GeneNetwork uses elasticsearch (ES) for all things considered 'state'. One example is user collections, another is user management.

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

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"

ES provides support for checking its health:

curl -XGET http://localhost:9200/_cluster/health?pretty=true

{
  "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
}

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_inbytes" : 46892794 }, "fielddata" : { "memory_size" : "0b", "memory_sizeinbytes" : 0, "evictions" : 0 }, "query_cache" : { "memory_size" : "0b", "memory_sizeinbytes" : 0, "total_count" : 0, "hit_count" : 0, "miss_count" : 0, "cache_size" : 0, "cache_count" : 0, "evictions" : 0 }, "completion" : { "size" : "0b", "size_inbytes" : 0 }, "segments" : { "count" : 24, "memory" : "157.3kb", "memory_inbytes" : 161112, "terms_memory" : "122.6kb", "terms_{memoryinbytes}" : 125569, "stored_fieldsmemory" : "15.3kb", "stored_{fieldsmemoryinbytes}" : 15728, "term_{vectorsmemory}" : "0b", "term_{vectorsmemoryinbytes}" : 0, "norms_memory" : "10.8kb", "norms_{memoryinbytes}" : 11136, "points_memory" : "111b", "points_{memoryinbytes}" : 111, "doc_valuesmemory" : "8.3kb", "doc_{valuesmemoryinbytes}" : 8568, "index_writermemory" : "0b", "index_{writermemoryinbytes}" : 0, "version_mapmemory" : "0b", "version_{mapmemoryinbytes}" : 0, "fixed_bitset" : "0b", "fixed_{bitsetmemoryinbytes}" : 0, "max_{unsafeautoidtimestamp}" : -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_inbytes" : 135189286912, "free" : "48.3gb", "free_inbytes" : 51922628608, "used" : "77.5gb", "used_inbytes" : 83266658304, "free_percent" : 38, "used_percent" : 62 } }, "process" : { "cpu" : { "percent" : 0 }, "open_{filedescriptors}" : { "min" : 415, "max" : 415, "avg" : 415 } }, "jvm" : { "max_uptime" : "1.9d", "max_{uptimeinmillis}" : 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_usedinbytes" : 1214872032, "heap_max" : "23.8gb", "heap_maxinbytes" : 25656426496 }, "threads" : 110 }, "fs" : { "total" : "786.4gb", "total_inbytes" : 844400918528, "free" : "246.5gb", "free_inbytes" : 264688160768, "available" : "206.5gb", "available_inbytes" : 221771468800 }, "plugins" : [ ], "network_types" : { "transport_types" : { "netty4" : 1 }, "http_types" : { "netty4" : 1 } } } } #+BEGIN_SRC json