+def make_builder(joborder, hints, requirements, runtimeContext):
+ return Builder(
+ job=joborder,
+ files=[], # type: List[Dict[Text, Text]]
+ bindings=[], # type: List[Dict[Text, Any]]
+ schemaDefs={}, # type: Dict[Text, Dict[Text, Any]]
+ names=None, # type: Names
+ requirements=requirements, # type: List[Dict[Text, Any]]
+ hints=hints, # type: List[Dict[Text, Any]]
+ resources={}, # type: Dict[str, int]
+ mutation_manager=None, # type: Optional[MutationManager]
+ formatgraph=None, # type: Optional[Graph]
+ make_fs_access=None, # type: Type[StdFsAccess]
+ fs_access=None, # type: StdFsAccess
+ job_script_provider=runtimeContext.job_script_provider, # type: Optional[Any]
+ timeout=runtimeContext.eval_timeout, # type: float
+ debug=runtimeContext.debug, # type: bool
+ js_console=runtimeContext.js_console, # type: bool
+ force_docker_pull=runtimeContext.force_docker_pull, # type: bool
+ loadListing="", # type: Text
+ outdir="", # type: Text
+ tmpdir="", # type: Text
+ stagedir="", # type: Text
+ )
+
+def search_schemadef(name, reqs):
+ for r in reqs:
+ if r["class"] == "SchemaDefRequirement":
+ for sd in r["types"]:
+ if sd["name"] == name:
+ return sd
+ return None
+
+primitive_types_set = frozenset(("null", "boolean", "int", "long",
+ "float", "double", "string", "record",
+ "array", "enum"))
+
+def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discovered):
+ if isinstance(inputschema, Sequence) and not isinstance(inputschema, basestring):
+ # union type, collect all possible secondaryFiles
+ for i in inputschema:
+ set_secondary(fsaccess, builder, i, secondaryspec, primary, discovered)
+ return
+
+ if isinstance(inputschema, basestring):
+ sd = search_schemadef(inputschema, reversed(builder.hints+builder.requirements))
+ if sd:
+ inputschema = sd
+ else:
+ return
+
+ if "secondaryFiles" in inputschema:
+ # set secondaryFiles, may be inherited by compound types.
+ secondaryspec = inputschema["secondaryFiles"]
+
+ if (isinstance(inputschema["type"], (Mapping, Sequence)) and
+ not isinstance(inputschema["type"], basestring)):
+ # compound type (union, array, record)
+ set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered)
+
+ elif (inputschema["type"] == "record" and
+ isinstance(primary, Mapping)):
+ #
+ # record type, find secondary files associated with fields.
+ #
+ for f in inputschema["fields"]:
+ p = primary.get(shortname(f["name"]))
+ if p:
+ set_secondary(fsaccess, builder, f, secondaryspec, p, discovered)
+
+ elif (inputschema["type"] == "array" and
+ isinstance(primary, Sequence)):
+ #
+ # array type, find secondary files of elements
+ #
+ for p in primary:
+ set_secondary(fsaccess, builder, {"type": inputschema["items"]}, secondaryspec, p, discovered)
+
+ elif (inputschema["type"] == "File" and
+ secondaryspec and
+ isinstance(primary, Mapping) and
+ primary.get("class") == "File" and
+ "secondaryFiles" not in primary):
+ #
+ # Found a file, check for secondaryFiles
+ #
+ primary["secondaryFiles"] = []
+ for i, sf in enumerate(aslist(secondaryspec)):
+ pattern = builder.do_eval(sf["pattern"], context=primary)
+ if pattern is None:
+ continue
+ sfpath = substitute(primary["location"], pattern)
+ required = builder.do_eval(sf.get("required"), context=primary)
+
+ if fsaccess.exists(sfpath):
+ primary["secondaryFiles"].append({"location": sfpath, "class": "File"})
+ elif required:
+ raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
+ "Required secondary file '%s' does not exist" % sfpath)
+
+ primary["secondaryFiles"] = cmap(primary["secondaryFiles"])
+ if discovered is not None:
+ discovered[primary["location"]] = primary["secondaryFiles"]
+ elif inputschema["type"] not in primitive_types_set:
+ set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered)
+
+def discover_secondary_files(fsaccess, builder, inputs, job_order, discovered=None):
+ for inputschema in inputs:
+ primary = job_order.get(shortname(inputschema["id"]))
+ if isinstance(primary, (Mapping, Sequence)):
+ set_secondary(fsaccess, builder, inputschema, None, primary, discovered)
+