From 9e8a6bcd74fe7fa306af59bf5b69bfdd32bc2693 Mon Sep 17 00:00:00 2001
From: Miquel Duran-Frigola <miquelduranfrigola@gmail.com>
Date: Tue, 27 Jun 2023 13:28:24 +0200
Subject: [PATCH] update version [skip ci]

---
 ersilia/_static_version.py   |  2 +-
 ersilia/hub/pull/pull.py     |  2 +-
 ersilia/serve/autoservice.py |  3 +++
 ersilia/serve/services.py    |  8 ++++----
 ersilia/utils/docker.py      | 17 ++++++++++++++---
 5 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/ersilia/_static_version.py b/ersilia/_static_version.py
index 9eaa0426..a543ebb1 100644
--- a/ersilia/_static_version.py
+++ b/ersilia/_static_version.py
@@ -1 +1 @@
-version = "0.1.16"
+version = "0.1.17"
diff --git a/ersilia/hub/pull/pull.py b/ersilia/hub/pull/pull.py
index d791740d..ee52385a 100644
--- a/ersilia/hub/pull/pull.py
+++ b/ersilia/hub/pull/pull.py
@@ -97,7 +97,7 @@ def pull(self):
                         DOCKERHUB_ORG, self.model_id, DOCKERHUB_LATEST_TAG
                     )
                 )
-            # except:
+            # except: #TODO add better error
             #    raise DockerImageArchitectureNotAvailableError(model=self.model_id)
         else:
             self.logger.info("Image {0} is not available".format(self.image_name))
diff --git a/ersilia/serve/autoservice.py b/ersilia/serve/autoservice.py
index 6d776856..0ba74a2f 100644
--- a/ersilia/serve/autoservice.py
+++ b/ersilia/serve/autoservice.py
@@ -290,8 +290,10 @@ def clean_docker_containers(self):
         self.logger.debug("Silencing docker containers if necessary")
         dm = DockerManager(config_json=self.config_json)
         if dm.is_inside_docker():
+            self.logger.debug("It is inside docker")
             return
         if dm.is_installed():
+            self.logger.debug("It is not inside docker")
             dm.stop_containers(self.model_id)
 
     def serve(self):
@@ -311,6 +313,7 @@ def close(self):
             os.remove(tmp_file)
         self.clean_temp_dir()
         self.clean_docker_containers()
+        self.service.close()
 
     def api(
         self, api_name, input, output=DEFAULT_OUTPUT, batch_size=DEFAULT_BATCH_SIZE
diff --git a/ersilia/serve/services.py b/ersilia/serve/services.py
index 7c872549..b34c1a52 100644
--- a/ersilia/serve/services.py
+++ b/ersilia/serve/services.py
@@ -460,7 +460,7 @@ def __init__(self, model_id, config_json=None, preferred_port=None):
         self.image_name = "{0}/{1}:{2}".format(
             DOCKERHUB_ORG, self.model_id, DOCKERHUB_LATEST_TAG
         )
-        self.logger.debug("Staring Docker Daemon service")
+        self.logger.debug("Starting Docker Daemon service")
         self.tmp_folder = tempfile.mkdtemp(prefix="ersilia-")
         self.logger.debug(
             "Creating temporary folder {0} and mounting as volume in container".format(
@@ -507,7 +507,9 @@ def _stop_all_containers_of_image(self):
                     "Stopping and removing container {0}".format(container.name)
                 )
                 container.stop()
+                self.logger.debug("Container stopped")
                 container.remove()
+                self.logger.debug("Container removed")
 
     def _get_apis(self):
         file_name = os.path.join(
@@ -575,7 +577,5 @@ def api(self, api_name, input):
         return self._api_with_url(api_name=api_name, input=input)
 
     def close(self):
-        self.logger.debug(
-            "Stopping and removing container {0}".format(self.container_id)
-        )
+        self.logger.debug("Stopping and removing container")
         self._stop_all_containers_of_image()
diff --git a/ersilia/utils/docker.py b/ersilia/utils/docker.py
index 62fd4bee..0c258aa0 100644
--- a/ersilia/utils/docker.py
+++ b/ersilia/utils/docker.py
@@ -149,14 +149,25 @@ def remove(name):
         run_command(cmd)
 
     @staticmethod
-    def cp_from_container(name, img_path, local_path):
+    def cp_from_container(name, img_path, local_path, org=None, img=None, tag=None):
         local_path = os.path.abspath(local_path)
-        cmd = "docker cp %s:%s %s" % (name, img_path, local_path)
+        tmp_file = os.path.join(tempfile.mkdtemp(prefix="ersilia-"), "tmp.txt")
+        cmd = "docker cp %s:%s %s &> %s" % (name, img_path, local_path, tmp_file)
         run_command(cmd)
+        with open(tmp_file, "r") as f:
+            output = f.read()
+        if "No such container" in output:
+            img_name = "{0}/{1}:{2}".format(org, img, tag)
+            cmd = "docker run --platform linux/amd64 -d --name={0} {1}".format(
+                name, img_name
+            )
+            run_command(cmd)
+            cmd = "docker cp %s:%s %s" % (name, img_path, local_path)
+            run_command(cmd)
 
     def cp_from_image(self, img_path, local_path, org, img, tag):
         name = self.run(org, img, tag, name=None)
-        self.cp_from_container(name, img_path, local_path)
+        self.cp_from_container(name, img_path, local_path, org=org, img=img, tag=tag)
         self.remove(name)
 
     @staticmethod