diff options
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/README.org | 2 | ||||
| -rw-r--r-- | doc/elasticsearch.org | 247 |
2 files changed, 0 insertions, 249 deletions
diff --git a/doc/README.org b/doc/README.org index 1236016e..8839aefc 100644 --- a/doc/README.org +++ b/doc/README.org @@ -81,14 +81,12 @@ GeneNetwork2 with : source ~/opt/guix-pull/etc/profile : git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics : cd ~/guix-bioinformatics -: git pull : env GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2 you probably also need guix-past (the upstream channel for older packages): : git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past : cd ~/guix-past -: git pull : env GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2 ignore the warnings. Guix should install the software without trying diff --git a/doc/elasticsearch.org b/doc/elasticsearch.org deleted file mode 100644 index 864a8363..00000000 --- a/doc/elasticsearch.org +++ /dev/null @@ -1,247 +0,0 @@ -* 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 |