ElasticSearch forgets my analyzer

create-index.sh

curl -XPUT 'http://localhost:9200/clinical_trials/' -d '{
    "analysis" : {
        "analyzer" : {
            "lowercase_keyword" : {
                "type" : "custom",
                "tokenizer" : "keyword",
                "filter" : ["lowercase", "trim"]
            }
        }
    }
}'

curl -XPUT 'http://localhost:9200/clinical_trials/trial/_mapping' -d '{
    "trial" : {
        "properties" : {
            "overall_status" : {
                "type" : "string",
                "analyzer" : "lowercase_keyword"
            },
            "phase" : {
                "type" : "string",
                "analyzer" : "lowercase_keyword"
            },
            "condition" : {
                "type" : "string",
                "analyzer" : "lowercase_keyword"
            },
            "gender" : {
                "type" : "string",
                "analyzer" : "lowercase_keyword"
            },
            "intervention" : {
                "properties" : {
                    "intervention_name" : {
                        "type" : "string",
                        "analyzer" : "lowercase_keyword"
                    },
                    "intervention_type" : {
                        "type" : "string",
                        "analyzer" : "lowercase_keyword"
                    }
                }
            },
            "location_countries" : {
                "properties" : {
                    "country" : {
                        "type" : "string",
                        "analyzer" : "lowercase_keyword"
                    }
                }
            },
            "eligibility" : {
                "properties" : {
                    "minimum_age_years" : {
                        "type" : "double"
                    },
                    "maximum_age_years" : {
                        "type" : "double"
                    }
                }
            },
            "intervention_filter": {
                "type" : "string",
                "analyzer" : "lowercase_keyword"
            }
        }
    }
}
'

elasticsearch.yml

##################### ElasticSearch Configuration Example #####################

# This file contains an overview of various configuration settings,
# targeted at operations staff. Application developers should
# consult the guide at <http://elasticsearch.org/guide>.
#
# The installation procedure is covered at
# <http://elasticsearch.org/guide/reference/setup/installation.html>.
#
# ElasticSearch comes with reasonable defaults for most settings,
# so you can try it out without bothering with configuration.
#
# Most of the time, these defaults are just fine for running a production
# cluster. If you're fine-tuning your cluster, or wondering about the
# effect of certain configuration option, please _do ask_ on the
# mailing list or IRC channel [http://elasticsearch.org/community].

# Any element in the configuration can be replaced with environment variables
# by placing them in ${...} notation. For example:
#
# node.rack: ${RACK_ENV_VAR}

# See <http://elasticsearch.org/guide/reference/setup/configuration.html>
# for information on supported formats and syntax for the configuration file.


################################### Cluster ###################################

# Cluster name identifies your cluster for auto-discovery. If you're running
# multiple clusters on the same network, make sure you're using unique names.
#
cluster.name: kevin-development


#################################### Node #####################################

# Node names are generated dynamically on startup, so you're relieved
# from configuring them manually. You can tie this node to a specific name:
#
# node.name: "Franz Kafka"

# Every node can be configured to allow or deny being eligible as the master,
# and to allow or deny to store the data.
#
# Allow this node to be eligible as a master node (enabled by default):
#
# node.master: true
#
# Allow this node to store data (enabled by default):
#
# node.data: true

# You can exploit these settings to design advanced cluster topologies.
#
# 1. You want this node to never become a master node, only to hold data.
#    This will be the "workhorse" of your cluster.
#
# node.master: false
# node.data: true
#
# 2. You want this node to only serve as a master: to not store any data and
#    to have free resources. This will be the "coordinator" of your cluster.
#
# node.master: true
# node.data: false
#
# 3. You want this node to be neither master nor data node, but
#    to act as a "search load balancer" (fetching data from nodes,
#    aggregating results, etc.)
#
# node.master: false
# node.data: false

# Use the Cluster Health API [http://localhost:9200/_cluster/health], the
# Node Info API [http://localhost:9200/_cluster/nodes] or GUI tools
# such as <http://github.com/lukas-vlcek/bigdesk> and
# <http://mobz.github.com/elasticsearch-head> to inspect the cluster state.

# A node can have generic attributes associated with it, which can later be used
# for customized shard allocation filtering, or allocation awareness. An attribute
# is a simple key value pair, similar to node.key: value, here is an example:
#
# node.rack: rack314

# By default, multiple nodes are allowed to start from the same installation location
# to disable it, set the following:
# node.max_local_storage_nodes: 1


#################################### Index ####################################

# You can set a number of options (such as shard/replica options, mapping
# or analyzer definitions, translog settings, ...) for indices globally,
# in this file.
#
# Note, that it makes more sense to configure index settings specifically for
# a certain index, either when creating it or by using the index templates API.
#
# See <http://elasticsearch.org/guide/reference/index-modules/> and
# <http://elasticsearch.org/guide/reference/api/admin-indices-create-index.html>
# for more information.

# Set the number of shards (splits) of an index (5 by default):
#
# index.number_of_shards: 5

# Set the number of replicas (additional copies) of an index (1 by default):
#
# index.number_of_replicas: 1

# Note, that for development on a local machine, with small indices, it usually
# makes sense to "disable" the distributed features:
#
# index.number_of_shards: 1
# index.number_of_replicas: 0

# These settings directly affect the performance of index and search operations
# in your cluster. Assuming you have enough machines to hold shards and
# replicas, the rule of thumb is:
#
# 1. Having more *shards* enhances the _indexing_ performance and allows to
#    _distribute_ a big index across machines.
# 2. Having more *replicas* enhances the _search_ performance and improves the
#    cluster _availability_.
#
# The "number_of_shards" is a one-time setting for an index.
#
# The "number_of_replicas" can be increased or decreased anytime,
# by using the Index Update Settings API.
#
# ElasticSearch takes care about load balancing, relocating, gathering the
# results from nodes, etc. Experiment with different settings to fine-tune
# your setup.

# Use the Index Status API (<http://localhost:9200/A/_status>) to inspect
# the index status.


#################################### Paths ####################################

# Path to directory containing configuration (this file and logging.yml):
#
# path.conf: /path/to/conf

# Path to directory where to store index data allocated for this node.
#
path.data: /data/search/
#
# Can optionally include more than one location, causing data to be striped across
# the locations (à la RAID 0) on a file level, favouring locations with most free
# space on creation. For example:
#
# path.data: /path/to/data1,/path/to/data2

# Path to temporary files:
#
# path.work: /path/to/work

# Path to log files:
#
# path.logs: /path/to/logs

# Path to where plugins are installed:
#
# path.plugins: /path/to/plugins


#################################### Plugin ###################################

# If a plugin listed here is not installed for current node, the node will not start.
#
# plugin.mandatory: mapper-attachments,lang-groovy


################################### Memory ####################################

# ElasticSearch performs poorly when JVM starts swapping: you should ensure that
# it _never_ swaps.
#
# Set this property to true to lock the memory:
#
# bootstrap.mlockall: true

# Make sure that the ES_MIN_MEM and ES_MAX_MEM environment variables are set
# to the same value, and that the machine has enough memory to allocate
# for ElasticSearch, leaving enough memory for the operating system itself.
#
# You should also make sure that the ElasticSearch process is allowed to lock
# the memory, eg. by using `ulimit -l unlimited`.


############################## Network And HTTP ###############################

# ElasticSearch, by default, binds itself to the 0.0.0.0 address, and listens
# on port [9200-9300] for HTTP traffic and on port [9300-9400] for node-to-node
# communication. (the range means that if the port is busy, it will automatically
# try the next port).

# Set the bind address specifically (IPv4 or IPv6):
#
# network.bind_host: 192.168.0.1

# Set the address other nodes will use to communicate with this node. If not
# set, it is automatically derived. It must point to an actual IP address.
#
# network.publish_host: 192.168.0.1

# Set both 'bind_host' and 'publish_host':
#
# network.host: 192.168.0.1

# Set a custom port for the node to node communication (9300 by default):
#
# transport.tcp.port: 9300

# Enable compression for all communication between nodes (disabled by default):
#
# transport.tcp.compress: true

# Set a custom port to listen for HTTP traffic:
#
# http.port: 9200

# Set a custom allowed content length:
#
# http.max_content_length: 100mb

# Disable HTTP completely:
#
# http.enabled: false


################################### Gateway ###################################

# The gateway allows for persisting the cluster state between full cluster
# restarts. Every change to the state (such as adding an index) will be stored
# in the gateway, and when the cluster starts up for the first time,
# it will read its state from the gateway.

# There are several types of gateway implementations. For more information,
# see <http://elasticsearch.org/guide/reference/modules/gateway>.

# The default gateway type is the "local" gateway (recommended):
#
# gateway.type: local

# Settings below control how and when to start the initial recovery process on
# a full cluster restart (to reuse as much local data as possible when using shared
# gateway).

# Allow recovery process after N nodes in a cluster are up:
#
# gateway.recover_after_nodes: 1

# Set the timeout to initiate the recovery process, once the N nodes
# from previous setting are up (accepts time value):
#
# gateway.recover_after_time: 5m

# Set how many nodes are expected in this cluster. Once these N nodes
# are up (and recover_after_nodes is met), begin recovery process immediately
# (without waiting for recover_after_time to expire):
#
# gateway.expected_nodes: 2


############################# Recovery Throttling #############################

# These settings allow to control the process of shards allocation between
# nodes during initial recovery, replica allocation, rebalancing,
# or when adding and removing nodes.

# Set the number of concurrent recoveries happening on a node:
#
# 1. During the initial recovery
#
# cluster.routing.allocation.node_initial_primaries_recoveries: 4
#
# 2. During adding/removing nodes, rebalancing, etc
#
# cluster.routing.allocation.node_concurrent_recoveries: 2

# Set to throttle throughput when recovering (eg. 100mb, by default unlimited):
#
# indices.recovery.max_size_per_sec: 0

# Set to limit the number of open concurrent streams when
# recovering a shard from a peer:
#
# indices.recovery.concurrent_streams: 5


################################## Discovery ##################################

# Discovery infrastructure ensures nodes can be found within a cluster
# and master node is elected. Multicast discovery is the default.

# Set to ensure a node sees N other master eligible nodes to be considered
# operational within the cluster. Set this option to a higher value (2-4)
# for large clusters (>3 nodes):
#
# discovery.zen.minimum_master_nodes: 1

# Set the time to wait for ping responses from other nodes when discovering.
# Set this option to a higher value on a slow or congested network
# to minimize discovery failures:
#
# discovery.zen.ping.timeout: 3s

# See <http://elasticsearch.org/guide/reference/modules/discovery/zen.html>
# for more information.

# Unicast discovery allows to explicitly control which nodes will be used
# to discover the cluster. It can be used when multicast is not present,
# or to restrict the cluster communication-wise.
#
# 1. Disable multicast discovery (enabled by default):
#
# discovery.zen.ping.multicast.enabled: false
#
# 2. Configure an initial list of master nodes in the cluster
#    to perform discovery when new nodes (master or data) are started:
#
# discovery.zen.ping.unicast.hosts: ["host1", "host2:port", "host3[portX-portY]"]

# EC2 discovery allows to use AWS EC2 API in order to perform discovery.
#
# You have to install the cloud-aws plugin for enabling the EC2 discovery.
#
# See <http://elasticsearch.org/guide/reference/modules/discovery/ec2.html>
# for more information.
#
# See <http://elasticsearch.org/tutorials/2011/08/22/elasticsearch-on-ec2.html>
# for a step-by-step tutorial.


################################## Slow Log ##################################

# Shard level query and fetch threshold logging.

#index.search.slowlog.level: TRACE
#index.search.slowlog.threshold.query.warn: 10s
#index.search.slowlog.threshold.query.info: 5s
#index.search.slowlog.threshold.query.debug: 2s
#index.search.slowlog.threshold.query.trace: 500ms

#index.search.slowlog.threshold.fetch.warn: 1s
#index.search.slowlog.threshold.fetch.info: 800ms
#index.search.slowlog.threshold.fetch.debug: 500ms
#index.search.slowlog.threshold.fetch.trace: 200ms

################################## GC Logging ################################

#monitor.jvm.gc.ParNew.warn: 1000ms
#monitor.jvm.gc.ParNew.info: 700ms
#monitor.jvm.gc.ParNew.debug: 400ms

#monitor.jvm.gc.ConcurrentMarkSweep.warn: 10s
#monitor.jvm.gc.ConcurrentMarkSweep.info: 5s
#monitor.jvm.gc.ConcurrentMarkSweep.debug: 2s

post-data.sh

curl -XPOST 'http://localhost:9200/clinical_trials/trial/NCT01631617' -d '
{
"firstreceived_date": "2012-06-28T00:00:00",
"is_fda_regulated": false,
"location_countries": {
"country": "United States"
},
"reference": [
{
"pmid": "20847294",
"citation": "Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4554-61. Epub 2010 Sep 16."
},
{
"pmid": "21482860",
"citation": "Fanelli M, Kupperman E, Lautenbach E, Edelstein PH, Margolis DJ. Antibiotics, acne, and Staphylococcus aureus colonization. Arch Dermatol. 2011 Aug;147(8):917-21. Epub 2011 Apr 11."
},
{
"pmid": "20352091",
"citation": "Jakobsson HE, Jernberg C, Andersson AF, Sjölund-Karlsson M, Jansson JK, Engstrand L. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One. 2010 Mar 24;5(3):e9836."
}
],
"overall_contact_backup": {
"phone": "(301) 402-7452",
"last_name": "Heidi H Kong, M.D.",
"email": "konghe@mail.nih.gov"
},
"completion_date": "2015-06-01T00:00:00",
"has_expanded_access": false,
"intervention": [
{
"intervention_name": "Trimethoprim/sulfamethoxazole",
"description": "N/A",
"intervention_type": "Drug"
},
{
"intervention_name": "Cephalexin",
"description": "N/A",
"intervention_type": "Drug"
},
{
"intervention_name": "Doxycycline",
"description": "N/A",
"intervention_type": "Drug"
},
{
"intervention_name": "Sodium hypochlorite (bleach)",
"description": "N/A",
"intervention_type": "Other"
}
],
"primary_completion_date": "2015-06-01T00:00:00",
"location": [
{
"status": "Recruiting",
"contact": {
"phone": "888-624-1937",
"last_name": "For more information at the NIH Clinical Center contact National Cancer Institute Referral Office"
},
"facility": {
"name": "National Institutes of Health Clinical Center, 9000 Rockville Pike",
"address": {
"city": "Bethesda",
"state": "Maryland",
"zip": "20892",
"country": "United States"
}
}
}
],
"number_of_arms": "1",
"start_date": "2012-06-01T00:00:00",
"id_info": {
"org_study_id": "120159",
"secondary_id": "12-C-0159",
"nct_id": "NCT01631617"
},
"study_type": "Interventional",
"official_title": "Effects of Treatments on the Microbiome in Healthy Volunteers and Patients With Atopic Dermatitis",
"brief_title": "Effects of Treatments on Atopic Dermatitis"
}
'

query.sh

curl -XGET 'localhost:9200/clinical_trials/_search?pretty=true' -d '
{
    "query" : {
        "term" : { "brief_title" : "dermatitis" }
    },
    "filter" : {
        "term" : { "country" : "united states" }
    },
    "facets" : {
        "tag" : {
            "terms" : { "field" : "country" }
        }
    }
}
'