Resolved conflict

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