From ee710a4ed141c89f3ba6e38606bb86a7d5370154 Mon Sep 17 00:00:00 2001
From: Patrik Smeds <patrik.smeds@gmail.com>
Date: Wed, 7 May 2025 14:51:13 -0400
Subject: [PATCH 1/2] function used to import an invocation archive. Needs API
 updates before it can be merged.

---
 bioblend/_tests/TestGalaxyInvocations.py  |   9 ++++++
 bioblend/_tests/data/example3.rocrate.zip | Bin 0 -> 11109 bytes
 bioblend/galaxy/invocations/__init__.py   |  34 ++++++++++++++++++++++
 3 files changed, 43 insertions(+)
 create mode 100644 bioblend/_tests/data/example3.rocrate.zip

diff --git a/bioblend/_tests/TestGalaxyInvocations.py b/bioblend/_tests/TestGalaxyInvocations.py
index 6f4b1a302..8dfd9fecc 100644
--- a/bioblend/_tests/TestGalaxyInvocations.py
+++ b/bioblend/_tests/TestGalaxyInvocations.py
@@ -112,6 +112,15 @@ def test_get_invocation_jobs_summary(self):
         assert len(step_jobs_summary) == 1
         assert step_jobs_summary[0]["populated_state"] == "ok"
 
+    @test_util.skip_unless_galaxy("release_23.0")
+    def test_import_invocation_archive(self):
+        new_history = self.gi.histories.create_history(name="My History")
+        test_file = test_util.get_abspath(os.path.join("data", "example3.rocrate.zip"))
+        import_response = self.gi.invocations.import_invocation(
+            history_id=new_history["id"], model_store_format="rocrate.zip", file_path=test_file
+        )
+        assert "model_class" in import_response[0] and import_response[0]["model_class"] == "WorkflowInvocation"
+
     @test_util.skip_unless_galaxy("release_19.09")
     @test_util.skip_unless_tool("cat1")
     @test_util.skip_unless_tool("cat")
diff --git a/bioblend/_tests/data/example3.rocrate.zip b/bioblend/_tests/data/example3.rocrate.zip
new file mode 100644
index 0000000000000000000000000000000000000000..6ed84a307faba950b923017837aec4d2d3b937f8
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diff --git a/bioblend/galaxy/invocations/__init__.py b/bioblend/galaxy/invocations/__init__.py
index 67b912577..2bb7ff8ec 100644
--- a/bioblend/galaxy/invocations/__init__.py
+++ b/bioblend/galaxy/invocations/__init__.py
@@ -2,6 +2,7 @@
 Contains possible interactions with the Galaxy workflow invocations
 """
 
+import base64
 import logging
 from typing import (
     Any,
@@ -267,6 +268,39 @@ def cancel_invocation(self, invocation_id: str) -> dict[str, Any]:
         url = self._make_url(invocation_id)
         return self._delete(url=url)
 
+    def import_invocation(
+        self, history_id: str, model_store_format: str, file_path: Optional[str] = None, url: Optional[str] = None
+    ) -> Any:
+        """
+        Import a invocation from an archive on disk or a URL.
+
+        :type history_id
+        :param history_id: id of the history where the invocation will be imported
+
+        :type model_store_format
+        :param model_store_format: archive type that will be imported
+
+        :type file_path: str
+        :param file_path: Path to exported history archive on disk.
+
+        :type url: str
+        :param url: URL for an exported history archive
+
+        :rtype: dict or list of dicts
+        :return: if the import is successful, a list of dictionaries will be returned; otherwise, a single dictionary will be returned.
+        """
+        payload: dict[str, Any] = {
+            "history_id": history_id,
+            "model_store_format": model_store_format,
+        }
+        if file_path:
+            with open(file_path, "rb") as reader:
+                payload["store_content_uri"] = "base64://" + base64.b64encode(reader.read()).decode("utf-8")
+        else:
+            payload["store_content_uri"] = url
+        url = "/".join((self._make_url(), "from_store"))
+        return self._post(url=url, payload=payload)
+
     def show_invocation_step(self, invocation_id: str, step_id: str) -> dict[str, Any]:
         """
         See the details of a particular workflow invocation step.

From e82eca98fdefcfb2da387bb19ad53b9b5d136bc1 Mon Sep 17 00:00:00 2001
From: Patrik Smeds <patrik.smeds@gmail.com>
Date: Fri, 30 May 2025 12:12:50 -0400
Subject: [PATCH 2/2] modify import function to use tus client to upload files,
 instead of reading it into memory

---
 bioblend/_tests/TestGalaxyInvocations.py |  7 +++++--
 bioblend/galaxy/invocations/__init__.py  | 18 ++++++++++++++----
 2 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/bioblend/_tests/TestGalaxyInvocations.py b/bioblend/_tests/TestGalaxyInvocations.py
index 8dfd9fecc..669ad9da8 100644
--- a/bioblend/_tests/TestGalaxyInvocations.py
+++ b/bioblend/_tests/TestGalaxyInvocations.py
@@ -112,12 +112,15 @@ def test_get_invocation_jobs_summary(self):
         assert len(step_jobs_summary) == 1
         assert step_jobs_summary[0]["populated_state"] == "ok"
 
-    @test_util.skip_unless_galaxy("release_23.0")
+    @test_util.skip_unless_galaxy("release_25.01")
     def test_import_invocation_archive(self):
         new_history = self.gi.histories.create_history(name="My History")
         test_file = test_util.get_abspath(os.path.join("data", "example3.rocrate.zip"))
         import_response = self.gi.invocations.import_invocation(
-            history_id=new_history["id"], model_store_format="rocrate.zip", file_path=test_file
+            history_id=new_history["id"],
+            model_store_format="rocrate.zip",
+            file_path=test_file,
+            upload_url="/upload/resumable_upload",
         )
         assert "model_class" in import_response[0] and import_response[0]["model_class"] == "WorkflowInvocation"
 
diff --git a/bioblend/galaxy/invocations/__init__.py b/bioblend/galaxy/invocations/__init__.py
index 2bb7ff8ec..23b17ed04 100644
--- a/bioblend/galaxy/invocations/__init__.py
+++ b/bioblend/galaxy/invocations/__init__.py
@@ -2,7 +2,6 @@
 Contains possible interactions with the Galaxy workflow invocations
 """
 
-import base64
 import logging
 from typing import (
     Any,
@@ -269,7 +268,13 @@ def cancel_invocation(self, invocation_id: str) -> dict[str, Any]:
         return self._delete(url=url)
 
     def import_invocation(
-        self, history_id: str, model_store_format: str, file_path: Optional[str] = None, url: Optional[str] = None
+        self,
+        history_id: str,
+        model_store_format: str,
+        file_path: Optional[str] = None,
+        url: Optional[str] = None,
+        upload_url: str = "/invocations/resumable_upload",
+        chunk_size: int = CHUNK_SIZE,
     ) -> Any:
         """
         Import a invocation from an archive on disk or a URL.
@@ -286,6 +291,9 @@ def import_invocation(
         :type url: str
         :param url: URL for an exported history archive
 
+        :type chunk_size: int
+        :param chunk_size: Number of bytes to send in each chunk
+
         :rtype: dict or list of dicts
         :return: if the import is successful, a list of dictionaries will be returned; otherwise, a single dictionary will be returned.
         """
@@ -294,8 +302,10 @@ def import_invocation(
             "model_store_format": model_store_format,
         }
         if file_path:
-            with open(file_path, "rb") as reader:
-                payload["store_content_uri"] = "base64://" + base64.b64encode(reader.read()).decode("utf-8")
+            uploader = self.gi.get_tus_uploader(path=file_path, url=upload_url, chunk_size=chunk_size)
+            uploader.upload()
+            assert uploader.session_id
+            payload["store_content_uri"] = f"tus://{uploader.session_id}"
         else:
             payload["store_content_uri"] = url
         url = "/".join((self._make_url(), "from_store"))