fix: avoid incomplete remote files in case of errors and automatically retry download and upload

setup.py

@@ -79,6 +79,7 @@
         "tabulate",
         "yte >=1.0,<2.0",
         "jinja2 >=3.0,<4.0",
+        "retry",
     ],
     extras_require={
         "reports": ["jinja2", "networkx", "pygments", "pygraphviz"],
@@ -92,7 +93,7 @@
         "pep": [
             "peppy",
             "eido",
-        ]
+        ],
     },
     classifiers=[
         "Development Status :: 5 - Production/Stable",

snakemake/dag.py

@@ -2247,18 +2247,19 @@ def get_outputs_with_changes(self, change_type):
                     changed.extend(list(job.outputs_older_than_script_or_notebook()))
         return changed
 
-    def warn_about_changes(self):
-        for change_type in ["code", "input", "params"]:
-            changed = self.get_outputs_with_changes(change_type)
-            if changed:
-                rerun_trigger = ""
-                if not ON_WINDOWS:
-                    rerun_trigger = f"\n    To trigger a re-run, use 'snakemake -R $(snakemake --list-{change_type}-changes)'."
-                logger.warning(
-                    f"The {change_type} used to generate one or several output files has changed:\n"
-                    f"    To inspect which output files have changes, run 'snakemake --list-{change_type}-changes'."
-                    f"{rerun_trigger}"
-                )
+    def warn_about_changes(self, quiet=False):
+        if not quiet:
+            for change_type in ["code", "input", "params"]:
+                changed = self.get_outputs_with_changes(change_type)
+                if changed:
+                    rerun_trigger = ""
+                    if not ON_WINDOWS:
+                        rerun_trigger = f"\n    To trigger a re-run, use 'snakemake -R $(snakemake --list-{change_type}-changes)'."
+                    logger.warning(
+                        f"The {change_type} used to generate one or several output files has changed:\n"
+                        f"    To inspect which output files have changes, run 'snakemake --list-{change_type}-changes'."
+                        f"{rerun_trigger}"
+                    )
 
     def __str__(self):
         return self.dot()

snakemake/remote/AzBlob.py

@@ -15,7 +15,11 @@
 
 # module specific
 from snakemake.exceptions import WorkflowError, AzureFileException
-from snakemake.remote import AbstractRemoteObject, AbstractRemoteProvider
+from snakemake.remote import (
+    AbstractRemoteObject,
+    AbstractRemoteProvider,
+    AbstractRemoteRetryObject,
+)
 
 # service provider support
 try:
@@ -60,7 +64,7 @@ def available_protocols(self):
         return ["ab://"]
 
 
-class RemoteObject(AbstractRemoteObject):
+class RemoteObject(AbstractRemoteRetryObject):
     def __init__(self, *args, keep_local=False, provider=None, **kwargs):
         super(RemoteObject, self).__init__(
             *args, keep_local=keep_local, provider=provider, **kwargs
@@ -95,7 +99,7 @@ def size(self):
             return self._as.blob_size(self.container_name, self.blob_name)
         return self._iofile.size_local
 
-    def download(self):
+    def _download(self):
         if self.exists():
             os.makedirs(os.path.dirname(self.local_file()), exist_ok=True)
             self._as.download_from_azure_storage(
@@ -105,7 +109,7 @@ def download(self):
             return self.local_file()
         return None
 
-    def upload(self):
+    def _upload(self):
         self._as.upload_to_azure_storage(
             container_name=self.container_name,
             blob_name=self.blob_name,

snakemake/remote/EGA.py

@@ -14,9 +14,14 @@
 from requests.auth import HTTPBasicAuth
 
 
-from snakemake.remote import AbstractRemoteObject, AbstractRemoteProvider
+from snakemake.remote import (
+    AbstractRemoteObject,
+    AbstractRemoteProvider,
+    check_deprecated_retry,
+)
 from snakemake.exceptions import WorkflowError
 from snakemake.common import lazy_property
+from snakemake.logging import logger
 
 
 EGAFileInfo = namedtuple("EGAFileInfo", ["size", "status", "id", "checksum"])
@@ -30,7 +35,7 @@ def __init__(
         keep_local=False,
         stay_on_remote=False,
         is_default=False,
-        retry=5,
+        retry=None,
         **kwargs
     ):
         super().__init__(
@@ -40,7 +45,7 @@ def __init__(
             is_default=is_default,
             **kwargs
         )
-        self.retry = retry
+        check_deprecated_retry(retry)
         self._token = None
         self._expires = None
         self._file_cache = dict()
@@ -193,7 +198,7 @@ def _credentials(cls, name):
             )
 
 
-class RemoteObject(AbstractRemoteObject):
+class RemoteObject(AbstractRemoteRetryObject):
     # === Implementations of abstract class members ===
     def _stats(self):
         return self.provider.get_files(self.parts.dataset)[self.parts.path]
@@ -209,7 +214,7 @@ def mtime(self):
         # Hence, the files are always considered to be "ancient".
         return 0
 
-    def download(self):
+    def _download(self):
         stats = self._stats()
 
         r = self.provider.api_request(

snakemake/remote/FTP.py

@@ -179,7 +179,7 @@ def size(self):
         else:
             return self._iofile.size_local
 
-    def download(self, make_dest_dirs=True):
+    def _download(self, make_dest_dirs=True):
         with self.connection_pool.item() as ftpc:
             if self.exists():
                 # if the destination path does not exist
@@ -197,7 +197,7 @@ def download(self, make_dest_dirs=True):
                     "The file does not seem to exist remotely: %s" % self.local_file()
                 )
 
-    def upload(self):
+    def _upload(self):
         with self.connection_pool.item() as ftpc:
             ftpc.synchronize_times()
             ftpc.upload(source=self.local_path, target=self.remote_path)

snakemake/remote/GS.py

@@ -220,7 +220,7 @@ def size(self):
             return self._iofile.size_local
 
     @retry.Retry(predicate=google_cloud_retry_predicate, deadline=600)
-    def download(self):
+    def _download(self):
         """Download with maximum retry duration of 600 seconds (10 minutes)"""
         if not self.exists():
             return None
@@ -251,7 +251,7 @@ def _download_directory(self):
         return self.local_file()
 
     @retry.Retry(predicate=google_cloud_retry_predicate)
-    def upload(self):
+    def _upload(self):
         try:
             if not self.bucket.exists():
                 self.bucket.create()

snakemake/remote/HTTP.py

@@ -209,7 +209,7 @@ def size(self):
         else:
             return self._iofile.size_local
 
-    def download(self, make_dest_dirs=True):
+    def _download(self, make_dest_dirs=True):
         with self.httpr(stream=True) as httpr:
             if self.exists():
                 # Find out if the source file is gzip compressed in order to keep
@@ -237,7 +237,7 @@ def download(self, make_dest_dirs=True):
                     "The file does not seem to exist remotely: %s" % self.remote_file()
                 )
 
-    def upload(self):
+    def _upload(self):
         raise HTTPFileException(
             "Upload is not permitted for the HTTP remote provider. Is an output set to HTTP.remote()?"
         )

snakemake/remote/NCBI.py

@@ -139,7 +139,7 @@ def size(self):
         else:
             return self._iofile.size_local
 
-    def download(self):
+    def _download(self):
         if self.exists():
             self._ncbi.fetch_from_ncbi(
                 [self.accession],
@@ -155,7 +155,7 @@ def download(self):
                 "The record does not seem to exist remotely: %s" % self.accession
             )
 
-    def upload(self):
+    def _upload(self):
         raise NCBIFileException(
             "Upload is not permitted for the NCBI remote provider. Is an output set to NCBI.RemoteProvider.remote()?"
         )

snakemake/remote/S3.py

@@ -11,7 +11,11 @@
 import concurrent.futures
 
 # module-specific
-from snakemake.remote import AbstractRemoteObject, AbstractRemoteProvider
+from snakemake.remote import (
+    AbstractRemoteObject,
+    AbstractRemoteProvider,
+    AbstractRemoteRetryObject,
+)
 from snakemake.exceptions import WorkflowError, S3FileException
 from snakemake.utils import os_sync
 
@@ -59,7 +63,7 @@ def available_protocols(self):
         return ["s3://"]
 
 
-class RemoteObject(AbstractRemoteObject):
+class RemoteObject(AbstractRemoteRetryObject):
     """This is a class to interact with the AWS S3 object store."""
 
     def __init__(self, *args, keep_local=False, provider=None, **kwargs):
@@ -97,11 +101,11 @@ def size(self):
         else:
             return self._iofile.size_local
 
-    def download(self):
+    def _download(self):
         self._s3c.download_from_s3(self.s3_bucket, self.s3_key, self.local_file())
         os_sync()  # ensure flush to disk
 
-    def upload(self):
+    def _upload(self):
         self._s3c.upload_to_s3(
             self.s3_bucket,
             self.local_file(),

snakemake/remote/SFTP.py

@@ -120,7 +120,7 @@ def size(self):
         else:
             return self._iofile.size_local
 
-    def download(self, make_dest_dirs=True):
+    def _download(self, make_dest_dirs=True):
         with self.connection_pool.item() as sftpc:
             if self.exists():
                 # if the destination path does not exist
@@ -156,7 +156,7 @@ def mkdir_remote_path(self):
                     sftpc.mkdir(part)
                     sftpc.chdir(part)
 
-    def upload(self):
+    def _upload(self):
         if self.provider.mkdir_remote:
             self.mkdir_remote_path()
 

snakemake/remote/XRootD.py

@@ -8,7 +8,11 @@
 import re
 
 from stat import S_ISREG
-from snakemake.remote import AbstractRemoteObject, AbstractRemoteProvider
+from snakemake.remote import (
+    AbstractRemoteObject,
+    AbstractRemoteProvider,
+    AbstractRemoteRetryObject,
+)
 from snakemake.exceptions import WorkflowError, XRootDFileException
 
 try:
@@ -51,7 +55,7 @@ def available_protocols(self):
         return ["root://", "roots://", "rootk://"]
 
 
-class RemoteObject(AbstractRemoteObject):
+class RemoteObject(AbstractRemoteRetryObject):
     """This is a class to interact with XRootD servers."""
 
     def __init__(
@@ -89,11 +93,11 @@ def size(self):
         else:
             return self._iofile.size_local
 
-    def download(self):
+    def _download(self):
         assert not self.stay_on_remote
         self._xrd.copy(self.remote_file(), self.file())
 
-    def upload(self):
+    def _upload(self):
         assert not self.stay_on_remote
         self._xrd.copy(self.file(), self.remote_file())
 

snakemake/remote/__init__.py

@@ -9,8 +9,11 @@
 import re
 from functools import partial
 from abc import ABCMeta, abstractmethod
-from wrapt import ObjectProxy
 from contextlib import contextmanager
+import shutil
+
+from wrapt import ObjectProxy
+from retry import retry
 
 try:
     from connection_pool import ConnectionPool
@@ -22,6 +25,7 @@
 import collections
 
 # module-specific
+from snakemake.exceptions import WorkflowError
 import snakemake.io
 from snakemake.logging import logger
 from snakemake.common import parse_uri
@@ -225,12 +229,29 @@ def mtime(self):
     def size(self):
         pass
 
+    def download(self):
+        try:
+            return self._download()
+        except Exception as e:
+            local_path = self.local_file()
+            if os.path.exists(local_path):
+                if os.path.isdir(local_path):
+                    shutil.rmtree(local_path)
+                os.remove(local_path)
+            raise WorkflowError(e)
+
+    def upload(self):
+        try:
+            self._upload()
+        except Exception as e:
+            raise WorkflowError(e)
+
     @abstractmethod
-    def download(self, *args, **kwargs):
+    def _download(self, *args, **kwargs):
         pass
 
     @abstractmethod
-    def upload(self, *args, **kwargs):
+    def _upload(self, *args, **kwargs):
         pass
 
     @abstractmethod
@@ -253,7 +274,17 @@ def local_touch_or_create(self):
         self._iofile.touch_or_create()
 
 
-class DomainObject(AbstractRemoteObject):
+class AbstractRemoteRetryObject(AbstractRemoteObject):
+    @retry(tries=3, delay=3, backoff=2, logger=logger)
+    def download(self):
+        return super().download()
+
+    @retry(tries=3, delay=3, backoff=2, logger=logger)
+    def upload(self):
+        super().upload()
+
+
+class DomainObject(AbstractRemoteRetryObject):
     """This is a mixin related to parsing components
     out of a location path specified as
     (host|IP):port/remote/location
@@ -474,3 +505,10 @@ def remote(self, value, *args, provider_kws=None, **kwargs):
 
 
 AUTO = AutoRemoteProvider()
+
+
+def check_deprecated_retry(retry):
+    if retry:
+        logger.warning(
+            "Using deprecated retry argument. Snakemake now always uses 3 retries on download and upload."
+        )