refactored the zipping to hopefully not change dir, removed minio due…

… to PyO3 build errors
intbio-ncl · Sep 12, 2024 · afad372 · afad372
1 parent 72fd7ac
commit afad372
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Showing 4 changed files with 28 additions and 120 deletions.
diff --git a/Cargo.toml b/Cargo.toml
@@ -27,8 +27,6 @@ url = "2.2"
 zip = "0.6.6"
 walkdir = "2"
 reqwest = { version = "0.11", features =  ["blocking", "json"], default-features = false}
-minio = {git="https://github.com/minio/minio-rs.git"}
-tokio = "1.38.0"
 
 [dev-dependencies]
 tempfile = "3.9"

diff --git a/src/ro_crate/transfer/minio.rs b/src/ro_crate/transfer/minio.rs
diff --git a/src/ro_crate/transfer/mod.rs b/src/ro_crate/transfer/mod.rs
diff --git a/src/ro_crate/write.rs b/src/ro_crate/write.rs
@@ -5,7 +5,6 @@
 
 use crate::ro_crate::read::read_crate;
 use crate::ro_crate::rocrate::RoCrate;
-use std::env;
 use std::fmt;
 use std::fs::{self, File};
 use std::io::{self, Write};
@@ -303,28 +302,27 @@ pub fn zip_crate_external(
 fn update_zip_ids(rocrate: &mut RoCrate, id: PathBuf, zip_id: &str) {
     let id_str = id.to_str().unwrap_or_default();
 
-    // NOTE: this only really checks for extended length path failures - others may be present so this can
-    // be refactored when needed
-    // base update on direct match
-    if rocrate.update_id_recursive(id_str, zip_id).is_none() {
-        // if fail - check if the ID string contains the '\\?\' prefix
-        if id_str.starts_with(r"\\?\") {
-            let stripped_id = &id_str[4..];
-            if let Some(_) = rocrate.update_id_recursive(stripped_id, zip_id) {
-            } else {
-                // if win extend length not an issue, check \\ stripping
-                if id_str.contains("\\\\") {
-                    if let Some(_) = rocrate.update_id_recursive(stripped_id, zip_id) {}
-                } else {
-                    if let Some(_) = rocrate.update_id_recursive(stripped_id, zip_id) {}
-                }
-            }
-        } else {
+    // Try updating based on a direct match
+    if rocrate.update_id_recursive(id_str, zip_id).is_some() {
+        return;
+    }
+
+    // Handle Windows extended-length path prefixes (\\?\)
+    if id_str.starts_with(r"\\?\") {
+        let stripped_id = &id_str[4..];
+
+        // Attempt to update using the stripped path
+        if rocrate.update_id_recursive(stripped_id, zip_id).is_some() {
+            return;
+        }
+
+        // Handle paths with '\\' by replacing them with a single '\'
+        if id_str.contains("\\\\") {
+            let normalized_id = stripped_id.replace("\\\\", "\\");
+            rocrate.update_id_recursive(&normalized_id, zip_id);
         }
-    } else {
     }
 }
-
 /// Identifies file paths that are not relative to the given RO-Crate directory.
 ///
 /// When preparing an RO-Crate for zipping, it's important to include all related files, even those
@@ -339,38 +337,28 @@ fn update_zip_ids(rocrate: &mut RoCrate, id: PathBuf, zip_id: &str) {
 fn get_nonrelative_paths(ids: &Vec<&String>, crate_dir: &Path) -> Vec<PathBuf> {
     let mut nonrels: Vec<PathBuf> = Vec::new();
 
+    // Get the absolute path of the crate directory
     let rocrate_path = get_absolute_path(crate_dir).unwrap();
-    let root_dir = rocrate_path.parent();
-    // Extract the directory part of the path
-    if let Some(directory_path) = root_dir {
-        // Try to change the current working directory
-        let _ = env::set_current_dir(directory_path);
-    } else {
-    }
 
-    // Iterate over all the ids, check the paths are relative to crate.
-    // If not relative to crate and a file, then grab, add to extern folder
-    // and zip
+    // Iterate over all the ids, check if the paths are relative to the crate.
     for id in ids.iter() {
+        // Skip IDs that are fragment references (i.e., starting with '#')
         if id.starts_with('#') {
             continue;
         }
+
+        // Resolve the absolute path of the current ID
         if let Some(path) = get_absolute_path(Path::new(id)) {
+            // Check if the path exists
             if path.exists() {
-                let nonrel = is_outside_base_folder(root_dir.unwrap(), &path);
-                if nonrel {
-                    if id.starts_with(".") {
-                        nonrels.push(id.into());
-                    } else {
-                        nonrels.push(path);
-                    }
+                // Check if the path is outside the base crate directory
+                if is_outside_base_folder(&rocrate_path, &path) {
+                    nonrels.push(path);
                 }
-            } else {
             }
-        } else {
-            continue;
         }
     }
+
     nonrels
 }
 /// Converts a relative path to an absolute one, if possible.