basic set of functions for ETN data access

[stijnvanhoey]

@jreubens @PieterjanVerhelst as we discussed:

As a replacement of the current getLWData function, we aim to go to a minimal set of functions for the data access. Each of these functions target a specific set of data-tables, comparable to the online ETN data portal.

Apart from a make_connection function, the first set of functions that we will focus on are. For each function, we define the required filters as function inputs that will be embedded to query the existing views:

get_projects()

get_deployments(
    netwerk-project,
    active)               # open deployments, default ALL  

get_animals(
    netwerk-project,   # i.e. projectlist
    animal_project,   # i.e. tagprojectlist
    species)

get_tags(
    animal_project)   # i.e. tagprojectlist

get_receivers
    netwerk-project)    # i.e. projectlist

get_detections(
    animal_project,
    netwerk-project,
    start_date,
    end_date,
    station,
    get_tags,
    ...?)

By default, we return all the available columns in the database views/tables; but maybe this will be too much. @jreubens you could maybe define a subset of columns for each output that are really out of scope for any of the ETN users?

[jreubens]

@stijnvanhoey
below you can find an overview of all the header I would keep included. It is still quite a lot, thus if this is still too much, let me know and I'll see whether I can do a further reduction...
From projects, detections and tags I kept all the headers.
From the other ones I removed some redundant ones

vliz.detections_view

colnames(tabel)
"receiver" "transmitter" "transmitter_name"
"transmitter_serial" "sensor_value" "sensor_unit"
"sensor2_value" "sensor2_unit" "station_name"
"datetime" "id_pk" "qc_flag"
"file" "latitude" "longitude"
"deployment_fk" "scientific_name" "location_name"
"deployment_station_name" "deploy_date_time" "animal_project_name"
"animal_project_code" "animal_moratorium" "network_project_name"
"network_project_code" "network_moratorium" "signal_to_noise_ratio"
"detection_file_id" "tag_sensor_type" "tag_intercept"
"tag_slope" "sensor_value_depth_meters"

vliz.tags

colnames(tabel)
"serial_number" "type" "model" "id_code" "tag_code_space"
"owner_pi" "owner_organization" "id_pk" "activation_date" "min_delay"
"max_delay" "power" "end_date" "file" "estimated_lifetime"
"sensor_type" "frequency" "acoustic_tag_type" "min_delay_step2" "max_delay_step2"
"power_step2" "min_delay_step3" "max_delay_step3" "power_step3" "duration_step1"
"duration_step2" "duration_step3" "manufacturer_fk" "intercept" "slope"
"owner_group_fk"

animals_view

colnames(tabel)
"projectname" "projectmember"
"tag_code_space" "person_id"
animal_id" "scientific_name"
"common_name" "length"
"length_type" "length_units"
"length2" "length2_type"
"length2_units" "weight_units"
"age" "age_units"
"sex" "life_stage"
"capture_location" "capture_depth"
"utc_release_date_time" "comments"
"est_tag_life" "wild_or_hatchery"
"stock" "dna_sample_taken"
"treatment_type" "dissolved_oxygen"
"date_of_surgery"
"id_pk" "catched_date_time"
"capture_latitude" "capture_longitude"
"release_latitude" "release_longitude"
"recapture_date" "implant_type"
"implant_method" "date_modified"
"date_created" "release_location"
"length3" "length3_type"
"length3_units" "length4"
"length4_type" "length4_units"
"weight" "end_date_tag"
"capture_method" "project_fk"
"animal_tag_release_id_pk"

vliz.deployments_view

colnames(tabel)
"receiver" "receiver_status" "projectname"
"projectcode" "projectmember" "drop_dead_date"
"download_date_time" "deploy_date_time" "recover_date_time"
"bottom_depth" "sync_date_time" "data_downloaded"
"time_drift" "comments" "id_pk"
"receiver_fk" "location_name" "location_manager"
"location_description" "deploy_lat" "deploy_long"
"recover_lat" "recover_long" "station_name"
"intended_lat" "intended_long" "date_created"
"date_modified" "battery_install_date" "ar_battery_install_date"
"distance_to_mouth" "source" "transmit_profile"
"transmit_power_output" "log_temperature_stats_period" "log_temperature_sample_period"
"log_tilt_sample_period" "log_noise_stats_period" "log_noise_sample_period"
"log_depth_stats_period" "log_depth_sample_period" "project_fk"
"mooring_type"

vliz.receivers

colnames(tabel)
"serial_number" "model_number"
"expected_battery_life" "id_pk"
"receiver" "owner_organization" "built_in_tag_fk"
"status" "receiver_type" "manufacturer_fk"
"owner_group_fk"

[PieterjanVerhelst]

@jreubens I think some fields in animals are redundant. Although everything can have its purpose for someone in the future, I think the listed column names below will only rarely be used. If one column appears to be more important than previously thought, it can be added to the function at a later stage.

"wild_or_hatchery"
"stock" "dna_sample_taken"
"treatment_type" "dissolved_oxygen"
"date_of_surgery"
"id_pk"
"implant_type"
"implant_method" "date_modified"
"date_created"
"capture_method"
"animal_tag_release_id_pk"

[jreubens]

some can indeed be removed I guess
but I want to keep the following...
"wild_or_hatchery"
"stock"
"dna_sample_taken"
"date_of_surgery"
"implant_type"
"implant_method"
"capture_method"

for some projects this might be important in the near future...

[stijnvanhoey]

For the moment, I propose to keep the full table views as output to the user without any filtering. We can show in a vignette/tutorial how to quickly select columns as a user, based on the given result. OK?

[stijnvanhoey]

Closing this issue here, as the basic functions are currently available.