toil 9.0.0__py3-none-any.whl → 9.1.0__py3-none-any.whl

toil/lib/checksum.py

@@ -0,0 +1,88 @@
+# Copyright (C) 2015-2021 Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import logging
+import hashlib
+
+from io import BytesIO
+from typing import BinaryIO, Union, List, TYPE_CHECKING
+
+from toil.lib.aws.config import S3_PART_SIZE
+
+if TYPE_CHECKING:
+    # mypy complaint: https://github.com/python/typeshed/issues/2928
+    from hashlib import _Hash
+
+
+logger = logging.getLogger(__name__)
+
+
+class ChecksumError(Exception):
+    """Raised when a download does not contain the correct data."""
+
+
+class Etag:
+    """A hasher for s3 etags."""
+    def __init__(self, chunk_size: int) -> None:
+        self.etag_bytes: int = 0
+        self.etag_parts: List[bytes] = []
+        self.etag_hasher: "_Hash" = hashlib.md5()
+        self.chunk_size: int = chunk_size
+
+    def update(self, chunk: bytes) -> None:
+        if self.etag_bytes + len(chunk) > self.chunk_size:
+            chunk_head = chunk[:self.chunk_size - self.etag_bytes]
+            chunk_tail = chunk[self.chunk_size - self.etag_bytes:]
+            self.etag_hasher.update(chunk_head)
+            self.etag_parts.append(self.etag_hasher.digest())
+            self.etag_hasher = hashlib.md5()
+            self.etag_hasher.update(chunk_tail)
+            self.etag_bytes = len(chunk_tail)
+        else:
+            self.etag_hasher.update(chunk)
+            self.etag_bytes += len(chunk)
+
+    def hexdigest(self) -> str:
+        if self.etag_bytes:
+            self.etag_parts.append(self.etag_hasher.digest())
+            self.etag_bytes = 0
+        if len(self.etag_parts) > 1:
+            etag = hashlib.md5(b"".join(self.etag_parts)).hexdigest()
+            return f'{etag}-{len(self.etag_parts)}'
+        else:
+            return self.etag_hasher.hexdigest()
+
+
+hashers = {'sha1':    hashlib.sha1(),
+           'sha256':  hashlib.sha256(),
+           'etag': Etag(chunk_size=S3_PART_SIZE)}
+
+
+def compute_checksum_for_file(local_file_path: str, algorithm: str = 'sha1') -> str:
+    with open(local_file_path, 'rb') as fh:
+        checksum_result = compute_checksum_for_content(fh, algorithm=algorithm)
+    return checksum_result
+
+
+def compute_checksum_for_content(fh: Union[BinaryIO, BytesIO], algorithm: str = 'sha1') -> str:
+    """
+    Note: Chunk size matters for s3 etags, and must be the same to get the same hash from the same object.
+    Therefore this buffer is not modifiable throughout Toil.
+    """
+    hasher: "_Hash" = hashers[algorithm]  # type: ignore
+    contents = fh.read(S3_PART_SIZE)
+    while contents != b'':
+        hasher.update(contents)
+        contents = fh.read(S3_PART_SIZE)
+
+    return f'{algorithm}${hasher.hexdigest()}'

toil/lib/conversions.py

@@ -2,40 +2,28 @@
 Conversion utilities for mapping memory, disk, core declarations from strings to numbers and vice versa.
 Also contains general conversion functions
 """
-
 import math
-from typing import Optional, SupportsInt, Union
+import urllib.parse
+
+from typing import Optional, SupportsInt, Union, List
+
+KIB = 1024
+MIB = 1024 ** 2
+GIB = 1024 ** 3
+TIB = 1024 ** 4
+PIB = 1024 ** 5
+EIB = 1024 ** 6
+
+KB = 1000
+MB = 1000 ** 2
+GB = 1000 ** 3
+TB = 1000 ** 4
+PB = 1000 ** 5
+EB = 1000 ** 6
 
 # See https://en.wikipedia.org/wiki/Binary_prefix
-BINARY_PREFIXES = [
-    "ki",
-    "mi",
-    "gi",
-    "ti",
-    "pi",
-    "ei",
-    "kib",
-    "mib",
-    "gib",
-    "tib",
-    "pib",
-    "eib",
-]
-DECIMAL_PREFIXES = [
-    "b",
-    "k",
-    "m",
-    "g",
-    "t",
-    "p",
-    "e",
-    "kb",
-    "mb",
-    "gb",
-    "tb",
-    "pb",
-    "eb",
-]
+BINARY_PREFIXES = ['ki', 'mi', 'gi', 'ti', 'pi', 'ei', 'kib', 'mib', 'gib', 'tib', 'pib', 'eib']
+DECIMAL_PREFIXES = ['b', 'k', 'm', 'g', 't', 'p', 'e', 'kb', 'mb', 'gb', 'tb', 'pb', 'eb']
 VALID_PREFIXES = BINARY_PREFIXES + DECIMAL_PREFIXES
 
 
@@ -185,3 +173,17 @@ def strtobool(val: str) -> bool:
 def opt_strtobool(b: Optional[str]) -> Optional[bool]:
     """Convert an optional string representation of bool to None or bool"""
     return b if b is None else strtobool(b)
+
+
+def modify_url(url: str, remove: List[str]) -> str:
+    """
+    Given a valid URL string, split out the params, remove any offending
+    params in 'remove', and return the cleaned URL.
+    """
+    scheme, netloc, path, query, fragment = urllib.parse.urlsplit(url)
+    params = urllib.parse.parse_qs(query)
+    for param_key in remove:
+        if param_key in params:
+            del params[param_key]
+    query = urllib.parse.urlencode(params, doseq=True)
+    return urllib.parse.urlunsplit((scheme, netloc, path, query, fragment))

toil/lib/directory.py

@@ -0,0 +1,217 @@
+# Copyright (C) 2015-2025 Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import json
+import base64
+
+from urllib.parse import quote, unquote
+
+from typing import Iterator, Optional, Union
+
+TOIL_DIR_URI_SCHEME = "toildir:"
+
+
+DirectoryContents = dict[str, Union[str, "DirectoryContents"]]
+
+
+def check_directory_dict_invariants(contents: DirectoryContents) -> None:
+    """
+    Make sure a directory structure dict makes sense. Throws an error
+    otherwise.
+
+    Currently just checks to make sure no empty-string keys exist.
+    """
+
+    for name, item in contents.items():
+        if name == "":
+            raise RuntimeError(
+                "Found nameless entry in directory: " + json.dumps(contents, indent=2)
+            )
+        if isinstance(item, dict):
+            check_directory_dict_invariants(item)
+
+
+def decode_directory(
+    dir_path: str,
+) -> tuple[DirectoryContents, Optional[str], str, Optional[str], Optional[str]]:
+    """
+    Decode a directory from a "toildir:" path to a directory (or a file in it).
+
+    :returns: the decoded directory dict, the remaining part of the path (which
+        may be None), an identifier string for the directory (which is the
+        stored name URI if one was provided), and the name URI and source task
+        info.
+    """
+    if not dir_path.startswith(TOIL_DIR_URI_SCHEME):
+        raise RuntimeError(f"Cannot decode non-directory path: {dir_path}")
+
+    # We will decode the directory and then look inside it
+
+    # Since this was encoded by upload_directory we know the
+    # next pieces are encoded source URL, encoded source task, and JSON
+    # describing the directory structure, and it can't contain any slashes.
+    #
+    # So split on slash to separate all that from the path components within
+    # the directory to whatever we're trying to get.
+    parts = dir_path[len(TOIL_DIR_URI_SCHEME) :].split("/", 1)
+
+    # Before the first slash is the encoded data describing the directory contents
+    encoded_name, encoded_source, dir_data = parts[0].split(":")
+    # Decode the name and source, replacing empty string with None again.
+    name: Optional[str] = unquote(encoded_name) or None
+    source: Optional[str] = unquote(encoded_source) or None
+    
+    # We need the unique key identifying this directory, which is where it came
+    # from if stored, or the encoded data itself otherwise.
+    # TODO: Is this too complicated?
+    directory_identifier = name if name is not None else dir_data
+
+    # Decode what to download
+    contents = json.loads(
+        base64.urlsafe_b64decode(dir_data.encode("utf-8")).decode("utf-8")
+    )
+
+    check_directory_dict_invariants(contents)
+
+    if len(parts) == 1 or parts[1] == "/":
+        # We didn't have any subdirectory
+        return contents, None, directory_identifier, name, source
+    else:
+        # We have a path below this
+        return contents, parts[1], directory_identifier, name, source
+
+def encode_directory(contents: DirectoryContents, name: Optional[str] = None, source: Optional[str] = None) -> str:
+    """
+    Encode a directory from a "toildir:" path to a directory (or a file in it).
+
+    :param contents: the directory dict, which is a dict from name to URI for a
+        file or dict for a subdirectory.
+    :param name: the path or URI the directory belongs at, including its
+        basename. May not be empty if set.
+    :param source: the name of a workflow component that uploaded the
+        directory. May not be empty if set.
+    """
+
+    check_directory_dict_invariants(contents)
+
+    parts = [
+        TOIL_DIR_URI_SCHEME[:-1],
+        quote(name or "", safe=""),
+        quote(source or "", safe=""),
+        base64.urlsafe_b64encode(
+            json.dumps(contents).encode("utf-8")
+        ).decode("utf-8"),
+    ]
+
+    return ":".join(parts)
+
+
+def directory_item_exists(dir_path: str) -> bool:
+    """
+    Checks that a URL to a Toil directory or thing in it actually exists.
+
+    Assumes that all the pointed-to URLs exist; just checks tha tthe thing is
+    actually in the encoded directory structure.
+    """
+
+    try:
+        get_directory_item(dir_path)
+    except FileNotFoundError:
+        return False
+    return True
+
+def get_directory_contents_item(contents: DirectoryContents, remaining_path: Optional[str]) -> Union[DirectoryContents, str]:
+    """
+    Get a subdirectory or file from a decoded directory and remaining path.
+    """
+
+    if remaining_path is None:
+        return contents
+    
+    here: Union[str, DirectoryContents] = contents
+    for part in remaining_path.split("/"):
+        if not isinstance(here, dict):
+            # We're trying to go inside a file
+            raise FileNotFoundError(remaining_path)
+        if part not in here:
+            # We've hit a nonexistent path component
+            raise FileNotFoundError(remaining_path)
+        here = here[part]
+    # If we get here we successfully looked up the thing in the structure
+    return here
+
+def get_directory_item(dir_path: str) -> Union[DirectoryContents, str]:
+    """
+    Get a subdirectory or file from a URL pointing to or into a toildir: directory.
+    """
+
+    contents, remaining_path, _, _, _ = decode_directory(dir_path)
+    
+    try:
+        return get_directory_contents_item(contents, remaining_path)
+    except FileNotFoundError:
+        # Rewrite file not found to be about the full thing we went to look up.
+        raise FileNotFoundError(dir_path)
+
+def directory_contents_items(contents: DirectoryContents) -> Iterator[tuple[str, Union[str, None]]]:
+    """
+    Yield each file or directory under the given contents, including itself.
+
+    Yields parent items before children.
+
+    Yields each item as a str path from the root (possibly empty), and either a
+        str value for files or a None for directories.
+
+    The path won't have trailing slashes.
+    """
+
+    # Yield the thing itself
+    yield ("", None)
+
+    for k, v in contents.items():
+        if isinstance(v, str):
+            # Yield a file
+            yield (k, v)
+        else:
+            # Recurse on the directory
+            for child_path, child_value in directory_contents_items(v):
+                yield (f"{k}/{child_path}", child_value)
+
+def directory_items(dir_path: str) -> Iterator[tuple[str, Union[str, None]]]:
+    """
+    Yield each file or directory under the given path, including itself.
+
+    Yields parent items before children.
+
+    Yields each item as a str path from the root (possibly empty), and either a
+        str value for files or a None for directories.
+
+    The path won't have trailing slashes.
+    """
+
+    item = get_directory_item(dir_path)
+
+    if isinstance(item, str):
+        # Only one item and it's this file
+        yield ("", item)
+    else:
+        # It's a directory in there.
+        yield from directory_contents_items(item)
+
+        
+
+
+
+
+

toil/lib/ec2.py

@@ -1,11 +1,19 @@
 import logging
 import time
-from base64 import b64encode
+from base64 import b64encode, b64decode
+import binascii
 from collections.abc import Generator, Iterable, Mapping
-from typing import TYPE_CHECKING, Any, Callable, Optional, Union
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Callable,
+    Literal,
+    Optional,
+    Union,
+)
 
 from toil.lib.aws.session import establish_boto3_session
-from toil.lib.aws.utils import flatten_tags
+from toil.lib.aws.utils import flatten_tags, boto3_pager
 from toil.lib.exceptions import panic
 from toil.lib.retry import (
     ErrorCondition,
@@ -29,6 +37,19 @@ a_short_time = 5
 a_long_time = 60 * 60
 logger = logging.getLogger(__name__)
 
+def is_base64(value: str) -> bool:
+    """
+    Return True if value is base64-decodeable, and False otherwise.
+    """
+    try:
+        b64decode(
+            value.encode("utf-8"),
+            validate=True
+        )
+        return True
+    except binascii.Error:
+        return False
+
 
 class UserError(RuntimeError):
     def __init__(self, message=None, cause=None):
@@ -129,7 +150,7 @@ def wait_instances_running(
             elif i["State"]["Name"] == "running":
                 if i["InstanceId"] in running_ids:
                     raise RuntimeError(
-                        "An instance was already added to the list of running instance IDs. Maybe there is a duplicate."
+                        f"Instance {i['InstanceId']} was already added to the list of running instance IDs. Maybe there is a duplicate."
                     )
                 running_ids.add(i["InstanceId"])
                 yield i
@@ -151,12 +172,15 @@ def wait_instances_running(
         time.sleep(seconds)
         for attempt in retry_ec2():
             with attempt:
-                described_instances = boto3_ec2.describe_instances(
+                # describe_instances weirdly really describes reservations
+                reservations = boto3_pager(
+                    boto3_ec2.describe_instances,
+                    "Reservations",
                     InstanceIds=list(pending_ids)
                 )
                 instances = [
                     instance
-                    for reservation in described_instances["Reservations"]
+                    for reservation in reservations
                     for instance in reservation["Instances"]
                 ]
 
@@ -184,6 +208,9 @@ def wait_spot_requests_active(
 
     if timeout is not None:
         timeout = time.time() + timeout
+
+    # These hold spot instance request IDs.
+    # Not to be confused with instance IDs.
     active_ids = set()
     other_ids = set()
     open_ids = None
@@ -201,34 +228,37 @@ def wait_spot_requests_active(
             batch = []
             for r in requests:
                 r: "SpotInstanceRequestTypeDef"  # pycharm thinks it is a string
+                assert isinstance(r, dict), f"Found garbage posing as a spot request: {r}"
                 if r["State"] == "open":
-                    open_ids.add(r["InstanceId"])
-                    if r["Status"] == "pending-evaluation":
-                        eval_ids.add(r["InstanceId"])
-                    elif r["Status"] == "pending-fulfillment":
-                        fulfill_ids.add(r["InstanceId"])
+                    open_ids.add(r["SpotInstanceRequestId"])
+                    if r["Status"]["Code"] == "pending-evaluation":
+                        eval_ids.add(r["SpotInstanceRequestId"])
+                    elif r["Status"]["Code"] == "pending-fulfillment":
+                        fulfill_ids.add(r["SpotInstanceRequestId"])
                     else:
                         logger.info(
                             "Request %s entered status %s indicating that it will not be "
-                            "fulfilled anytime soon.",
-                            r["InstanceId"],
-                            r["Status"],
+                            "fulfilled anytime soon. (Message: %s)",
+                            r["SpotInstanceRequestId"],
+                            r["Status"]["Code"],
+                            r["Status"].get("Message"),
                         )
                 elif r["State"] == "active":
-                    if r["InstanceId"] in active_ids:
+                    if r["SpotInstanceRequestId"] in active_ids:
                         raise RuntimeError(
                             "A request was already added to the list of active requests. Maybe there are duplicate requests."
                         )
-                    active_ids.add(r["InstanceId"])
+                    active_ids.add(r["SpotInstanceRequestId"])
                     batch.append(r)
                 else:
-                    if r["InstanceId"] in other_ids:
+                    if r["SpotInstanceRequestId"] in other_ids:
                         raise RuntimeError(
                             "A request was already added to the list of other IDs. Maybe there are duplicate requests."
                         )
-                    other_ids.add(r["InstanceId"])
+                    other_ids.add(r["SpotInstanceRequestId"])
                     batch.append(r)
             if batch:
+                logger.debug("Found %d new active/other spot requests", len(batch))
                 yield batch
             logger.info(
                 "%i spot requests(s) are open (%i of which are pending evaluation and %i "
@@ -247,8 +277,10 @@ def wait_spot_requests_active(
             time.sleep(sleep_time)
             for attempt in retry_ec2(retry_while=spot_request_not_found):
                 with attempt:
-                    requests = boto3_ec2.describe_spot_instance_requests(
-                        SpotInstanceRequestIds=list(open_ids)
+                    requests = boto3_pager(
+                        boto3_ec2.describe_spot_instance_requests,
+                        "SpotInstanceRequests",
+                        SpotInstanceRequestIds=list(open_ids),
                     )
     except BaseException:
         if open_ids:
@@ -264,14 +296,20 @@ def create_spot_instances(
     boto3_ec2: "EC2Client",
     price,
     image_id,
-    spec,
+    spec: dict[Literal["LaunchSpecification"], dict[str, Any]],
     num_instances=1,
     timeout=None,
     tentative=False,
-    tags=None,
+    tags: dict[str, str] = None,
 ) -> Generator["DescribeInstancesResultTypeDef", None, None]:
     """
     Create instances on the spot market.
+
+    The "UserData" field in "LaunchSpecification" in spec MUST ALREADY BE
+    base64-encoded. It will NOT be automatically encoded.
+
+    :param tags: Dict from tag key to tag value of tags to apply to the
+        request.
     """
 
     def spotRequestNotFound(e):
@@ -280,20 +318,27 @@ def create_spot_instances(
     spec["LaunchSpecification"].update(
         {"ImageId": image_id}
     )  # boto3 image id is in the launch specification
+
+    user_data = spec["LaunchSpecification"].get("UserData", "")
+    assert is_base64(user_data), f"Spot user data needs to be base64-encoded: {user_data}"
+
     for attempt in retry_ec2(
         retry_for=a_long_time, retry_while=inconsistencies_detected
     ):
         with attempt:
             requests_dict = boto3_ec2.request_spot_instances(
-                SpotPrice=price, InstanceCount=num_instances, **spec
+                SpotPrice=str(price), InstanceCount=num_instances, **spec
             )
             requests = requests_dict["SpotInstanceRequests"]
 
+    assert isinstance(requests, list)
+
     if tags is not None:
+        flat_tags = flatten_tags(tags)
         for requestID in (request["SpotInstanceRequestId"] for request in requests):
             for attempt in retry_ec2(retry_while=spotRequestNotFound):
                 with attempt:
-                    boto3_ec2.create_tags(Resources=[requestID], Tags=tags)
+                    boto3_ec2.create_tags(Resources=[requestID], Tags=flat_tags)
 
     num_active, num_other = 0, 0
     # noinspection PyUnboundLocalVariable,PyTypeChecker
@@ -310,7 +355,7 @@ def create_spot_instances(
             else:
                 logger.info(
                     "Request %s in unexpected state %s.",
-                    request["InstanceId"],
+                    request["SpotInstanceRequestId"],
                     request["State"],
                 )
                 num_other += 1
@@ -324,7 +369,14 @@ def create_spot_instances(
                         boto3_ec2.modify_instance_metadata_options(
                             InstanceId=instance_id, HttpPutResponseHopLimit=3
                         )
-            yield boto3_ec2.describe_instances(InstanceIds=instance_ids)
+            # We can't use the normal boto3_pager here because we're weirdly
+            # specced as yielding the pages ourselves.
+            # TODO: Change this to just yield instance descriptions instead.
+            page = boto3_ec2.describe_instances(InstanceIds=instance_ids)
+            while page.get("NextToken") is not None:
+                yield page
+                page = boto3_ec2.describe_instances(InstanceIds=instance_ids, NextToken=page["NextToken"])
+            yield page
     if not num_active:
         message = "None of the spot requests entered the active state"
         if tentative:
@@ -335,6 +387,9 @@ def create_spot_instances(
         logger.warning("%i request(s) entered a state other than active.", num_other)
 
 
+# TODO: Get rid of this and use create_instances instead.
+# Right now we need it because we have code that needs an InstanceTypeDef for
+# either a spot or an ondemand instance.
 def create_ondemand_instances(
     boto3_ec2: "EC2Client",
     image_id: str,
@@ -344,7 +399,19 @@ def create_ondemand_instances(
     """
     Requests the RunInstances EC2 API call but accounts for the race between recently created
     instance profiles, IAM roles and an instance creation that refers to them.
+
+    The "UserData" field in spec MUST NOT be base64 encoded; it will be
+    base64-encoded by boto3 automatically. See
+    <https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/ec2/client/run_instances.html>.
+
+    Replaced by create_instances.
     """
+
+    user_data: str = spec.get("UserData", "")
+    if user_data:
+        # Hope any real user data contains some characters not allowed in base64
+        assert not is_base64(user_data), f"On-demand user data needs to not be base64-encoded: {user_data}"
+
     instance_type = spec["InstanceType"]
     logger.info("Creating %s instance(s) ... ", instance_type)
     boto_instance_list = []
@@ -434,12 +501,13 @@ def create_instances(
     Not to be confused with "run_instances" (same input args; returns a dictionary):
       https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/ec2.html#EC2.Client.run_instances
 
-    Tags, if given, are applied to the instances, and all volumes.
+    :param user_data: non-base64-encoded user data to control instance startup.
+    :param tags: if given, these tags are applied to the instances, and all volumes.
     """
     logger.info("Creating %s instance(s) ... ", instance_type)
 
-    if isinstance(user_data, str):
-        user_data = user_data.encode("utf-8")
+    if isinstance(user_data, bytes):
+        user_data = user_data.decode("utf-8")
 
     request = {
         "ImageId": image_id,

toil/lib/exceptions.py

@@ -18,6 +18,7 @@ import sys
 from typing import Optional
 import logging
 from urllib.parse import ParseResult
+from types import TracebackType
 
 
 # TODO: isn't this built in to Python 3 now?
@@ -56,7 +57,7 @@ class panic:
         raise_(exc_type, exc_value, traceback)
 
 
-def raise_(exc_type, exc_value, traceback) -> None:
+def raise_(exc_type: Optional[type[BaseException]], exc_value: Optional[BaseException], traceback: Optional[TracebackType]) -> None:
     if exc_value is not None:
         exc = exc_value
     else:

toil/lib/expando.py

@@ -67,10 +67,10 @@ class Expando(dict):
     ...
     KeyError: 'foo'
 
-    >>> del o.foo
+    >>> del o.foo # doctest: +IGNORE_EXCEPTION_DETAIL
     Traceback (most recent call last):
     ...
-    AttributeError: foo
+    AttributeError: 'Expando' object has no attribute 'foo'
 
     And copied: