RE2022-272: Add a bulk version of genbank_to_genome in GFU (#208)

* add a bulk version of genbank_to_genome in GFU

.github/workflows/kb_sdk_test.yaml

@@ -63,4 +63,5 @@ jobs:
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true

GenomeFileUtil.spec

@@ -21,6 +21,8 @@ module GenomeFileUtil {
 
     /*
     genome_name - becomes the name of the object
+    workspace_id - the immutable, numeric ID of the target workspace. Always prefer
+        providing the ID over the name.
     workspace_name - the name of the workspace it gets saved to.
     source - Source of the file typically something like RefSeq or Ensembl
     taxon_ws_name - where the reference taxons are : ReferenceTaxons
@@ -42,6 +44,7 @@ module GenomeFileUtil {
     typedef structure {
         File file;
 
+        int workspace_id;
         string genome_name;
         string workspace_name;
 
@@ -65,6 +68,46 @@ module GenomeFileUtil {
     funcdef genbank_to_genome(GenbankToGenomeParams params)
                 returns (GenomeSaveResult result) authentication required;
 
+    typedef structure {
+        File file;
+        string genome_name;
+
+        string source;
+        string taxon_wsname;
+        string taxon_id;
+
+        string release;
+        string generate_ids_if_needed;
+        int    genetic_code;
+        string scientific_name;
+        usermeta metadata;
+        boolean generate_missing_genes;
+        string use_existing_assembly;
+    } GenbankToGenomeInput;
+
+    typedef structure {
+        int workspace_id;
+        list<GenbankToGenomeInput> inputs;
+    } GenbanksToGenomesParams;
+
+    typedef structure {
+        string genome_ref;
+        string assembly_ref;
+        string assembly_path;
+        Workspace.object_info assembly_info;
+        Workspace.object_info genome_info;
+    } GenbankToGenomeSaveResult;
+
+    /* Results for the genbanks_to_genomes function.
+        results - the results of the save operation in the same order as the input.
+    */
+    typedef structure {
+        list<GenbankToGenomeSaveResult> results;
+    } GenbanksToGenomesSaveResults;
+
+    funcdef genbanks_to_genomes(GenbanksToGenomesParams params)
+                returns (GenbanksToGenomesSaveResults results) authentication required;
+
     /*
         is_gtf - optional flag switching export to GTF format (default is 0,
             which means GFF)

RELEASE_NOTES.md

@@ -5,6 +5,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.11.7] - 2024-02-14
+
+### Added
+
+- The `genbanks_to_genomes` method was added to allow users to upload multiple
+genome objects at once
+
 ## [0.11.6] - 2022-01-29
 Fixed performance issue with FastaGFF impacting metagenome uploads
 

kbase.yml

@@ -8,7 +8,7 @@ service-language:
     python
 
 module-version:
-    0.11.6
+    0.11.7
 
 owners:
-    [jkbaumohl, tgu2]
+    [jkbaumohl, tgu2, sijiex]

lib/GenomeFileUtil/GenomeFileUtilServer.py

@@ -342,6 +342,10 @@ def __init__(self):
                              name='GenomeFileUtil.genbank_to_genome',
                              types=[dict])
         self.method_authentication['GenomeFileUtil.genbank_to_genome'] = 'required'  # noqa
+        self.rpc_service.add(impl_GenomeFileUtil.genbanks_to_genomes,
+                             name='GenomeFileUtil.genbanks_to_genomes',
+                             types=[dict])
+        self.method_authentication['GenomeFileUtil.genbanks_to_genomes'] = 'required'  # noqa
         self.rpc_service.add(impl_GenomeFileUtil.genome_to_gff,
                              name='GenomeFileUtil.genome_to_gff',
                              types=[dict])