- implement shape in Rust
- implement more readers - fix downloading of bioformats jar - (mostly) compatible with python version
This commit is contained in:
w.pomp
@@ -1,131 +1,177 @@
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#[cfg(not(feature = "python"))]
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use j4rs::{JvmBuilder, MavenArtifact, MavenArtifactRepo, MavenSettings, errors::J4RsError};
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#[cfg(not(feature = "python"))]
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use retry::{delay, delay::Exponential, retry};
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use std::error::Error;
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#[cfg(not(feature = "python"))]
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use std::fmt::Display;
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#[cfg(not(feature = "python"))]
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use std::fmt::Formatter;
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#[cfg(not(feature = "python"))]
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use std::path::PathBuf;
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#[cfg(not(feature = "python"))]
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use std::{env, fs};
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#[cfg(feature = "bioformats_java")]
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const BIOFORMATS_VERSION: &str = "8.5.0";
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#[cfg(feature = "python")]
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use j4rs::Jvm;
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#[cfg(feature = "bioformats_java")]
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mod bioformats {
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use std::error::Error;
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use std::fmt::{Display, Formatter};
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#[cfg(feature = "movie")]
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use ffmpeg_sidecar::download::auto_download;
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#[derive(Clone, Debug)]
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pub(crate) enum BuildError {
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J4rsVersionNotFound,
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}
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#[cfg(not(feature = "python"))]
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#[derive(Clone, Debug)]
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enum BuildError {
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BioFormatsNotDownloaded,
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}
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impl Display for BuildError {
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fn fmt(&self, fmt: &mut Formatter) -> Result<(), std::fmt::Error> {
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match self {
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Self::J4rsVersionNotFound => write!(fmt, "J4rsVersion not found in Cargo.lock"),
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}
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}
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}
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#[cfg(not(feature = "python"))]
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impl Display for BuildError {
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fn fmt(&self, fmt: &mut Formatter) -> Result<(), std::fmt::Error> {
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write!(fmt, "Bioformats package not downloaded")
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impl Error for BuildError {}
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fn get_j4rs_version() -> Result<String, Box<dyn Error>> {
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let manifest_dir = std::env::var("CARGO_MANIFEST_DIR").expect("CARGO_MANIFEST_DIR not set");
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let lock_path = std::path::Path::new(&manifest_dir).join("Cargo.lock");
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let lock_toml = std::fs::read_to_string(&lock_path)?;
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let value: toml::Value = toml::from_str(&lock_toml)?;
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if let Some(packages) = value.get("package").and_then(|v| v.as_array()) {
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for package in packages {
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if let (Some(name), Some(version)) = (
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package.get("name").and_then(|v| v.as_str()),
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package.get("version"),
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) && name == "j4rs"
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{
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return Ok(version
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.to_string()
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.strip_prefix("\"")
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.and_then(|v| v.strip_suffix("\""))
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.ok_or(BuildError::J4rsVersionNotFound)?
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.to_string());
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}
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}
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}
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Err(Box::new(BuildError::J4rsVersionNotFound {}))
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}
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pub(crate) fn build() -> Result<(), Box<dyn Error>> {
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let j4rs_version = get_j4rs_version()?;
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let out_dir = std::env::var("OUT_DIR")?;
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let dest_path = std::path::Path::new(&out_dir).join("constants.rs");
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let contents = format!(
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r#"
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/// Generated by build.rs
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pub(super) const J4RS_VERSION: &str = "{}";
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pub(super) const BIOFORMATS_VERSION: &str = "{}";
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"#,
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j4rs_version,
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crate::BIOFORMATS_VERSION,
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);
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std::fs::write(&dest_path, contents)?;
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Ok(())
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}
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}
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#[cfg(not(feature = "python"))]
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impl Error for BuildError {}
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#[cfg(all(not(feature = "python"), feature = "bioformats_java"))]
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mod no_python_bioformats {
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use j4rs::errors::J4RsError;
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use j4rs::{JvmBuilder, MavenArtifact, MavenArtifactRepo, MavenSettings};
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use retry::delay::Exponential;
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use retry::{delay, retry};
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use std::error::Error;
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use std::fmt::{Display, Formatter};
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fn main() -> Result<(), Box<dyn Error>> {
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#[derive(Clone, Debug)]
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pub(crate) enum BuildError {
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BioFormatsNotDownloaded,
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}
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impl Display for BuildError {
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fn fmt(&self, fmt: &mut Formatter) -> Result<(), std::fmt::Error> {
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write!(fmt, "Bioformats package not downloaded")
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}
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}
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impl Error for BuildError {}
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pub(crate) fn build() -> Result<(), Box<dyn Error>> {
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retry(
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Exponential::from_millis(1000).map(delay::jitter).take(4),
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deploy_java_artifacts,
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)?;
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let path = default_jassets_path()?;
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if !path.join("bioformats_package-8.5.0.jar").exists() {
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Err(BuildError::BioFormatsNotDownloaded)?;
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}
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Ok(())
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}
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fn default_jassets_path() -> Result<std::path::PathBuf, J4RsError> {
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let is_build_script = std::env::var("OUT_DIR").is_ok();
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let mut start_path = if is_build_script {
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std::path::PathBuf::from(std::env::var("OUT_DIR")?)
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} else {
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std::env::current_exe()?
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};
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start_path = std::fs::canonicalize(start_path)?;
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while start_path.pop() {
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for entry in std::fs::read_dir(&start_path)? {
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let path = entry?.path();
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if path.file_name().map(|x| x == "jassets").unwrap_or(false) {
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return Ok(path);
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}
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}
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}
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Err(J4RsError::GeneralError(
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"Can not find jassets directory".to_string(),
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))
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}
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fn deploy_java_artifacts() -> Result<(), J4RsError> {
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let jvm = JvmBuilder::new()
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.skip_setting_native_lib()
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.with_maven_settings(MavenSettings::new(vec![MavenArtifactRepo::from(
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"openmicroscopy::https://artifacts.openmicroscopy.org/artifactory/ome.releases",
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)]))
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.build()?;
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jvm.deploy_artifact(&MavenArtifact::from("ome:bioformats_package:8.5.0"))?;
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#[cfg(feature = "gpl-formats")]
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jvm.deploy_artifact(&MavenArtifact::from("ome:formats-gpl:8.5.0"))?;
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Ok(())
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}
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}
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#[cfg(all(feature = "python", feature = "bioformats_java"))]
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mod python_bioformats {
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pub(crate) fn build() -> Result<(), Box<dyn std::error::Error>> {
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let py_src_path = std::env::current_dir()?.join("py").join("ndbioimage");
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let py_jassets_path = py_src_path.join("jassets");
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let py_deps_path = py_src_path.join("deps");
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if py_jassets_path.exists() {
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std::fs::remove_dir_all(&py_jassets_path)?;
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}
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if py_deps_path.exists() {
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std::fs::remove_dir_all(&py_deps_path)?;
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}
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j4rs::Jvm::copy_j4rs_libs_under(py_src_path.to_str().unwrap())?;
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Ok(())
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}
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}
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fn main() -> Result<(), Box<dyn std::error::Error>> {
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println!("cargo::rerun-if-changed=build.rs");
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if std::env::var("DOCS_RS").is_err() {
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#[cfg(feature = "movie")]
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auto_download()?;
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ffmpeg_sidecar::download::auto_download()?;
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#[cfg(not(feature = "python"))]
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{
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retry(
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Exponential::from_millis(1000).map(delay::jitter).take(4),
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deploy_java_artifacts,
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)?;
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let path = default_jassets_path()?;
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if !path.join("bioformats_package-8.3.0.jar").exists() {
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Err(BuildError::BioFormatsNotDownloaded)?;
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}
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}
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#[cfg(feature = "bioformats_java")]
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bioformats::build()?;
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#[cfg(feature = "python")]
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{
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let py_src_path = std::env::current_dir()?.join("py").join("ndbioimage");
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let py_jassets_path = py_src_path.join("jassets");
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let py_deps_path = py_src_path.join("deps");
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if py_jassets_path.exists() {
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std::fs::remove_dir_all(&py_jassets_path)?;
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}
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if py_deps_path.exists() {
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std::fs::remove_dir_all(&py_deps_path)?;
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}
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#[cfg(all(not(feature = "python"), feature = "bioformats_java"))]
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no_python_bioformats::build()?;
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Jvm::copy_j4rs_libs_under(py_src_path.to_str().unwrap())?;
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// rename else maturin will ignore them
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for file in std::fs::read_dir(&py_deps_path)? {
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let f = file?.path().to_str().unwrap().to_string();
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if !f.ends_with("_") {
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std::fs::rename(&f, std::format!("{f}_"))?;
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}
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}
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// remove so we don't include too much accidentally
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for file in std::fs::read_dir(&py_jassets_path)? {
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let f = file?.path();
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if !f.file_name().unwrap().to_str().unwrap().starts_with("j4rs") {
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std::fs::remove_file(&f)?;
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}
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}
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}
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#[cfg(all(feature = "python", feature = "bioformats_java"))]
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python_bioformats::build()?;
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}
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Ok(())
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}
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#[cfg(not(feature = "python"))]
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fn default_jassets_path() -> Result<PathBuf, J4RsError> {
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let is_build_script = env::var("OUT_DIR").is_ok();
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let mut start_path = if is_build_script {
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PathBuf::from(env::var("OUT_DIR")?)
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} else {
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env::current_exe()?
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};
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start_path = fs::canonicalize(start_path)?;
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while start_path.pop() {
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for entry in std::fs::read_dir(&start_path)? {
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let path = entry?.path();
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if path.file_name().map(|x| x == "jassets").unwrap_or(false) {
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return Ok(path);
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}
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}
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}
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Err(J4RsError::GeneralError(
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"Can not find jassets directory".to_owned(),
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))
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}
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#[cfg(not(feature = "python"))]
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fn deploy_java_artifacts() -> Result<(), J4RsError> {
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let jvm = JvmBuilder::new()
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.skip_setting_native_lib()
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.with_maven_settings(MavenSettings::new(vec![MavenArtifactRepo::from(
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"openmicroscopy::https://artifacts.openmicroscopy.org/artifactory/ome.releases",
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)]))
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.build()?;
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jvm.deploy_artifact(&MavenArtifact::from("ome:bioformats_package:8.3.0"))?;
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#[cfg(feature = "gpl-formats")]
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jvm.deploy_artifact(&MavenArtifact::from("ome:formats-gpl:8.3.0"))?;
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Ok(())
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}
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