I'm seeing a bus error on cargo run when attempting to load the spatialite extension with rusqlite:
Finished dev [unoptimized + debuginfo] target(s) in 1.19s
Running `target/debug/rust-spatialite-example`
[1] 33253 bus error cargo run --verbose
My suspicion is that there's a mismatch of sqlite version and spatialite and that they need to be built together rather than using the bundled feature of rusqlite, though it seems like that'd result in a different error?
Here's how things are set up:
Cargo.toml
[package]
name = "rust-spatialite-example"
version = "0.0.0"
edition = "2021"
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
[dependencies]
rusqlite = { version = "0.28.0", features = ["load_extension", "bundled"] }
init.sql
CREATE TABLE place (
id INTEGER PRIMARY KEY,
name TEXT NOT NULL
);
SELECT AddGeometryColumn('place', 'geom', 4326, 'POINT', 'XY', 0);
SELECT CreateSpatialIndex('place', 'geom');
main.rs
use rusqlite::{Connection, Result, LoadExtensionGuard};
#[derive(Debug)]
struct Place {
id: i32,
name: String,
geom: String,
}
fn load_spatialite(conn: &Connection) -> Result<()> {
unsafe {
let _guard = LoadExtensionGuard::new(conn)?;
conn.load_extension("/opt/homebrew/Cellar/libspatialite/5.0.1_2/lib/mod_spatialite", None)
}
}
fn main() -> Result<()> {
let conn = Connection::open("./geo.db")?;
load_spatialite(&conn)?;
// ... sql statements that aren't executed
Ok(())
}
Running:
cat init.sql | spatialite geo.db
cargo run
The mod_spatialite path is correct (there's an expected SqliteFailure error when that path is wrong). I tried explicitly setting sqlite3_modspatialite_init as the entry point and the behavior stayed the same.
Related
i'm new to nf-core/nextflow and needless to say the documentation does not reflect what might be actually implemented. But i'm defining the basic pipeline below:
nextflow.enable.dsl=2
process RUNBLAST{
input:
val thr
path query
path db
path output
output:
path output
script:
"""
blastn -query ${query} -db ${db} -out ${output} -num_threads ${thr}
"""
}
workflow{
//println "I want to BLAST $params.query to $params.dbDir/$params.dbName using $params.threads CPUs and output it to $params.outdir"
RUNBLAST(params.threads,params.query,params.dbDir, params.output)
}
Then i'm executing the pipeline with
nextflow run main.nf --query test2.fa --dbDir blast/blastDB
Then i get the following error:
N E X T F L O W ~ version 22.10.6
Launching `main.nf` [dreamy_hugle] DSL2 - revision: c388cf8f31
Error executing process > 'RUNBLAST'
Error executing process > 'RUNBLAST'
Caused by:
Not a valid path value: 'test2.fa'
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
I know test2.fa exists in the current directory:
(nfcore) MN:nf-core-basicblast jraygozagaray$ ls
CHANGELOG.md conf other.nf
CITATIONS.md docs pyproject.toml
CODE_OF_CONDUCT.md lib subworkflows
LICENSE main.nf test.fa
README.md modules test2.fa
assets modules.json work
bin nextflow.config workflows
blast nextflow_schema.json
I also tried with "file" instead of path but that is deprecated and raises other kind of errors.
It'll be helpful to know how to fix this to get myself started with the pipeline building process.
Shouldn't nextflow copy the file to the execution path?
Thanks
You get the above error because params.query is not actually a path value. It's probably just a simple String or GString. The solution is to instead supply a file object, for example:
workflow {
query = file(params.query)
BLAST( query, ... )
}
Note that a value channel is implicitly created by a process when it is invoked with a simple value, like the above file object. If you need to be able to BLAST multiple query files, you'll instead need a queue channel, which can be created using the fromPath factory method, for example:
params.query = "${baseDir}/data/*.fa"
params.db = "${baseDir}/blastdb/nt"
params.outdir = './results'
db_name = file(params.db).name
db_path = file(params.db).parent
process BLAST {
publishDir(
path: "{params.outdir}/blast",
mode: 'copy',
)
input:
tuple val(query_id), path(query)
path db
output:
tuple val(query_id), path("${query_id}.out")
"""
blastn \\
-num_threads ${task.cpus} \\
-query "${query}" \\
-db "${db}/${db_name}" \\
-out "${query_id}.out"
"""
}
workflow{
Channel
.fromPath( params.query )
.map { file -> tuple(file.baseName, file) }
.set { query_ch }
BLAST( query_ch, db_path )
}
Note that the usual way to specify the number of threads/cpus is using cpus directive, which can be configured using a process selector in your nextflow.config. For example:
process {
withName: BLAST {
cpus = 4
}
}
main.rs:
#[async_std::main]
async fn main() -> Result<(),sqlx::Error> {
use sqlx::Connect;
let mut conn = sqlx::SqliteConnection::connect("sqlite:///home/ace/hello_world/test.db").await?;
let row = sqlx::query!("SELECT * FROM tbl").fetch_all(&conn).await?;
println!("{}{}",row.0,row.1);
Ok(())
}
Cargo.toml:
[package]
name = "hello_world"
version = "0.1.0"
authors = ["ace"]
edition = "2018"
[dependencies]
async-std = {version = "1", features = ["attributes"]}
sqlx = { version="0.3.5", default-features=false, features=["runtime-async-std","macros","sqlite"] }
bash session:
ace#SLAB:~/hello_world$ sqlite test.db
SQLite version 2.8.17
Enter ".help" for instructions
sqlite> create table tbl ( num integer, chr varchar );
sqlite> insert into tbl values (1,'ok');
sqlite> .quit
ace#SLAB:~/hello_world$ pwd
/home/ace/hello_world
ace#SLAB:~/hello_world$ export DATABASE_URL=sqlite:///home/ace/hello_world/test.db
ace#SLAB:~/hello_world$ cargo run
Compiling hello_world v0.1.0 (/home/ace/hello_world)
error: failed to connect to database: file is not a database
--> src/main.rs:8:12
|
8 | let row = sqlx::query!("SELECT * FROM tbl").fetch_all(&conn).await?;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
= note: this error originates in a macro (in Nightly builds, run with -Z macro-backtrace for more info)
error: aborting due to previous error
error: could not compile `hello_world`.
To learn more, run the command again with --verbose.
ace#SLAB:~/hello_world$ rustc --version
rustc 1.44.0 (49cae5576 2020-06-01)
ace#SLAB:~/hello_world$ uname -r
5.4.0-33-generic
ace#SLAB:~/hello_world$ cat /etc/os-release | head -2
NAME="Ubuntu"
VERSION="20.04 LTS (Focal Fossa)"
ace#SLAB:~/hello_world$
Also tried using DATABASE_URL "sqlite::memory:" (both in environment variable and in main.rs) with system table "sqlite_master". Got different error:
error[E0277]: the trait bound `&sqlx_core::sqlite::connection::SqliteConnection: sqlx_core::executor::RefExecutor<'_>` is not satisfied
... but it must have gotten partway to success because when I used table name "Xsqlite_master" with memory db, it complained that there was no such table.
Tried "sqlite://home"(etc) and every other number of slashes, zero through 4. Tried several hundred other things. :(
Thank you!
There maybe several more things to try:
Try sqlite3 /home/ace/hello_world/test.db to double verify that the DB does exist. Make sure tbl table is defined there .schema tbl
Try DB path with a single slash i.e. sqlite:/home/ace/hello_world/test.db
Lastly try using the query function not the macro https://docs.rs/sqlx/0.3.5/sqlx/fn.query.html to see if it works.
I am attempting to build a small terminal emulator and am running into some interesting type conflicts with libc. When I am attempting to set up the slave portion of the pty connection I need to create the slave with a system call to ptsname() in order to get the name for the pts so I can access it. However, I get a type error saying that libc::ptsname() requires an i32 for the input. This is in direct conflict with the man page that says it should be passed a file descriptor. I'm just wondering if I can convert the libc::c_int that I have for a file descriptor into a i32 to pass into ptsname.
The code is as follows :
use libc::{self, c_int, grantpt, posix_openpt, ptsname, unlockpt, O_RDWR};
use std::os::unix::io::FromRawFd;
use std::process::{Child, Command, Stdio};
#[derive(Debug)]
pub struct Pty {
process: Child,
fd: i32,
}
fn create_pty(process: &str) -> Pty {
let master: c_int;
unsafe {
// create master/slave pair of fd
master = posix_openpt(O_RDWR);
if master == -1 {
panic!("Failed to posix_openpt");
}
// set slave ownership and mode as master
let mut result = grantpt(master);
if result == -1 {
panic!("Failed to grantpt");
}
// unlock slave
result = unlockpt(master);
if result == -1 {
panic!("Failed to unlockpt");
}
}
let slave: c_int = ptsname(master as i32);
slave = libc::open(slave);
let mut builder = Command::new(process);
match builder.spawn() {
Ok(process) => {
let pty = Pty {
process,
fd: master,
};
pty
}
Err(e) => {
panic!("Failed to create pty: {}", e);
}
}
}
fn main() {
let shell = "/bin/bish";
let pty = create_pty(shell);
println!("{:?}", pty);
}
and the console output(The second error can be ignored for now):
error[E0308]: mismatched types
--> src/main.rs:42:24
|
42 | let slave: c_int = ptsname(master as i32);
| ^^^^^^^^^^^^^^^^^^^^^^ expected i32, found *-ptr
|
= note: expected type `i32`
found type `*mut i8`
error[E0060]: this function takes at least 2 parameters but 1 parameter was supplied
--> src/main.rs:43:13
|
43 | slave = libc::open(slave);
| ^^^^^^^^^^^^^^^^^ expected at least 2 parameters
error: aborting due to 2 previous errors
Some errors have detailed explanations: E0060, E0308.
For more information about an error, try `rustc --explain E0060`.
error: could not compile `experiment`.
It's not saying that it requires an input of i32, but rather that you're asking that ptsname(master as i32); has the type i32. This might be a bit confusing because c_int is an alias for i32, so it sounds like it's asking for an unrelated type.
The problem is that you're giving slave the type c_int, when ptsname returns *mut c_char (c_char is also an alias, this time for i8).
I'm having an issue with getting SBT Subprojects to recognize commands provided by plugins. I have the following plugin source:
object DemoPlugin extends AutoPlugin {
override lazy val projectSettings = Seq(commands += demoCommand)
lazy val demoCommand =
Command.command("demo") { (state: State) =>
println("Demo Plugin!")
state
}
}
Which is used by a project configured as follows:
lazy val root = project in file(".")
lazy val sub = (project in file("sub")).
enablePlugins(DemoPlugin).
settings(
//...
)
The plugin is, of course, listed in project/plugins.sbt. However, when I open up sbt in the project, I see the following:
> sub/commands
[info] List(sbt.SimpleCommand#413d2cd1)
> sub/demo
[error] Expected ':' (if selecting a configuration)
[error] Not a valid key: demo (similar: doc)
[error] sub/demo
Even stranger, using consoleProject, I can see that the command in the project is the one defined by DemoPlugin!
scala> (commands in sub).eval.map { c => c.getClass.getMethod("name").invoke(c) }
res0: Seq[Object] = List(demo)
I'm looking to be able to type sub/demo, and have it perform the demo command. Any help would be much appreciated!
Commands aren't per-project. They only work for the top-level project.
It's also recommended to try and use tasks, or if needed input tasks where you might want to use a command.
If you really need a command, there's a way to have a sort of "holder" task, see the answer to Can you access a SBT SettingKey inside a Command?
I have a SBT multi project which includes two sub projects. One is an ordinary Scala web server project and the other is just some web files. With my self written SBT plugin I can run Gulp on the web project. This Gulp task runs asynchronous. So with
sbt "web/webAppStart" "server/run"
I can start the Gulp development web server and my Scala backend server in parallel. Now I want to create a new task, that combines them both. So afterwards
sbt dev
for example should do the same. Here is what I tried so far:
// Build.sbt (only the relevant stuff)
object Build extends sbt.Build {
lazy val runServer: InputKey[Unit] = run in server in Compile
lazy val runWeb: TaskKey[Unit] = de.choffmeister.sbt.WebAppPlugin.webAppStart
lazy val dev = InputKey[Unit]("dev", "Starts a development web server")
// Scala backend project
lazy val server = (project in file("project-server"))
// Web frontend project
lazy val web = (project in file("project-web"))
// Root project
lazy val root = (project in file("."))
.settings(dev <<= (runServer) map { (_) => {
// do nothing
})
.aggregate(server, web)
This works so far. Now I don't have any idea, how to make dev also depend on the runWeb task. If I just add the runWeb task like
.settings(dev <<= (runWeb, runServer) map { (_, _) => {
// do nothing
})
then I get the error
[error] /Users/choffmeister/Development/shop/project/Build.scala:59:value map is not a member of (sbt.TaskKey[Unit], sbt.InputKey[Unit])
[error] .settings(dev <<= (runWeb, runServer) map { (_, _) =>
[error] ^
[error] one error found
[error] (compile:compile) Compilation failed
Can anyone help me with this please?
The optimal solution would pass the arguments given to dev to the runServer task. But I could also live with making dev a TaskKey[Unit] and then hard code to run runServer with no arguments.
tl;dr Use .value macro to execute dependent tasks or just alias the task sequence.
Using .value macro
Your case seems overly complicated to my eyes because of the pre-0.13 syntax (<<=) and the use of project/Build.scala (that often confuse not help people new to sbt).
You should just execute the two tasks in another as follows:
dev := {
runWeb.value
runServer.value
}
The complete example:
lazy val server = project
lazy val runServer = taskKey[Unit]("runServer")
runServer := {
println("runServer")
(run in server in Compile).value
}
lazy val runWeb = taskKey[Unit]("runWeb")
runWeb := {
println("runWeb")
}
lazy val dev = taskKey[Unit]("dev")
dev := {
println("dev")
}
dev <<= dev dependsOn (runServer, runWeb)
Using alias command
sbt offers alias command that...
[sbt-learning-space]> help alias
alias
Prints a list of defined aliases.
alias name
Prints the alias defined for `name`.
alias name=value
Sets the alias `name` to `value`, replacing any existing alias with that name.
Whenever `name` is entered, the corresponding `value` is run.
If any argument is provided to `name`, it is appended as argument to `value`.
alias name=
Removes the alias for `name`.
Just define what tasks/command you want to execute in an alias as follows:
addCommandAlias("devAlias", ";runServer;runWeb")
Use devAlias as if it were a built-in task:
[sbt-learning-space]> devAlias
runServer
[success] Total time: 0 s, completed Jan 25, 2015 6:30:15 PM
runWeb
[success] Total time: 0 s, completed Jan 25, 2015 6:30:15 PM