fix issue with having paths in github repos

cwlkernel/CoreExecutor.py

@@ -23,7 +23,7 @@
 from cwltool.process import add_sizes
 from cwltool.provenance import ResearchObject
 from cwltool.stdfsaccess import StdFsAccess
-from cwltool.utils import CWLObjectType, visit_class
+from cwltool.utils import CWLObjectType, visit_class, DEFAULT_TMP_PREFIX
 from ruamel import yaml
 
 from .IOManager import IOFileManager
@@ -42,9 +42,17 @@ def __init__(self, root_directory: str,
         )
         self.runtime_context.outdir = root_directory
         self.runtime_context.basedir = root_directory
-        self.runtime_context.default_stdin = DEVNULL
         self.runtime_context.default_stdout = DEVNULL
         self.runtime_context.default_stderr = DEVNULL
+        # If on MacOS platform, TMPDIR must be set to be under one of the
+        # shared volumes in Docker for Mac
+        # More info: https://dockstore.org/docs/faq
+        if sys.platform == "darwin":
+            default_mac_path = "/private/tmp/docker_tmp"
+            if self.runtime_context.tmp_outdir_prefix == DEFAULT_TMP_PREFIX:
+                self.runtime_context.tmp_outdir_prefix = default_mac_path
+            if self.runtime_context.tmpdir_prefix == DEFAULT_TMP_PREFIX:
+                self.runtime_context.tmpdir_prefix = default_mac_path
 
 
 class ProvenanceFactory(JupyterFactory):

cwlkernel/IOManager.py

@@ -32,6 +32,7 @@ def read(self, relative_path: str) -> bytes:
 
     def write(self, relative_path: str, binary_data: bytes, metadata=None) -> str:
         real_path = os.path.realpath(os.path.join(self.ROOT_DIRECTORY, relative_path))
+        Path(os.path.dirname(real_path)).mkdir(exist_ok=True, parents=True)
         with open(real_path, 'wb') as f:
             self._files_registry[real_path] = metadata if metadata is not None else {}
             f.write(binary_data)

cwlkernel/cwlrepository/cwlrepository.py

@@ -35,17 +35,14 @@ def validate(self, tool: WorkflowComponent):
                 if 'id' not in output:
                     raise MissingIdError(f'Missing id for outputs: {output}')
 
-        def register_tool(self, tool: WorkflowComponent) -> None:
+        def register_tool(self, tool: WorkflowComponent, relative_directory: Optional[Path] = None) -> None:
             self.validate(tool)
             if tool.id in self._registry:
                 raise KeyError(f'Dublicate key error: {tool.id}')
-            path = Path(self._file_repository.write(f'{tool.id}.cwl', tool.to_yaml().encode()))
+            relative_directory = relative_directory.as_posix() if relative_directory is not None else f'{tool.id}.cwl'
+            path = Path(self._file_repository.write(relative_directory, tool.to_yaml().encode()))
             self._registry[tool.id] = (deepcopy(tool), path)
 
-        # def register_tools(self, *args):
-        #     for tool in args:
-        #         self.register_tool(tool)
-
         def get_by_id(self, tool_id: str) -> Optional[WorkflowComponent]:
             comp = self._registry.get(tool_id, None)
             return comp[0] if comp is not None else None

cwlkernel/kernel_magics.py

@@ -328,7 +328,8 @@ def github_import(kernel: CWLKernel, url: str):
             file_data = f.read()
         cwl_component = cwl_factory.get_workflow_component(file_data)
         cwl_component._id = os.path.splitext(os.path.basename(cwl_file))[0]
-        kernel.workflow_repository.register_tool(cwl_component)
+        relative_dir = Path(os.path.relpath(cwl_file, kernel._github_resolver._local_root_directory.as_posix()))
+        kernel.workflow_repository.register_tool(cwl_component, relative_dir)
         kernel.send_response(kernel.iopub_socket, 'stream',
                              {'name': 'stdout', 'text': f"tool '{cwl_component.id}' registered\n"})