Merge pull request #127 from refgenie/dev

v0.11.1

docs/changelog.md

@@ -2,6 +2,10 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.11.1] - 2021-06-01
+### Fixed
+- issue with missing `assets` section in `RefGenConf.list` method. This situation occured after setting genome identity for nonexistent genome
+
 ## [0.11.0] - 2021-04-27
 ### Added
 - `RefGenConf.populate` function to support `refgenie populate`

refgenconf/_version.py

@@ -1 +1 @@
-__version__ = "0.11.0"
+__version__ = "0.11.1"

refgenconf/refgenconf.py

@@ -326,6 +326,7 @@ def list(self, genome=None, order=None, include_tags=False):
                         ),
                     )
                     for g in refgens
+                    if CFG_ASSETS_KEY in self[CFG_GENOMES_KEY][g]
                 ]
             )
         self.run_plugins(POST_LIST_HOOK)
@@ -338,6 +339,7 @@ def list(self, genome=None, order=None, include_tags=False):
                     ),
                 )
                 for g in refgens
+                if CFG_ASSETS_KEY in self[CFG_GENOMES_KEY][g]
             ]
         )
 

tests/test_listing.py

@@ -27,6 +27,26 @@ def test_multiple_genomes(self, ro_rgc, all_genomes):
             ro_rgc.list().keys()
         )
 
+    def test_no_asset_section(self, ro_rgc):
+        """
+        Verify listing works even if the 'assets' section is missing in the config.
+        This situation may occur after setting genome identity for nonexistent genome.
+        """
+        # get the original genomes count
+        ori_genomes_count = len(ro_rgc.genomes)
+        # set test alias, which will create an empty genome section
+        ro_rgc.set_genome_alias(
+            genome="test_alias",
+            digest="test_digest",
+            create_genome=True,
+        )
+        # check if list works and skips the empty genome
+        assert len(ro_rgc.list().keys()) == ori_genomes_count
+        # clean up
+        ro_rgc.remove_genome_aliases(digest="test_digest")
+        with ro_rgc as r:
+            del r["genomes"]["test_digest"]
+
 
 class ListByGenomeTest:
     def test_returns_entire_mapping_when_no_genonome_specified(self, my_rgc):