Merge github.com:genenetwork/genenetwork2 into acenteno

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