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authorzsloan2018-10-01 16:16:56 +0000
committerzsloan2018-10-01 16:16:56 +0000
commitdabf5838abe99d1a394db344b2bee65a1e460cec (patch)
tree10cb7c550db2d9f0ecd69aadeb36af926b3d0805
parenta3365dae23f204e489939d3defc55edc1b4872d8 (diff)
parentb2a7886df64073042a89b466cc103f9bbf06827a (diff)
downloadgenenetwork2-dabf5838abe99d1a394db344b2bee65a1e460cec.tar.gz
Resolved conflict
-rw-r--r--doc/README.org2
-rw-r--r--doc/elasticsearch.org206
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py24
3 files changed, 223 insertions, 9 deletions
diff --git a/doc/README.org b/doc/README.org
index f290480d..cc141098 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -259,7 +259,7 @@ if that works run genenetwork after setting SQL_URI to something like
* Running ElasticSearch
-In order to start up elasticsearch, use the following command:
+In order to start up elasticsearch, change user to "elasticsearch" and use the following command:
: env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch
diff --git a/doc/elasticsearch.org b/doc/elasticsearch.org
index 18adfc8b..864a8363 100644
--- a/doc/elasticsearch.org
+++ b/doc/elasticsearch.org
@@ -1,5 +1,12 @@
* 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
@@ -39,3 +46,202 @@ 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
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index c6f5e1d5..769688ff 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -3,11 +3,15 @@ import os, math, string, random, json
from base import webqtlConfig
from base.trait import GeneralTrait
from base.data_set import create_dataset
-from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR
+from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, WEBSERVER_MODE
import utility.logger
logger = utility.logger.getLogger(__name__ )
+GEMMAOPTS = "-debug"
+if WEBSERVER_MODE == 'PROD':
+ GEMMAOPTS = "-no-check"
+
def run_gemma(this_dataset, samples, vals, covariates, use_loco, maf=0.01):
"""Generates p-values for each marker using GEMMA"""
@@ -34,7 +38,7 @@ def run_gemma(this_dataset, samples, vals, covariates, use_loco, maf=0.01):
if use_loco == "True":
k_output_filename = this_dataset.group.name + "_K_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
- generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -gk -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+ generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
genofile_name,
flat_files('genotype/bimbam'),
genofile_name,
@@ -45,7 +49,7 @@ def run_gemma(this_dataset, samples, vals, covariates, use_loco, maf=0.01):
logger.debug("k_command:" + generate_k_command)
os.system(generate_k_command)
- gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (TEMPDIR,
+ gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- '+GEMMAOPTS+' -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (TEMPDIR,
k_output_filename,
flat_files('genotype/bimbam'),
genofile_name,
@@ -54,20 +58,24 @@ def run_gemma(this_dataset, samples, vals, covariates, use_loco, maf=0.01):
gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
if covariates != "":
- gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
+ gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf 0.1 > %s/gn2/%s.json' % (flat_files('mapping'),
this_dataset.group.name,
flat_files('genotype/bimbam'),
genofile_name,
TEMPDIR,
gwa_output_filename)
else:
- gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+ gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
genofile_name,
TEMPDIR,
gwa_output_filename)
else:
+<<<<<<< HEAD
gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'),
+=======
+ gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('genotype/bimbam'),
+>>>>>>> b2a7886df64073042a89b466cc103f9bbf06827a
genofile_name,
flat_files('genotype/bimbam'),
genofile_name,
@@ -78,12 +86,12 @@ def run_gemma(this_dataset, samples, vals, covariates, use_loco, maf=0.01):
maf)
if covariates != "":
- gemma_command += ' -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('mapping'),
+ gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'),
this_dataset.group.name,
webqtlConfig.GENERATED_IMAGE_DIR,
genofile_name)
else:
- gemma_command += ' -outdir %s -debug -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
+ gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
genofile_name)
logger.debug("gemma_command:" + gemma_command)
@@ -219,4 +227,4 @@ def parse_loco_output(this_dataset, gwa_output_filename):
included_markers.append(line.split("\t")[1])
p_values.append(float(line.split("\t")[9]))
- return marker_obs \ No newline at end of file
+ return marker_obs