Default settings

docs/commands.md

@@ -1,3 +1,12 @@
+# Defaults
+
+This controls default choices for the `gen` command line
+
+- database
+ - This controls the default database for `gen` to work on, it is what is passed to the `--db` argument. 
+- collection
+ - This controls the default collection for `gen` to work on, it is what is passed to the `--name` argument.
+
 # Apply
 
 Apply operations to the current branch.

migrations/operations/01-initial/up.sql

@@ -1,3 +1,9 @@
+CREATE TABLE defaults (
+ id INTEGER PRIMARY KEY NOT NULL,
+ db_name TEXT,
+ collection_name TEXT
+) STRICT;
+
 CREATE TABLE operation_state (
  db_uuid TEXT PRIMARY KEY NOT NULL,
  operation_id INTEGER,
@@ -41,3 +47,5 @@ CREATE TABLE branch (
  FOREIGN KEY(current_operation_id) REFERENCES operation(id)
 ) STRICT;
 CREATE UNIQUE INDEX branch_uidx ON branch(db_uuid, name);
+
+INSERT INTO defaults values (1, NULL, NULL);

src/main.rs

@@ -8,10 +8,10 @@ use gen::get_connection;
 use gen::imports::fasta::import_fasta;
 use gen::imports::gfa::import_gfa;
 use gen::models::metadata;
-use gen::models::operations::{setup_db, Branch, Operation, OperationState};
+use gen::models::operations::{setup_db, Branch, OperationState};
 use gen::operation_management;
 use gen::updates::vcf::update_with_vcf;
-use rusqlite::types::Value;
+use rusqlite::{types::Value, Connection};
 use std::fmt::Debug;
 use std::path::PathBuf;
 use std::str;
@@ -26,6 +26,13 @@ struct Cli {
  command: Option<Commands>,
 }
 
+fn get_default_collection(conn: &Connection) -> Option<String> {
+ let mut stmt = conn
+ .prepare("select collection_name from defaults where id = 1")
+ .unwrap();
+ stmt.query_row((), |row| row.get(0)).unwrap()
+}
+
 #[derive(Subcommand)]
 enum Commands {
  /// Import a new sequence collection.
@@ -38,7 +45,7 @@ enum Commands {
  gfa: Option<String>,
  /// The name of the collection to store the entry under
  #[arg(short, long)]
- name: String,
+ name: Option<String>,
  /// Don't store the sequence in the database, instead store the filename
  #[arg(short, long, action)]
  shallow: bool,
@@ -47,7 +54,7 @@ enum Commands {
  Update {
  /// The name of the collection to update
  #[arg(short, long)]
- name: String,
+ name: Option<String>,
  /// A fasta file to insert
  #[arg(short, long)]
  fasta: Option<String>,
@@ -104,11 +111,19 @@ enum Commands {
  Export {
  /// The name of the collection to export
  #[arg(short, long)]
- name: String,
+ name: Option<String>,
  /// The name of the GFA file to export to
  #[arg(short, long)]
  gfa: String,
  },
+ Defaults {
+ /// The default database to use
+ #[arg(short, long)]
+ database: Option<String>,
+ /// The default collection to use
+ #[arg(short, long)]
+ collection: Option<String>,
+ },
 }
 
 fn main() {
@@ -120,11 +135,42 @@ fn main() {
  return;
  }
 
- let binding = cli.db.expect("No db specified.");
+ let operation_conn = get_operation_connection();
+ if let Some(Commands::Defaults {
+ database,
+ collection,
+ }) = &cli.command
+ {
+ if let Some(name) = database {
+ operation_conn
+ .execute("update defaults set db_name=?1 where id = 1", (name,))
+ .unwrap();
+ println!("Default database set to {name}");
+ }
+ if let Some(name) = collection {
+ operation_conn
+ .execute(
+ "update defaults set collection_name=?1 where id = 1",
+ (name,),
+ )
+ .unwrap();
+ println!("Default collection set to {name}");
+ }
+ return;
+ }
+
+ let binding = cli.db.unwrap_or_else(|| {
+ let mut stmt = operation_conn
+ .prepare("select db_name from defaults where id = 1 and db_name is not null;")
+ .unwrap();
+ let row: Option<String> = stmt.query_row((), |row| row.get(0)).unwrap();
+ row.expect("No db specified and no default database chosen.")
+ });
  let db = binding.as_str();
  let conn = get_connection(db);
  let db_uuid = metadata::get_db_uuid(&conn);
- let operation_conn = get_operation_connection();
+
+ let default_collection = get_default_collection(&operation_conn);
 
  // initialize the selected database if needed.
  setup_db(&operation_conn, &db_uuid);
@@ -137,6 +183,9 @@ fn main() {
  shallow,
  }) => {
  conn.execute("BEGIN TRANSACTION", []).unwrap();
+ let name = &name.clone().unwrap_or_else(|| {
+ default_collection.expect("No collection specified and default not setup.")
+ });
  if fasta.is_some() {
  import_fasta(
  &fasta.clone().unwrap(),
@@ -162,6 +211,9 @@ fn main() {
  sample,
  }) => {
  conn.execute("BEGIN TRANSACTION", []).unwrap();
+ let name = &name.clone().unwrap_or_else(|| {
+ default_collection.expect("No collection specified and default not setup.")
+ });
  update_with_vcf(
  vcf,
  name,
@@ -173,10 +225,6 @@ fn main() {
 
  conn.execute("END TRANSACTION", []).unwrap();
  }
- Some(Commands::Init {}) => {
- config::get_or_create_gen_dir();
- println!("Gen repository initialized.");
- }
  Some(Commands::Operations { branch }) => {
  let current_op = OperationState::get_operation(&operation_conn, &db_uuid)
  .expect("Unable to read operation.");
@@ -288,10 +336,22 @@ fn main() {
  operation_management::checkout(&conn, &operation_conn, &db_uuid, branch, *id);
  }
  Some(Commands::Export { name, gfa }) => {
+ let name = &name.clone().unwrap_or_else(|| {
+ default_collection.expect("No collection specified and default not setup.")
+ });
  conn.execute("BEGIN TRANSACTION", []).unwrap();
  export_gfa(&conn, name, &PathBuf::from(gfa));
  conn.execute("END TRANSACTION", []).unwrap();
  }
  None => {}
+ // these will never be handled by this method as we search for them earlier.
+ Some(Commands::Init {}) => {
+ config::get_or_create_gen_dir();
+ println!("Gen repository initialized.");
+ }
+ Some(Commands::Defaults {
+ database,
+ collection,
+ }) => {}
  }
 }