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Merge pull request #16 from slebras/samples_config
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Samples and SampleSet indexers
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@jayrbolton
jayrbolton committed Jul 23, 2020
2 parents 13885e2 + 3dfda59 commit 04f8f5f
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198 changes: 198 additions & 0 deletions config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ ws_type_to_indexes:
KBaseMatrices.TraitMatrix: matrix
KBaseSets.GenomeSet: genomeset
KBaseMetagenomes.AnnotatedMetagenomeAssembly: annotated_metagenome_assembly
KBaseSets.SampleSet: sample_set

es_type_global_name: data

Expand Down Expand Up @@ -98,6 +99,9 @@ latest_versions:
annotated_metagenome_assembly_features: "annotated_metagenome_assembly_features_1"
annotated_metagenome_assembly_version: "annotated_metagenome_assembly_version_1"
annotated_metagenome_assembly_features_version: "annotated_metagenome_assembly_features_version_1"
sample_set: "sample_set_1"
sample_set_version: "sample_set_version_1"
sample: "sample_1"

# Map from unversioned alias to versioned indexes
aliases:
Expand Down Expand Up @@ -153,6 +157,12 @@ aliases:
- "annotated_metagenome_assembly_version_1"
annotated_metagenome_assembly_features_version:
- "annotated_metagenome_assembly_features_version_1"
sample_set:
- "sample_set_1"
sample_set_version:
- "sample_set_version_1"
sample:
- "sample_1"

# All ES type mappings
mappings:
Expand Down Expand Up @@ -633,3 +643,191 @@ mappings:
objtype: {type: keyword}
perm: {type: keyword}
permusers: {type: keyword}

"sample_set_1":
global_mappings: [ws_auth, ws_object]
properties:
description: {type: text}
sample_ids: {type: keyword}
sample_names: {type: keyword}
sample_versions: {type: integer}

"sample_set_version_1":
global_mappings: [ws_auth, ws_object]
properties:
description: {type: text}
sample_ids: {type: keyword}
sample_names: {type: keyword}
sample_versions: {type: integer}

"sample_1":
global_mappings: [ws_auth, ws_object]
properties:
save_date: {type: text}
sample_version: {type: integer}
name: {type: keyword}
parent_id: {type: keyword}
node_id: {type: keyword}
sample_name: {type: text}
material: {type: text}
field_name_informal_classification: {type: text}
location_description: {type: text}
locality_description: {type: text}
collection_method: {type: text}
purpose: {type: text}
navigation_type: {type: text}
primary_physiographic_feature: {type: text}
name_of_physiographic_feature: {type: text}
field_program_cruise: {type: text}
collector_chief_scientist: {type: text}
collection_date_precision: {type: text}
current_archive: {type: text}
related_identifiers: {type: text}
platform_type: {type: text}
zone: {type: text}
state_province: {type: text}
original_archive_contact: {type: text}
classification: {type: text}
vertical_datum: {type: text}
original_archive: {type: text}
platform_name: {type: text}
collection_time_end: {type: text}
county: {type: text}
size_unit: {type: text}
age_unit: {type: text}
locality: {type: text}
sample_description: {type: text}
collection_method_description: {type: text}
other_names: {type: text}
geological_unit: {type: text}
collector_chief_scientist_address: {type: text}
size: {type: text}
launch_platform_name: {type: text}
depth_scale: {type: text}
country: {type: text}
city_township: {type: text}
sub-object_type: {type: text}
launch_id: {type: text}
id: {type: text}
elevation_unit: {type: text}
elevation_start: {type: text}
latitude: {type: text}
collection_date: {type: text}
str:degrees: {type: text}
longitude: {type: text}
age_min: {type: text}
age_max: {type: text}
geological_age: {type: text}
collection_date_precision: {type: text}
collection_date_end: {type: text}
elevation_end: {type: text}
depth_in_core_max: {type: text}
depth_in_core_min: {type: text}
coordinate_precision?: {type: float}
current_archive_contact: {type: keyword}
easting_m: {type: float}
elevation_unit: {type: float}
igsn: {type: }
latitude_end: {type: float}
longitude_end: {type: float}
northing_m: {type: float}
parent_igsn: {type: keyword}
relation_type: {type: text}
release_date: {type: keyword}
sampleid: {type: keyword}
experiment_name: {type: keyword}
area_name: {type: keyword}
well_name: {type: keyword}
environmental_package: {type: text}
description: {type: text}
date: {type: text}
time_zone: {type: text}
geological_zone: {type: text}
recovery_factor: {type: text}
method: {type: text}
fraction: {type: text}
replicate: {type: text}
maturation_time: {type: text}
treatment: {type: text}
temperature_celsius: {type: text}
moisture: {type: text}
pore_water_extraction_microliters: {type: text}
conductivity_ms_cm: {type: text}
dapi_cell_count_cells_g: {type: text}
dna_picogreen_total_ng: {type: text}
total_carbon_mg_g_dry_weight: {type: text}
biomass_carbon_mg_g: {type: text}
total_nitrogen_mg_g_dry_weight: {type: text}
leucine_activity_ngc_day_cell: {type: text}
functional_area: {type: text}
type_of_well: {type: text}
ground_elevation_ft_amsl: {type: text}
installation_method: {type: text}
boring_ft_bgs: {type: text}
boring_refusal: {type: text}
boring_diameter_in: {type: text}
screen_type: {type: text}
well_casing_type: {type: text}
well_casing_od_in: {type: text}
well_casing_id_in: {type: text}
drive_casing_type: {type: text}
drive_casing_id_in: {type: text}
drive_casing_od_in: {type: text}
drive_casing_start_depth_ft_bgs: {type: text}
drive_casing_end_depth_ft_bgs: {type: text}
packing_type: {type: text}
packing_depth_start_ft_bgs: {type: text}
packing_depth_end_ft_bgs: {type: text}
topofweatheredbedrock_ft_bgs: {type: text}
topoffreshbedrock_ft_bgs: {type: text}
aquifer: {type: text}
fractures_cavities_waterbreaks: {type: text}
other_name: {type: text}
screened: {type: text}
open: {type: text}
well_status: {type: text}
condition: {type: text}
origination_or_plug_abandon: {type: text}
min_water_level_ft_amsl: {type: text}
average_water_level_ft_amsl: {type: text}
max_water_level_ft_amsl: {type: text}
upper_seal_type: {type: text}
upper_seal_start_depth_ft_bgs: {type: text}
upper_seal_end_depth_ft_bgs: {type: text}
lower_seal_type_ft_bgs: {type: text}
lower_seal_start_depth_ft_bgs: {type: text}
lower_seal_end_depth_ft_bgs: {type: text}
open_casing_type: {type: text}
open_casing_od_in: {type: text}
open_casing_id_in: {type: text}
open_casing_depth_ft_bgs: {type: text}
open_hole_diameter_in: {type: text}
open_hole_depth_ft_bgs: {type: text}
open_interval_start_depth_ft_bgs: {type: text}
open_interval_end_depth_ft_bgs: {type: text}
open_interval_diameter_in: {type: text}
rock_formation: {type: text}
depth: {type: text}
elevation: {type: text}
time: {type: text}
timezone: {type: text}
env_package: {type: text}
continent: {type: text}
region: {type: text}
biome: {type: text}
feature: {type: text}
aodc_cells_g: {type: float}
boncat_activity_cell_g: {type: float}
depth_cm_bgs: {type: float}
filter_micron: {type: float}
organic_carbon_mg_g_dry_weight: {type: float}
ph: {type: float}
redox_potential_?: {type: float}
screen_bottom_elevation_ft_amsl: {type: float}
screen_end_depth_ft_bgs: {type: float}
screen_start_depth_ft_bgs: {type: float}
screen_top_elevation_ft_amsl: {type: float}
screened_interval_ft: {type: float}
top_of_casing_elevation_ft_amsl: {type: float}
top_of_casing_stickup_ft: {type: float}
well_casing_depth_ft_bgs: {type: float}

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