Directus migration

[oolonek]

• Prepare a crate aiming to build a csv for the whole iNat (and relevant) taxonomy (e.g. OTL, Catalogue of Life). This will retrieve taxon metadata.

• Retrieve taxonomy mappings from Wikidata and store it to the database
  see https://qlever.cs.uni-freiburg.de/wikidata/37W9lU

• At the moment the way to pull iNaturalist observations is by using the following script https://github.com/digital-botanical-gardens-initiative/inat-fetcher. This need to be converted to a proper crate.
  This should retrieve only observation metadata

[oolonek]

We are looking at the current Field Data table.
This contains information from QField cloud via the API using the following script https://github.com/digital-botanical-gardens-initiative/qfieldcloud-fetcher

Currently the directus table has the following columns

Geographical coordinates are extracted and converted form QFiled cloud field and then appended to the pictures metadata using https://github.com/digital-botanical-gardens-initiative/Pictures_manager

#[cfg(feature = "64-column-tables")]
diesel::table! {
    #[sql_name = "Field_Data"] public.field_data(id) { id -> diesel::sql_types::Integer,
    status -> diesel::sql_types::Text
user_created -> diesel::sql_types::Nullable <
    diesel::sql_types::Uuid >
date_created -> diesel::sql_types::Nullable <
    diesel::sql_types::Timestamptz >
user_updated -> diesel::sql_types::Nullable <
    diesel::sql_types::Uuid >
date_updated -> diesel::sql_types::Nullable <
    diesel::sql_types::Timestamptz >
sample_name -> diesel::sql_types::Nullable <
    diesel::sql_types::Text >
sample_id -> diesel::sql_types::Text
picture_panel ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
picture_general ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
picture_detail ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
picture_cut ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
picture_panel_label ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
x_coord ->
    diesel::sql_types::Nullable < diesel::sql_types::Float >
y_coord ->
    diesel::sql_types::Nullable < diesel::sql_types::Float >
#[sql_name =
    "herbivory_(percent)"] herbivory_percent -> diesel::sql_types::Nullable <
    diesel::sql_types::Float >
#[sql_name = "temperature_(°C)"] temperature_celsius ->
    diesel::sql_types::Nullable < diesel::sql_types::Float >
geometry ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
latitude ->
    diesel::sql_types::Nullable < diesel::sql_types::Float >
longitude ->
    diesel::sql_types::Nullable < diesel::sql_types::Float >
match_name ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
ott_id ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
rank ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
#[sql_name = "wikidataID"]
    wikidata_id -> diesel::sql_types::Nullable < diesel::sql_types::Text >
unknown ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
qfield_project ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
collector_fullname ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
picture_free ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
no_name_on_list ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
name_proposition ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
comment_eco ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
soil_type ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
weather ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
comment_env ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
observation_subject ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
collector_inat ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
collector_orcid ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
date ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
taxon_name ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
is_wild ->
    diesel::sql_types::Nullable < diesel::sql_types::Integer >
inat_upload ->
    diesel::sql_types::Nullable < diesel::sql_types::Integer >
ipen ->
    diesel::sql_types::Nullable < diesel::sql_types::Text > }
}

Should be

#[cfg(feature = "64-column-tables")]
diesel::table! {
    #[sql_name = "Field_Data"] public.field_data(id) {
sample_name -> diesel::sql_types::Nullable <
    diesel::sql_types::Text >
//remind to change this sample_name 
sample_id -> diesel::sql_types::Text
//this is the EMI code
x_coord ->
    diesel::sql_types::Nullable < diesel::sql_types::Float >
y_coord ->
    diesel::sql_types::Nullable < diesel::sql_types::Float >
geometry ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
latitude ->
    diesel::sql_types::Nullable < diesel::sql_types::Float >
longitude ->
    diesel::sql_types::Nullable < diesel::sql_types::Float >

// the previous columns will be converted to one single FK pointing to the geographical coordinates table.
// here we have two systems the local and

collector_fullname ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
// will be mapped by FK to the user table


collector_inat ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
collector_orcid ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >

//will be mapped to Orcid_user and iNat_user tables

no_name_on_list ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
name_proposition ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
taxon_name ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >

// to be renormalized to taxa name suggestions

comment_env ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
comment_eco ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >


observation_subject ->
    diesel::sql_types::Nullable < diesel::sql_types::Text >
// FK to a plants parts / organs ontology table


is_wild ->
    diesel::sql_types::Nullable < diesel::sql_types::Integer >
// This is where we specify if the observation is made on a wild or cultivated organism

inat_upload ->
    diesel::sql_types::Nullable < diesel::sql_types::Integer >
}