Merge branch 'develop' into rjchallis/issue44

.bumpversion.cfg

@@ -1,8 +1,9 @@
 [bumpversion]
-current_version = 2.0.5
+current_version = 2.0.7
 commit = True
 tag = True
-message = 'Bump version: {current_version} → {new_version}'
+tag_name = {new_version}
+message = "Bump version: {current_version} → {new_version}"
 
 [bumpversion:file:setup.py]
 search = version="{current_version}"
@@ -13,8 +14,8 @@ search = version = "{current_version}"
 replace = version = "{new_version}"
 
 [bumpversion:file:README.rst]
-search = v{current_version}.
-replace = v{new_version}.
+search = {current_version}.
+replace = {new_version}.
 
 [bumpversion:file:docs/conf.py]
 search = version = release = "{current_version}"

README.rst

@@ -42,9 +42,9 @@ GenomeHubs
     :alt: Conda platforms
     :target: https://anaconda.org/tolkit/genomehubs
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/genomehubs/genomehubs/v2.0.5.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/genomehubs/genomehubs/2.0.7.svg
     :alt: Commits since latest release
-    :target: https://github.com/genomehubs/genomehubs/compare/v2.0.5...main
+    :target: https://github.com/genomehubs/genomehubs/compare/2.0.7...main
 
 .. |license| image:: https://anaconda.org/tolkit/genomehubs/badges/license.svg
     :alt: MIT License

conda-recipe/meta.yaml

@@ -1,12 +1,12 @@
 {% set name = "genomehubs" %}
-{% set version = "2.0.5" %}
+{% set version = "2.0.7" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  git_rev: v{{ version }}
+  git_rev: {{ version }}
   git_url: https://github.com/genomehubs/genomehubs.git
 
 build:

docs/conf.py

@@ -29,7 +29,7 @@
     version = release = get_distribution("genomehubs").version
 except Exception:
     traceback.print_exc()
-    version = release = "2.0.5"
+    version = release = "2.0.7"
 
 pygments_style = "trac"
 templates_path = ["."]

scripts/conda_build.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-VERSION=2.0.5
+VERSION=2.0.7
 
 case $(uname | tr '[:upper:]' '[:lower:]') in
   linux*)

setup.py

@@ -25,7 +25,7 @@ def read(*names, **kwargs):
 
 setup(
     name="genomehubs",  # Required
-    version="2.0.5",
+    version="2.0.7",
     description="GenomeHubs",  # Optional
     long_description="%s\n%s"
     % (

src/genomehubs/lib/attributes.py

@@ -12,42 +12,56 @@
 LOGGER = tolog.logger(__name__)
 
 
-def index_template(opts):
+def index_template(opts, *, index_type="attribute"):
     """Index template (includes name, mapping and types)."""
-    parts = ["attributes", opts["hub-name"], opts["hub-version"]]
+    parts = ["%ss" % index_type, opts["hub-name"], opts["hub-version"]]
     template = index_templator(parts, opts)
     return template
 
 
-def stream_attributes(group, attributes):
+def stream_attributes(group, attributes, *, index_type="attribute"):
     """Stream attributes for indexing."""
     for name, obj in attributes.items():
         ret = {"group": group, "name": name}
         for prop, value in obj.items():
             if not prop.startswith("taxon_"):
                 ret.update({prop: value})
-        yield "attribute-%s-%s" % (group, name), ret
+        yield "%s-%s-%s" % (index_type, group, name), ret
 
 
-def index(es, group, attributes, opts):
-    """Index a set of attributes."""
-    LOGGER.info("Indexing attributes")
-    template = index_template(opts)
-    stream = stream_attributes(group, attributes)
+def index(es, group, attributes, opts, *, index_type="attribute"):
+    """Index a set of attributes or names."""
+    LOGGER.info("Indexing %s" % index_type)
+    template = index_template(opts, index_type=index_type)
+    stream = stream_attributes(group, attributes, index_type=index_type)
     return template, stream
 
 
 def index_types(es, types_name, types, opts):
     """Index types into Elasticsearch."""
-    if "attributes" not in types:
-        return
-    if "defaults" in types:
-        for key, value in types["attributes"].items():
-            value = {**types["defaults"]["attributes"], **value}
-            types["attributes"][key] = value
-    template, stream = index(es, types_name, types["attributes"], opts)
-    load_mapping(es, template["name"], template["mapping"])
-    index_stream(es, template["index_name"], stream)
+    if "attributes" in types:
+        if "defaults" in types and "attributes" in types["defaults"]:
+            for key, value in types["attributes"].items():
+                value = {**types["defaults"]["attributes"], **value}
+                types["attributes"][key] = value
+        template, stream = index(
+            es, types_name, types["attributes"], opts, index_type="attribute"
+        )
+        load_mapping(es, template["name"], template["mapping"])
+        index_stream(es, template["index_name"], stream)
+    if "taxon_names" in types:
+        if "defaults" in types and "taxon_names" in types["defaults"]:
+            for key, value in types["names"].items():
+                value = {
+                    **types["defaults"]["taxon_names"],
+                    **value,
+                }
+                types["taxon_names"][key] = value
+        template, stream = index(
+            es, types_name, types["taxon_names"], opts, index_type="identifier"
+        )
+        load_mapping(es, template["name"], template["mapping"])
+        index_stream(es, template["index_name"], stream)
 
 
 def fetch_types(es, types_name, opts):

src/genomehubs/lib/btk.py

@@ -87,7 +87,7 @@ def describe_btk_files(meta):
     return files
 
 
-def btk_parser(_params, opts):
+def btk_parser(_params, opts, *args, **kwargs):
     """Parse BlobToolKit assemblies."""
     parsed = []
     analyses = []