fix silliness around dts manifest mapping

README.md

@@ -49,6 +49,16 @@ gzip, bzip2, md5sum, head, tail, wc
 
 in the docker container all of these should be available
 
+## Updating importer mapping types
+The types returned by the `importer_mappings` endpoint (see [Get Importer Mappings](#get-importer-mappings) below)
+are generated by the `GenerateMappings.py` script here: `staging_service/autodetect/GenerateMappings.py`. 
+Running this script will build the `supported_apps_w_extensions.json` file that should be placed in the
+`deployment/conf` directory.
+
+To add new mappings, update the `GenerateMappings.py` script. New file types and object types should be added
+to the `staging_service.autodetect.Mappings` module and included from there. See `GenerateMappings.py` 
+docstrings for more details.
+
 ## API
 
 all paths should be specified treating the user's home directory as root

deployment/conf/supported_apps_w_extensions.json

@@ -1102,34 +1102,34 @@
         }
       ]
     },
-    "smbl": {
+    "json": {
       "file_ext_type": [
-        "SBML"
+        "JSON"
       ],
       "mappings": [
         {
-          "id": "fba_model",
-          "title": "FBA Model",
+          "id": "import_specification",
+          "title": "Import Specification",
+          "app_weight": 1
+        },
+        {
+          "id": "escher_map",
+          "title": "EscherMap",
           "app_weight": 1
         }
       ]
     },
-    "json": {
+    "smbl": {
       "file_ext_type": [
-        "JSON"
+        "SBML"
       ],
       "mappings": [
         {
-          "id": "escher_map",
-          "title": "EscherMap",
-          "app_weight": 1
-        },
-        {
-          "id": "import_specification",
-          "title": "Import Specification",
+          "id": "fba_model",
+          "title": "FBA Model",
           "app_weight": 1
         }
       ]
     }
   }
-}
+}

staging_service/app.py

@@ -12,7 +12,7 @@
 
 from .app_error_formatter import format_import_spec_errors
 from .auth2Client import KBaseAuth2
-from .autodetect.Mappings import CSV, EXCEL, TSV, DTS_MANIFEST
+from .autodetect.Mappings import CSV, EXCEL, TSV, JSON
 from .AutoDetectUtils import AutoDetectUtils
 from .globus import assert_globusid_exists, is_globusid
 from .import_specifications.file_parser import (
@@ -48,7 +48,7 @@
     CSV: parse_csv,
     TSV: parse_tsv,
     EXCEL: parse_excel,
-    DTS_MANIFEST: parse_dts_manifest,
+    JSON: parse_dts_manifest,
 }
 
 _IMPSPEC_FILE_TO_WRITER = {

staging_service/autodetect/GenerateMappings.py

@@ -23,6 +23,15 @@
 * Note: We should serve the generated content from memory
 * Note: This doesn't handle if we want to have different output types based on file extensions
   feeding into the same app
+
+Adding new file types and app ids:
+* file types and app ids should be added to staging_service.autodetect.Mappings
+* file types should be all upper-case and represent the file suffix.
+* app ids should be in snake_case, and represent either an object import type, or some
+  internal application to be run on selection (i.e. decompress or import specification).
+* app ids that map to actual object import maps should match the app ids in the narrative
+  interface configuration here:
+  https://github.com/kbase/narrative/blob/main/kbase-extension/static/kbase/config/staging_upload.json
 """
 
 from collections import defaultdict
@@ -120,7 +129,7 @@
     fba_model_id,
     import_specification,
 ]
-file_format_to_app_mapping[JSON] = [escher_map_id]
+file_format_to_app_mapping[JSON] = [escher_map_id, import_specification]
 file_format_to_app_mapping[SBML] = [fba_model_id]
 
 app_id_to_extensions = defaultdict(list)

staging_service/autodetect/Mappings.py

@@ -7,9 +7,6 @@
 EXCEL = "EXCEL"
 ZIP = "CompressedFileFormatArchive"
 
-# Data Transfer Service Manifest format (which is a specific JSON format)
-DTS_MANIFEST = "JSON"
-
 # BIOINFORMATICS FORMATS
 FASTA = "FASTA"
 FASTQ = "FASTQ"
@@ -103,7 +100,6 @@ def _add_gzip(extension_list):
     # ],
     TSV: ["tsv"],  # See Note 1 below
     CSV: ["csv"],  # See Note 1 below,
-    DTS_MANIFEST: ["json"],
     JSON: ["json"],
     EXCEL: ["xls", "xlsx"],  # See Note 1 below
     ZIP: ["zip", "tar", "tgz", "tar.gz", "7z", "gz", "gzip", "rar"],