From 02fcfa615afb99186a5cd94bd79724327a903b1c Mon Sep 17 00:00:00 2001
From: slebras <8630227+slebras@users.noreply.github.com>
Date: Thu, 19 Sep 2019 16:21:09 -0700
Subject: [PATCH] adding default_search_alias, versioned ama indices, and
 "group_alias" field for creating aggregated aliases. (#7)

* adding group aliases and ama_vesion index mappings

* adding more support for ama fields

* adding default_search field

* changing default_search to default_search_alias

* consolidating alias fields

* Update config.yaml
---
 config.yaml | 114 ++++++++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 97 insertions(+), 17 deletions(-)

diff --git a/config.yaml b/config.yaml
index f2af853..e989bc9 100644
--- a/config.yaml
+++ b/config.yaml
@@ -1,4 +1,3 @@
-
 # genome features index name
 genome_features_current_index_name: genome_features
 
@@ -55,6 +54,7 @@ ws_subobjects:
   - "pangenome_orthologfamily:1"
   - "attribute_mapping:1"
   - "annotated_metagenome_assembly_features:1"
+  - "annotated_metagenome_assembly_features_version:1"
 
 # Generic, global type mappings. These can be reused in any index mappings below.
 global_mappings:
@@ -94,24 +94,62 @@ latest_versions:
   indexing_errors: "indexing_errors:1"
   annotated_metagenome_assembly: "annotated_metagenome_assembly:1"
   annotated_metagenome_assembly_features: "annotated_metagenome_assembly_features:1"
+  annotated_metagenome_assembly_version: "annotated_metagenome_assembly_version:1"
+  annotated_metagenome_assembly_features_version: "annotated_metagenome_assembly_features_version:1"
+
 
-# Aliases from any index to any name
+# map from alias to contained indices
 aliases:
-  "narrative:1": narrative
-  "reads:1": reads
-  "assembly:1": assembly
-  "genome:1": genome
-  "genome_features:2": genome_features
-  "pangenome:1": pangenome
-  "pangenome_orthologfamily:1": pangenome_orthologfamily
-  "taxon:1": taxon
-  "tree:1": tree
-  "matrix:1": matrix
-  "attribute_mapping:1": attribute_mapping
-  "genomeset:1": genomeset
-  "indexing_errors:1": indexing_errors
-  "annotated_metagenome_assembly:1": annotated_metagenome_assembly
-  "annotated_metagenome_assembly_features:1": annotated_metagenome_assembly_features
+  default_search:
+    - "narrative:1"
+    - "reads:1"
+    - "assembly:1"
+    - "genome:1"
+    - "pangenome:1"
+    - "pangenome_orthologfamily:1"
+    - "taxon:1"
+    - "tree:1"
+    - "matrix:1"
+    - "attribute_mapping:1"
+    - "genomeset:1"
+    - "indexing_errors:1"
+    - "annotated_metagenome_assembly:1"
+    - "annotated_metagenome_assembly_features:1"
+  narrative:
+    - "narrative:1"
+  reads:
+    - "reads:1"
+  assembly:
+    - "assembly:1"
+  genome:
+    - "genome:1"
+  genome_features:
+    - "genome_features:2"
+  pangenome:
+    - "pangenome:1"
+  pangenome_orthologfamily:
+    - "pangenome_orthologfamily:1"
+  taxon:
+    - "taxon:1"
+  tree:
+    - "tree:1"
+  matrix:
+    - "matrix:1"
+  attribute_mapping:
+    - "attribute_mapping:1"
+  genomeset:
+    - "genomeset:1"
+  indexing_errors:
+    - "indexing_errors:1"
+  annotated_metagenome_assembly:
+    - "annotated_metagenome_assembly:1"
+  annotated_metagenome_assembly_features:
+    - "annotated_metagenome_assembly_features:1"
+  annotated_metagenome_assembly_version:
+    - "annotated_metagenome_assembly_version:1"
+  annotated_metagenome_assembly_features_version:
+    - "annotated_metagenome_assembly_features_version:1"
+
 
 # All ES type mappings
 mappings:
@@ -321,6 +359,48 @@ mappings:
       annotated_metagenome_assembly_num_contigs: {type: integer}
       annotated_metagenome_assembly_gc_content: {type: float}
 
+  "annotated_metagenome_assembly_version:1":
+    global_mappings: [ws_auth, ws_object]
+    properties:
+      size: {type: integer}
+      source_id: {type: keyword}
+      source: {type: keyword}
+      gc_content: {type: float}
+      warnings: {type: keyword}
+      num_contigs: {type: integer}
+      mean_contig_length: {type: float}
+      external_source_origination_date: {type: keyword}
+      original_source_file_name: {type: keyword}
+      environment: {type: keyword}
+      num_features: {type: integer}
+      publication_authors: {type: keyword}
+      publication_titles: {type: keyword}
+      molecule_type: {type: keyword}
+      assembly_ref: {type: keyword}
+      notes: {type: text}
+
+  "annotated_metagenome_assembly_features_version:1":
+    global_mappings: [ws_subobject, ws_auth, ws_object]
+    properties:
+      id: {type: keyword}
+      type: {type: keyword}
+      size: {type: integer}
+      contig_ids: {type: keyword}
+      starts: {type: integer}
+      strands: {type: keyword}
+      stops: {type: integer}
+      functions: {type: keyword}
+      functional_descriptions: {type: keyword}
+      warnings: {type: keyword}
+      parent_gene: {type: keyword}
+      inference_data: {type: keyword}
+      dna_sequence: {type: text}
+      gc_content: {type: float}
+      annotated_metagenome_assembly_size: {type: integer}
+      annotated_metagenome_assembly_num_features: {type: integer}
+      annotated_metagenome_assembly_num_contigs: {type: integer}
+      annotated_metagenome_assembly_gc_content: {type: float}
+
   "indexing_errors:1":
     properties:
       evtype: {type: keyword}