Merge branch 'release_23.1' into release_23.2

dannon · Nov 29, 2023 · 59d48ff · 59d48ff
2 parents 8874d69 + cd46ff3
commit 59d48ff
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Showing 4 changed files with 25 additions and 3 deletions.
diff --git a/client/gulpfile.js b/client/gulpfile.js
@@ -120,6 +120,20 @@ function buildPlugins(callback, forceRebuild) {
             skipBuild = false;
         } else {
             if (fs.existsSync(hashFilePath)) {
+                const hashFileContent = fs.readFileSync(hashFilePath, "utf8").trim();
+                const isHash = /^[0-9a-f]{7,40}$/.test(hashFileContent); // Check for a 7 to 40 character hexadecimal string
+
+                if (!isHash) {
+                    console.log(`Hash file for ${pluginName} exists but does not have a valid git hash.`);
+                    skipBuild = false;
+                } else {
+                    skipBuild =
+                        child_process.spawnSync("git", ["diff", "--quiet", hashFileContent, "--", pluginDir], {
+                            stdio: "inherit",
+                            shell: true,
+                        }).status === 0;
+                }
+
                 skipBuild =
                     child_process.spawnSync("git", ["diff", "--quiet", `$(cat ${hashFilePath})`, "--", pluginDir], {
                         stdio: "inherit",

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
@@ -861,7 +861,14 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
         self.install_database_engine_options = get_database_engine_options(kwargs, model_prefix="install_")
         self.shared_home_dir = kwargs.get("shared_home_dir")
         self.cookie_path = kwargs.get("cookie_path")
-        self.tool_path = self._in_root_dir(self.tool_path)
+        if not running_from_source and kwargs.get("tool_path") is None:
+            try:
+                self.tool_path = str(files("galaxy.tools") / "bundled")
+            except ModuleNotFoundError:
+                # Might not be a full galaxy installation
+                self.tool_path = self._in_root_dir(self.tool_path)
+        else:
+            self.tool_path = self._in_root_dir(self.tool_path)
         self.tool_data_path = self._in_root_dir(self.tool_data_path)
         if not running_from_source and kwargs.get("tool_data_path") is None:
             self.tool_data_path = self._in_data_dir(self.schema.defaults["tool_data_path"])

diff --git a/lib/galaxy/files/sources/s3fs.py b/lib/galaxy/files/sources/s3fs.py
@@ -71,7 +71,8 @@ def _realize_to(self, source_path, native_path, user_context=None, opts: Optiona
         self._open_fs(user_context=user_context, opts=opts).download(bucket_path, native_path)
 
     def _write_from(self, target_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
-        raise NotImplementedError()
+        bucket_path = self._bucket_path(target_path)
+        self._open_fs(user_context=user_context, opts=opts).upload(native_path, bucket_path)
 
     def _bucket_path(self, path: str):
         if path.startswith("s3://"):

diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg
@@ -36,7 +36,7 @@ install_requires =
     galaxy-data
     galaxy-job-execution
     galaxy-tool-util
-    galaxy-util
+    galaxy-util[jstree,template]
     galaxy-web-framework
     galaxy-web-stack
     a2wsgi