_weight": 1
         }
       ]
     },
-    "smbl": {
+    "json": {
       "file_ext_type": [
-        "SBML"
+        "JSON"
       ],
       "mappings": [
         {
-          "id": "fba_model",
-          "title": "FBA Model",
+          "id": "escher_map",
+          "title": "EscherMap",
+          "app_weight": 1
+        },
+        {
+          "id": "dts_manifest",
+          "title": "Data Transfer Service Manifest",
           "app_weight": 1
         }
       ]
diff --git a/staging_service/autodetect/GenerateMappings.py b/staging_service/autodetect/GenerateMappings.py
index 4d2287f7..62e7cc1e 100644
--- a/staging_service/autodetect/GenerateMappings.py
+++ b/staging_service/autodetect/GenerateMappings.py
@@ -50,6 +50,7 @@
     ZIP,
     assembly_id,
     decompress_id,
+    dts_manifest,
     escher_map_id,
     expression_matrix_id,
     extension_to_file_format_mapping,
@@ -90,6 +91,7 @@
     phenotype_set_id: "Phenotype Set",
     escher_map_id: "EscherMap",
     import_specification: "Import Specification",
+    dts_manifest: "Data Transfer Service Manifest"
 }
 
 file_format_to_app_mapping = {}
@@ -129,7 +131,7 @@
     fba_model_id,
     import_specification,
 ]
-file_format_to_app_mapping[JSON] = [escher_map_id, import_specification]
+file_format_to_app_mapping[JSON] = [escher_map_id, dts_manifest]
 file_format_to_app_mapping[SBML] = [fba_model_id]
 
 app_id_to_extensions = defaultdict(list)
diff --git a/staging_service/autodetect/Mappings.py b/staging_service/autodetect/Mappings.py
index af08e54c..a063eb33 100644
--- a/staging_service/autodetect/Mappings.py
+++ b/staging_service/autodetect/Mappings.py
@@ -51,6 +51,10 @@
 # import_specification is not a "real" data type, but rather tells the narrative that the
 # file contains specifications for how to load one or more other staging area files.
 import_specification = "import_specification"
+# dts_manifest is also not a real data type, but functions like import_specification as
+# it tells the narrative that the file has specs for loading other staging area files
+# that came from the Data Transfer Service, and that this manifest follows that spec.
+dts_manifest = "dts_manifest"
 decompress_id = "decompress"
 metabolic_annotations_id = "metabolic_annotation"
 metabolic_annotations_bulk_id = "metabolic_annotation_bulk"