Initial commit

ersilia/hub/fetch/actions/get.py

@@ -18,7 +18,7 @@
 
 
 class ModelRepositoryGetter(BaseAction):
-    def __init__(self, model_id, config_json, force_from_github, force_from_s3):
+    def __init__(self, model_id, config_json, force_from_github, force_from_s3, repo_path):
         BaseAction.__init__(
             self, model_id=model_id, config_json=config_json, credentials_json=None
         )
@@ -28,6 +28,7 @@ def __init__(self, model_id, config_json, force_from_github, force_from_s3):
         self.org = self.cfg.HUB.ORG
         self.force_from_github = force_from_github
         self.force_from_s3 = force_from_s3
+        self.repo_path = repo_path
 
     def _dev_model_path(self):
         pt = Paths()
@@ -87,6 +88,23 @@ def _change_py_version_in_dockerfile_if_necessary(self):
             for s in S:
                 f.write(s + os.linesep)
 
+    @staticmethod
+    def _is_sudo():
+        return os.geteuid() == 0
+
+    def _remove_sudo_if_root(self):
+        path = self._model_path(model_id=self.model_id)
+        dockerfile_path = os.path.join(path, "Dockerfile")
+        if self.is_sudo():
+            self.logger.debug("User is root! Removing sudo commands")
+            with open(dockerfile_path, "r") as f:
+                content = f.read()
+                content = content.replace("RUN sudo ", "RUN ")
+            with open(dockerfile_path, "w") as f:
+                f.write(content)
+        else:
+            self.logger.debug("User is not root")
+
     @throw_ersilia_exception
     def get(self):
         """Copy model repository from local or download from S3 or GitHub"""
@@ -98,21 +116,25 @@ def get(self):
             )
             self._copy_from_local(dev_model_path, folder)
         else:
-            if self.force_from_github:
-                self._copy_from_github(folder)
+            if self.repo_path is not None:
+                self._copy_from_local(self.repo_path, folder)
             else:
-                try:
-                    self.logger.debug("Trying to download from S3")
-                    self._copy_zip_from_s3(folder)
-                except:
-                    self.logger.debug(
-                        "Could not download in zip format in S3. Downloading from GitHub repository."
-                    )
-                    if self.force_from_s3:
-                        raise S3DownloaderError(model_id=self.model_id)
-                    else:
-                        self._copy_from_github(folder)
+                if self.force_from_github:
+                    self._copy_from_github(folder)
+                else:
+                    try:
+                        self.logger.debug("Trying to download from S3")
+                        self._copy_zip_from_s3(folder)
+                    except:
+                        self.logger.debug(
+                            "Could not download in zip format in S3. Downloading from GitHub repository."
+                        )
+                        if self.force_from_s3:
+                            raise S3DownloaderError(model_id=self.model_id)
+                        else:
+                            self._copy_from_github(folder)
         self._change_py_version_in_dockerfile_if_necessary()
+        self._remove_sudo_if_root()
 
 
 #  TODO: work outside GIT LFS
@@ -158,6 +180,7 @@ def __init__(
             config_json=config_json,
             force_from_github=force_from_gihtub,
             force_from_s3=force_from_s3,
+            repo_path=repo_path
         )
         self.mpg = ModelParametersGetter(model_id=model_id, config_json=config_json)
 
@@ -167,17 +190,10 @@ def _get_repository(self):
     def _get_model_parameters(self):
         self.mpg.get()
 
-    def _copy_from_repo_path(self):
-        dst = self._model_path(self.model_id)
-        src = self.repo_path
-        shutil.copytree(src, dst)
-
     @throw_ersilia_exception
     def get(self):
+        self._get_repository()
         if self.repo_path is None:
-            self._get_repository()
             self._get_model_parameters()
-        else:
-            self._copy_from_repo_path()
         if not os.path.exists(self._model_path(self.model_id)):
             raise FolderNotFoundError(os.path.exists(self._model_path(self.model_id)))