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Diffstat (limited to 'doc/elasticsearch.org')
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1 files changed, 247 insertions, 0 deletions
diff --git a/doc/elasticsearch.org b/doc/elasticsearch.org new file mode 100644 index 00000000..864a8363 --- /dev/null +++ b/doc/elasticsearch.org @@ -0,0 +1,247 @@ +* Elasticsearch + +** Introduction + +GeneNetwork uses elasticsearch (ES) for all things considered +'state'. One example is user collections, another is user management. + +** Example + +To get the right environment, first you can get a python REPL with something like + +: env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ../etc/default_settings.py -cli python + +(make sure to use the correct GN2_PROFILE!) + +Next try + +#+BEGIN_SRC python + +from elasticsearch import Elasticsearch, TransportError + +es = Elasticsearch([{ "host": 'localhost', "port": '9200' }]) + +# Dump all data + +es.search("*") + +# To fetch an E-mail record from the users index + +record = es.search( + index = 'users', doc_type = 'local', body = { + "query": { "match": { "email_address": "myname@email.com" } } + }) + +# It is also possible to do wild card matching + +q = { "query": { "wildcard" : { "full_name" : "pjot*" } }} +es.search(index = 'users', doc_type = 'local', body = q) + +# To get elements from that record: + +record['hits']['hits'][0][u'_source']['full_name'] +u'Pjotr' + +record['hits']['hits'][0][u'_source']['email_address'] +u"myname@email.com" + +#+END_SRC + +** Health + +ES provides support for checking its health: + +: curl -XGET http://localhost:9200/_cluster/health?pretty=true + +#+BEGIN_SRC json + + + { + "cluster_name" : "asgard", + "status" : "yellow", + "timed_out" : false, + "number_of_nodes" : 1, + "number_of_data_nodes" : 1, + "active_primary_shards" : 5, + "active_shards" : 5, + "relocating_shards" : 0, + "initializing_shards" : 0, + "unassigned_shards" : 5 + } + +#+END_SRC + +Yellow means just one instance is running (no worries). + +To get full cluster info + +: curl -XGET "localhost:9200/_cluster/stats?human&pretty" + +#+BEGIN_SRC json +{ + "_nodes" : { + "total" : 1, + "successful" : 1, + "failed" : 0 + }, + "cluster_name" : "elasticsearch", + "timestamp" : 1529050366452, + "status" : "yellow", + "indices" : { + "count" : 3, + "shards" : { + "total" : 15, + "primaries" : 15, + "replication" : 0.0, + "index" : { + "shards" : { + "min" : 5, + "max" : 5, + "avg" : 5.0 + }, + "primaries" : { + "min" : 5, + "max" : 5, + "avg" : 5.0 + }, + "replication" : { + "min" : 0.0, + "max" : 0.0, + "avg" : 0.0 + } + } + }, + "docs" : { + "count" : 14579, + "deleted" : 0 + }, + "store" : { + "size" : "44.7mb", + "size_in_bytes" : 46892794 + }, + "fielddata" : { + "memory_size" : "0b", + "memory_size_in_bytes" : 0, + "evictions" : 0 + }, + "query_cache" : { + "memory_size" : "0b", + "memory_size_in_bytes" : 0, + "total_count" : 0, + "hit_count" : 0, + "miss_count" : 0, + "cache_size" : 0, + "cache_count" : 0, + "evictions" : 0 + }, + "completion" : { + "size" : "0b", + "size_in_bytes" : 0 + }, + "segments" : { + "count" : 24, + "memory" : "157.3kb", + "memory_in_bytes" : 161112, + "terms_memory" : "122.6kb", + "terms_memory_in_bytes" : 125569, + "stored_fields_memory" : "15.3kb", + "stored_fields_memory_in_bytes" : 15728, + "term_vectors_memory" : "0b", + "term_vectors_memory_in_bytes" : 0, + "norms_memory" : "10.8kb", + "norms_memory_in_bytes" : 11136, + "points_memory" : "111b", + "points_memory_in_bytes" : 111, + "doc_values_memory" : "8.3kb", + "doc_values_memory_in_bytes" : 8568, + "index_writer_memory" : "0b", + "index_writer_memory_in_bytes" : 0, + "version_map_memory" : "0b", + "version_map_memory_in_bytes" : 0, + "fixed_bit_set" : "0b", + "fixed_bit_set_memory_in_bytes" : 0, + "max_unsafe_auto_id_timestamp" : -1, + "file_sizes" : { } + } + }, + "nodes" : { + "count" : { + "total" : 1, + "data" : 1, + "coordinating_only" : 0, + "master" : 1, + "ingest" : 1 + }, + "versions" : [ + "6.2.1" + ], + "os" : { + "available_processors" : 16, + "allocated_processors" : 16, + "names" : [ + { + "name" : "Linux", + "count" : 1 + } + ], + "mem" : { + "total" : "125.9gb", + "total_in_bytes" : 135189286912, + "free" : "48.3gb", + "free_in_bytes" : 51922628608, + "used" : "77.5gb", + "used_in_bytes" : 83266658304, + "free_percent" : 38, + "used_percent" : 62 + } + }, + "process" : { + "cpu" : { + "percent" : 0 + }, + "open_file_descriptors" : { + "min" : 415, + "max" : 415, + "avg" : 415 + } + }, + "jvm" : { + "max_uptime" : "1.9d", + "max_uptime_in_millis" : 165800616, + "versions" : [ + { + "version" : "9.0.4", + "vm_name" : "OpenJDK 64-Bit Server VM", + "vm_version" : "9.0.4+11", + "vm_vendor" : "Oracle Corporation", + "count" : 1 + } + ], + "mem" : { + "heap_used" : "1.1gb", + "heap_used_in_bytes" : 1214872032, + "heap_max" : "23.8gb", + "heap_max_in_bytes" : 25656426496 + }, + "threads" : 110 + }, + "fs" : { + "total" : "786.4gb", + "total_in_bytes" : 844400918528, + "free" : "246.5gb", + "free_in_bytes" : 264688160768, + "available" : "206.5gb", + "available_in_bytes" : 221771468800 + }, + "plugins" : [ ], + "network_types" : { + "transport_types" : { + "netty4" : 1 + }, + "http_types" : { + "netty4" : 1 + } + } + } +} +#+BEGIN_SRC json |