toil 5.12.0__py3-none-any.whl → 6.1.0__py3-none-any.whl

toil/utils/toilStatus.py

@@ -12,12 +12,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Tool for reporting on job status."""
-from collections import defaultdict
 import logging
 import os
 import sys
-from functools import reduce
-import json
 from typing import Any, Dict, List, Optional, Set
 
 from toil.bus import replay_message_bus
@@ -85,7 +82,7 @@ class ToilStatus:
                 with job.getLogFileHandle(self.jobStore) as fH:
                     # TODO: This looks intended to be machine-readable, but the format is
                     #  unspecified and no escaping is done. But keep these tags around.
-                    print(StatsAndLogging.formatLogStream(fH, job_name=f"LOG_FILE_OF_JOB:{job} LOG:"))
+                    print(StatsAndLogging.formatLogStream(fH, stream_name=f"LOG_FILE_OF_JOB:{job} LOG:"))
             else:
                 print(f"LOG_FILE_OF_JOB: {job} LOG: Job has no log file")
 
@@ -320,7 +317,7 @@ class ToilStatus:
 
 def main() -> None:
     """Reports the state of a Toil workflow."""
-    parser = parser_with_common_options()
+    parser = parser_with_common_options(prog="toil status")
     parser.add_argument("--failIfNotComplete", action="store_true",
                         help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
                         default=False)

toil/version.py

@@ -1,14 +1,14 @@
-baseVersion = '5.12.0'
+baseVersion = '6.1.0'
 cgcloudVersion = '1.6.0a1.dev393'
-version = '5.12.0-6d5a5b83b649cd8adf34a5cfe89e7690c95189d3'
-cacheTag = 'cache-local-py3.9'
-mainCacheTag = 'cache-master-py3.9'
-distVersion = '5.12.0'
-exactPython = 'python3.9'
-python = 'python3.9'
-dockerTag = '5.12.0-6d5a5b83b649cd8adf34a5cfe89e7690c95189d3-py3.9'
-currentCommit = '6d5a5b83b649cd8adf34a5cfe89e7690c95189d3'
+version = '6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f'
+cacheTag = 'cache-local-py3.10'
+mainCacheTag = 'cache-master-py3.10'
+distVersion = '6.1.0'
+exactPython = 'python3.10'
+python = 'python3.10'
+dockerTag = '6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f-py3.10'
+currentCommit = '3f9cba3766e52866ea80d0934498f8c8f3129c3f'
 dockerRegistry = 'quay.io/ucsc_cgl'
 dockerName = 'toil'
 dirty = False
-cwltool_version = '3.1.20230601100705'
+cwltool_version = '3.1.20240112164112'

toil/wdl/utils.py

@@ -11,12 +11,10 @@
 # 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
+from typing import Iterable
 
-from toil.wdl.wdl_analysis import AnalyzeWDL
 
-
-def get_version(iterable) -> str:
+def get_version(iterable: Iterable[str]) -> str:
     """
     Get the version of the WDL document.
 
@@ -35,121 +33,3 @@ def get_version(iterable) -> str:
             break
     # only draft-2 doesn't contain the version declaration
     return 'draft-2'
-
-
-def get_analyzer(wdl_file: str) -> AnalyzeWDL:
-    """
-    Creates an instance of an AnalyzeWDL implementation based on the version.
-
-    :param wdl_file: The path to the WDL file.
-    """
-    with open(wdl_file) as f:
-        version = get_version(f)
-
-    if version == 'draft-2':
-        from toil.wdl.versions.draft2 import AnalyzeDraft2WDL
-        return AnalyzeDraft2WDL(wdl_file)
-    elif version == '1.0':
-        from toil.wdl.versions.v1 import AnalyzeV1WDL
-        return AnalyzeV1WDL(wdl_file)
-    elif version == 'development':
-        from toil.wdl.versions.dev import AnalyzeDevelopmentWDL
-        return AnalyzeDevelopmentWDL(wdl_file)
-    else:
-        raise RuntimeError(f"Unsupported WDL version: '{version}'.")
-
-
-def dict_from_JSON(JSON_file: str) -> dict:
-    """
-    Takes a WDL-mapped json file and creates a dict containing the bindings.
-
-    :param JSON_file: A required JSON file containing WDL variable bindings.
-    """
-    json_dict = {}
-
-    # TODO: Add context support for variables within multiple wdl files
-
-    with open(JSON_file) as data_file:
-        data = json.load(data_file)
-    for d in data:
-        if isinstance(data[d], str):
-            json_dict[d] = f'"{data[d]}"'
-        else:
-            json_dict[d] = data[d]
-    return json_dict
-
-
-def write_mappings(parser: AnalyzeWDL, filename: str = 'mappings.out') -> None:
-    """
-    Takes an AnalyzeWDL instance and writes the final task dict and workflow
-    dict to the given file.
-
-    :param parser: An AnalyzeWDL instance.
-    :param filename: The name of a file to write to.
-    """
-    from collections import OrderedDict
-
-    class Formatter:
-        def __init__(self):
-            self.types = {}
-            self.htchar = '\t'
-            self.lfchar = '\n'
-            self.indent = 0
-            self.set_formater(object, self.__class__.format_object)
-            self.set_formater(dict, self.__class__.format_dict)
-            self.set_formater(list, self.__class__.format_list)
-            self.set_formater(tuple, self.__class__.format_tuple)
-
-        def set_formater(self, obj, callback):
-            self.types[obj] = callback
-
-        def __call__(self, value, **args):
-            for key in args:
-                setattr(self, key, args[key])
-            formater = self.types[type(value) if type(value) in self.types else object]
-            return formater(self, value, self.indent)
-
-        def format_object(self, value, indent):
-            return repr(value)
-
-        def format_dict(self, value, indent):
-            items = [
-                self.lfchar + self.htchar * (indent + 1) + repr(key) + ': ' +
-                (self.types[type(value[key]) if type(value[key]) in self.types else object])(self, value[key],
-                                                                                             indent + 1)
-                for key in value]
-            return '{%s}' % (','.join(items) + self.lfchar + self.htchar * indent)
-
-        def format_list(self, value, indent):
-            items = [
-                self.lfchar + self.htchar * (indent + 1) + (
-                    self.types[type(item) if type(item) in self.types else object])(self, item, indent + 1)
-                for item in value]
-            return '[%s]' % (','.join(items) + self.lfchar + self.htchar * indent)
-
-        def format_tuple(self, value, indent):
-            items = [
-                self.lfchar + self.htchar * (indent + 1) + (
-                    self.types[type(item) if type(item) in self.types else object])(self, item, indent + 1)
-                for item in value]
-            return '(%s)' % (','.join(items) + self.lfchar + self.htchar * indent)
-
-    pretty = Formatter()
-
-    def format_ordereddict(self, value, indent):
-        items = [
-            self.lfchar + self.htchar * (indent + 1) +
-            "(" + repr(key) + ', ' + (self.types[
-                type(value[key]) if type(value[key]) in self.types else object
-            ])(self, value[key], indent + 1) + ")"
-            for key in value
-        ]
-        return 'OrderedDict([%s])' % (','.join(items) +
-                                      self.lfchar + self.htchar * indent)
-
-    pretty.set_formater(OrderedDict, format_ordereddict)
-
-    with open(filename, 'w') as f:
-        f.write(pretty(parser.tasks_dictionary))
-        f.write('\n\n\n\n\n\n')
-        f.write(pretty(parser.workflows_dictionary))