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|
* 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
|
