more docstrings

cwltool/cwlprov/ro.py

@@ -402,6 +402,7 @@ def guess_mediatype(
         return aggregates
 
     def add_uri(self, uri: str, timestamp: Optional[datetime.datetime] = None) -> Aggregate:
+        """Add the given URI to this RO."""
         self.self_check()
         aggr: Aggregate = {"uri": uri}
         aggr["createdOn"], aggr["createdBy"] = self._self_made(timestamp=timestamp)

cwltool/cwlrdf.py

@@ -1,10 +1,8 @@
-import urllib
-from codecs import StreamWriter
-from collections.abc import Iterator
-from typing import IO, Any, Optional, TextIO, Union, cast
+"""RDF output."""
+
+from typing import IO, Any
 
 from rdflib import Graph
-from rdflib.query import ResultRow
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.jsonld_context import makerdf
 from schema_salad.utils import ContextType
@@ -38,172 +36,6 @@ def lastpart(uri: Any) -> str:
     return uri2
 
 
-def dot_with_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> None:
-    qres = cast(
-        Iterator[ResultRow],
-        g.query(
-            """SELECT ?step ?run ?runtype
-           WHERE {
-              ?step cwl:run ?run .
-              ?run rdf:type ?runtype .
-           }"""
-        ),
-    )  # ResultRow because the query is of type SELECT
-
-    for step, run, _ in qres:
-        stdout.write(
-            '"{}" [label="{}"]\n'.format(lastpart(step), f"{lastpart(step)} ({lastpart(run)})")
-        )
-
-    qres = cast(
-        Iterator[ResultRow],
-        g.query(
-            """SELECT ?step ?inp ?source
-           WHERE {
-              ?wf Workflow:steps ?step .
-              ?step cwl:inputs ?inp .
-              ?inp cwl:source ?source .
-           }"""
-        ),
-    )  # ResultRow because the query is of type SELECT
-
-    for step, inp, source in qres:
-        stdout.write('"%s" [shape=box]\n' % (lastpart(inp)))
-        stdout.write('"{}" -> "{}" [label="{}"]\n'.format(lastpart(source), lastpart(inp), ""))
-        stdout.write('"{}" -> "{}" [label="{}"]\n'.format(lastpart(inp), lastpart(step), ""))
-
-    qres = cast(
-        Iterator[ResultRow],
-        g.query(
-            """SELECT ?step ?out
-           WHERE {
-              ?wf Workflow:steps ?step .
-              ?step cwl:outputs ?out .
-           }"""
-        ),
-    )  # ResultRow because the query is of type SELECT
-
-    for step, out in qres:
-        stdout.write('"%s" [shape=box]\n' % (lastpart(out)))
-        stdout.write('"{}" -> "{}" [label="{}"]\n'.format(lastpart(step), lastpart(out), ""))
-
-    qres = cast(
-        Iterator[ResultRow],
-        g.query(
-            """SELECT ?out ?source
-           WHERE {
-              ?wf cwl:outputs ?out .
-              ?out cwl:source ?source .
-           }"""
-        ),
-    )  # ResultRow because the query is of type SELECT
-
-    for out, source in qres:
-        stdout.write('"%s" [shape=octagon]\n' % (lastpart(out)))
-        stdout.write('"{}" -> "{}" [label="{}"]\n'.format(lastpart(source), lastpart(out), ""))
-
-    qres = cast(
-        Iterator[ResultRow],
-        g.query(
-            """SELECT ?inp
-           WHERE {
-              ?wf rdf:type cwl:Workflow .
-              ?wf cwl:inputs ?inp .
-           }"""
-        ),
-    )  # ResultRow because the query is of type SELECT
-
-    for (inp,) in qres:
-        stdout.write('"%s" [shape=octagon]\n' % (lastpart(inp)))
-
-
-def dot_without_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> None:
-    dotname: dict[str, str] = {}
-    clusternode = {}
-
-    stdout.write("compound=true\n")
-
-    subworkflows = set()
-    qres = cast(
-        Iterator[ResultRow],
-        g.query(
-            """SELECT ?run
-           WHERE {
-              ?wf rdf:type cwl:Workflow .
-              ?wf Workflow:steps ?step .
-              ?step cwl:run ?run .
-              ?run rdf:type cwl:Workflow .
-           } ORDER BY ?wf"""
-        ),
-    )  # ResultRow because the query is of type SELECT
-    for (run,) in qres:
-        subworkflows.add(run)
-
-    qres = cast(
-        Iterator[ResultRow],
-        g.query(
-            """SELECT ?wf ?step ?run ?runtype
-           WHERE {
-              ?wf rdf:type cwl:Workflow .
-              ?wf Workflow:steps ?step .
-              ?step cwl:run ?run .
-              ?run rdf:type ?runtype .
-           } ORDER BY ?wf"""
-        ),
-    )  # ResultRow because the query is of type SELECT
-
-    currentwf: Optional[str] = None
-    for wf, step, _run, runtype in qres:
-        if step not in dotname:
-            dotname[step] = lastpart(step)
-
-        if wf != currentwf:
-            if currentwf is not None:
-                stdout.write("}\n")
-            if wf in subworkflows:
-                if wf not in dotname:
-                    dotname[wf] = "cluster_" + lastpart(wf)
-                stdout.write(f'subgraph "{dotname[wf]}" {{ label="{lastpart(wf)}"\n')  # noqa: B907
-                currentwf = wf
-                clusternode[wf] = step
-            else:
-                currentwf = None
-
-        if str(runtype) != "https://w3id.org/cwl/cwl#Workflow":
-            stdout.write(
-                f'"{dotname[step]}" [label="{urllib.parse.urldefrag(str(step))[1]}"]\n'  # noqa: B907
-            )
-
-    if currentwf is not None:
-        stdout.write("}\n")
-
-    qres = cast(
-        Iterator[ResultRow],
-        g.query(
-            """SELECT DISTINCT ?src ?sink ?srcrun ?sinkrun
-           WHERE {
-              ?wf1 Workflow:steps ?src .
-              ?wf2 Workflow:steps ?sink .
-              ?src cwl:out ?out .
-              ?inp cwl:source ?out .
-              ?sink cwl:in ?inp .
-              ?src cwl:run ?srcrun .
-              ?sink cwl:run ?sinkrun .
-           }"""
-        ),
-    )  # ResultRow because the query is of type SELECT
-
-    for src, sink, srcrun, sinkrun in qres:
-        attr = ""
-        if srcrun in clusternode:
-            attr += 'ltail="%s"' % dotname[srcrun]
-            src = clusternode[srcrun]
-        if sinkrun in clusternode:
-            attr += ' lhead="%s"' % dotname[sinkrun]
-            sink = clusternode[sinkrun]
-        stdout.write(f'"{dotname[src]}" -> "{dotname[sink]}" [{attr}]\n')  # noqa: B907
-
-
 def printdot(
     wf: Process,
     ctx: ContextType,

cwltool/factory.py

@@ -27,6 +27,7 @@ def __init__(self, t: Process, factory: "Factory") -> None:
 
     def __call__(self, **kwargs):
         # type: (**Any) -> Union[str, Optional[CWLObjectType]]
+        """Invoke the tool."""
         runtime_context = self.factory.runtime_context.copy()
         runtime_context.basedir = os.getcwd()
         out, status = self.factory.executor(self.t, kwargs, runtime_context)

cwltool/job.py

@@ -100,6 +100,7 @@ def relink_initialworkdir(
 
 
 def neverquote(string: str, pos: int = 0, endpos: int = 0) -> Optional[Match[str]]:
+    """No-op."""
     return None
 
 

cwltool/resolver.py

@@ -11,6 +11,7 @@
 
 
 def resolve_local(document_loader: Optional[Loader], uri: str) -> Optional[str]:
+    """Use the local resolver to find the target of the URI."""
     pathpart, frag = urllib.parse.urldefrag(uri)
 
     try:
@@ -41,6 +42,7 @@ def resolve_local(document_loader: Optional[Loader], uri: str) -> Optional[str]:
 
 
 def tool_resolver(document_loader: Loader, uri: str) -> Optional[str]:
+    """Try both the local resolver and the GA4GH TRS resolver, in that order."""
     for r in [resolve_local, resolve_ga4gh_tool]:
         ret = r(document_loader, uri)
         if ret is not None:
@@ -63,6 +65,7 @@ def tool_resolver(document_loader: Loader, uri: str) -> Optional[str]:
 
 
 def resolve_ga4gh_tool(document_loader: Loader, uri: str) -> Optional[str]:
+    """Use the GA4GH TRS API to resolve a tool reference."""
     path, version = uri.partition(":")[::2]
     if not version:
         version = "latest"

cwltool/stdfsaccess.py

@@ -55,6 +55,7 @@ def listdir(self, fn: str) -> list[str]:
         return [abspath(urllib.parse.quote(entry), fn) for entry in os.listdir(self._abs(fn))]
 
     def join(self, path, *paths):  # type: (str, *str) -> str
+        """Join one or more path segments intelligently."""
         return os.path.join(path, *paths)
 
     def realpath(self, path: str) -> str: