' \
+ --only "https://galaxyproject.org/gxformat2/${schema}#WorkflowDoc" \
+ --only "https://galaxyproject.org/gxformat2/${schema}#GalaxyWorkflow" \
+ workflow.yml > "$out"
+
+ java_package="${PROJECT_DIRECTORY}/java"
+ schema-salad-tool \
+ --codegen java \
+ --codegen-target "$java_package" \
+ --codegen-examples examples \
+ workflow.yml
+ cd "$java_package"
+ mvn test
+ mvn javadoc:javadoc
+ cd "${PROJECT_DIRECTORY}"
+done
diff --git a/dev-requirements.txt b/dev-requirements.txt
index 6fa2c45..f4f3b7f 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,3 +1,6 @@
+# Optional dependencies
+schema-salad
+
# For testing
tox
nose
diff --git a/gxformat2/lint.py b/gxformat2/lint.py
new file mode 100644
index 0000000..a429175
--- /dev/null
+++ b/gxformat2/lint.py
@@ -0,0 +1,110 @@
+"""Workflow linting entry point - main script."""
+import os
+import sys
+
+from gxformat2._yaml import ordered_load
+from gxformat2.linting import LintContext
+
+EXIT_CODE_SUCCESS = 0
+EXIT_CODE_LINT_FAILED = 1
+EXIT_CODE_FORMAT_ERROR = 2
+EXIT_CODE_FILE_PARSE_FAILED = 3
+
+LINT_FAILED_NO_OUTPUTS = "Workflow contained no outputs"
+LINT_FAILED_OUTPUT_NO_LABEL = "Workflow contained output without a label"
+
+
+def ensure_key(lint_context, has_keys, key, has_class=None, has_value=None):
+ if key not in has_keys:
+ lint_context.error("expected to find key [{key}] but absent", key=key)
+ return None
+
+ value = has_keys[key]
+ return ensure_key_has_value(lint_context, has_keys, key, value, has_class=has_class, has_value=has_value)
+
+
+def ensure_key_if_present(lint_context, has_keys, key, default=None, has_class=None):
+ if key not in has_keys:
+ return default
+
+ value = has_keys[key]
+ return ensure_key_has_value(lint_context, has_keys, key, value, has_class=has_class, has_value=None)
+
+
+def ensure_key_has_value(lint_context, has_keys, key, value, has_class=None, has_value=None):
+ if has_class is not None and not isinstance(value, has_class):
+ lint_context.error("expected value [{value}] with key [{key}] to be of class {clazz}", key=key, value=value, clazz=has_class)
+ if has_value is not None and value != has_value:
+ lint_context.error("expected value [{value}] with key [{key}] to be {expected_value}", key=key, value=value, expected_value=has_value)
+ return value
+
+
+def lint_ga(lint_context, workflow_dict, path=None):
+ """Lint a native/legacy style Galaxy workflow and populate the corresponding LintContext."""
+ ensure_key(lint_context, workflow_dict, "format-version", has_value="0.1")
+ ensure_key(lint_context, workflow_dict, "a_galaxy_workflow", has_value="true")
+
+ native_steps = ensure_key(lint_context, workflow_dict, "steps", has_class=dict) or {}
+
+ found_outputs = False
+ found_output_without_label = False
+ for order_index_str, step in native_steps.items():
+ if not order_index_str.isdigit():
+ lint_context.error("expected step_key to be integer not [{value}]", value=order_index_str)
+
+ workflow_outputs = ensure_key_if_present(lint_context, step, "workflow_outputs", default=[], has_class=list)
+ for workflow_output in workflow_outputs:
+ found_outputs = True
+
+ print(workflow_output)
+ if not workflow_output.get("label"):
+ found_output_without_label = True
+
+ step_type = step.get("type")
+ if step_type == "subworkflow":
+ subworkflow = ensure_key(lint_context, step, "subworkflow", has_class=dict)
+ lint_ga(lint_context, subworkflow)
+
+ if not found_outputs:
+ lint_context.warn(LINT_FAILED_NO_OUTPUTS)
+
+ if found_output_without_label:
+ lint_context.warn(LINT_FAILED_OUTPUT_NO_LABEL)
+
+
+def lint_format2(lint_context, workflow_dict, path=None):
+ """Lint a Format 2 Galaxy workflow and populate the corresponding LintContext."""
+ from gxformat2.schema.v19_09 import load_document
+ from schema_salad.exceptions import SchemaSaladException
+ try:
+ load_document("file://" + os.path.normpath(path))
+ except SchemaSaladException as e:
+ lint_context.error("Validation failed " + str(e))
+
+
+def main(argv):
+ """Script entry point for linting workflows."""
+ path = argv[1]
+ with open(path, "r") as f:
+ try:
+ workflow_dict = ordered_load(f)
+ except Exception:
+ return EXIT_CODE_FILE_PARSE_FAILED
+ workflow_class = workflow_dict.get("class")
+ lint_func = lint_format2 if workflow_class == "GalaxyWorkflow" else lint_ga
+ lint_context = LintContext()
+ lint_func(lint_context, workflow_dict, path=path)
+ lint_context.print_messages()
+ if lint_context.found_errors:
+ return EXIT_CODE_FORMAT_ERROR
+ elif lint_context.found_warns:
+ return EXIT_CODE_LINT_FAILED
+ else:
+ return EXIT_CODE_SUCCESS
+
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv))
+
+
+__all__ = ('main', 'lint_format2', 'lint_ga')
diff --git a/gxformat2/linting.py b/gxformat2/linting.py
new file mode 100644
index 0000000..cf712fb
--- /dev/null
+++ b/gxformat2/linting.py
@@ -0,0 +1,58 @@
+"""Generic utilities for linting.
+
+Largely derived in large part from galaxy.tool_util.lint.
+"""
+LEVEL_ALL = "all"
+LEVEL_WARN = "warn"
+LEVEL_ERROR = "error"
+
+
+class LintContext(object):
+ """Track running status (state) of linting."""
+
+ def __init__(self, level=LEVEL_WARN):
+ """Create LintContext with specified 'level' (currently unused)."""
+ self.level = level
+ self.found_errors = False
+ self.found_warns = False
+
+ # self.valid_messages = []
+ # self.info_messages = []
+ self.warn_messages = []
+ self.error_messages = []
+
+ def __handle_message(self, message_list, message, *args, **kwds):
+ if kwds or args:
+ message = message.format(*args, **kwds)
+ message_list.append(message)
+
+ # def valid(self, message, *args, **kwds):
+ # self.__handle_message(self.valid_messages, message, *args, **kwds)
+
+ # def info(self, message, *args, **kwds):
+ # self.__handle_message(self.info_messages, message, *args, **kwds)
+
+ def error(self, message, *args, **kwds):
+ """Track a linting error - a serious problem with the artifact preventing execution."""
+ self.__handle_message(self.error_messages, message, *args, **kwds)
+
+ def warn(self, message, *args, **kwds):
+ """Track a linting warning - a deviation from best practices."""
+ self.__handle_message(self.warn_messages, message, *args, **kwds)
+
+ def print_messages(self):
+ """Print error messages and update state at the end of linting."""
+ for message in self.error_messages:
+ self.found_errors = True
+ print(".. ERROR: %s" % message)
+
+ if self.level != LEVEL_ERROR:
+ for message in self.warn_messages:
+ self.found_warns = True
+ print(".. WARNING: %s" % message)
+
+ if self.level == LEVEL_ALL:
+ for message in self.info_messages:
+ print(".. INFO: %s" % message)
+ for message in self.valid_messages:
+ print(".. CHECK: %s" % message)
diff --git a/gxformat2/schema/__init__.py b/gxformat2/schema/__init__.py
new file mode 100644
index 0000000..51581e4
--- /dev/null
+++ b/gxformat2/schema/__init__.py
@@ -0,0 +1,5 @@
+"""Parsers for workflows dervied from schema-salad descriptions and codegen.
+
+Python files in this package probably shouldn't be modified manually. See
+build_schema.sh for more information.
+"""
diff --git a/gxformat2/schema/v19_09.py b/gxformat2/schema/v19_09.py
new file mode 100644
index 0000000..588c7bf
--- /dev/null
+++ b/gxformat2/schema/v19_09.py
@@ -0,0 +1,2718 @@
+#
+# This file was autogenerated using schema-salad-tool --codegen=python
+# The code itself is released under the Apache 2.0 license and the help text is
+# subject to the license of the original schema.
+#
+import copy
+import os
+import re
+import uuid # pylint: disable=unused-import # noqa: F401
+from typing import (
+ Any,
+ Dict,
+ List,
+ MutableMapping,
+ MutableSequence,
+ Optional,
+ Sequence,
+ Tuple,
+ Type,
+ Union,
+)
+
+from six import iteritems, string_types, text_type
+from six.moves import StringIO, urllib
+from typing_extensions import Text # pylint: disable=unused-import
+
+from ruamel import yaml
+from ruamel.yaml.comments import CommentedMap
+from schema_salad.ref_resolver import Fetcher
+from schema_salad.sourceline import SourceLine, add_lc_filename
+from schema_salad.exceptions import SchemaSaladException, ValidationException
+
+# move to a regular typing import when Python 3.3-3.6 is no longer supported
+
+_vocab = {} # type: Dict[Text, Text]
+_rvocab = {} # type: Dict[Text, Text]
+
+
+class Savable(object):
+ @classmethod
+ def fromDoc(cls, _doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Savable
+ pass
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Text]
+ pass
+
+
+class LoadingOptions(object):
+ def __init__(
+ self,
+ fetcher=None, # type: Optional[Fetcher]
+ namespaces=None, # type: Optional[Dict[Text, Text]]
+ fileuri=None, # type: Optional[Text]
+ copyfrom=None, # type: Optional[LoadingOptions]
+ original_doc=None, # type: Optional[Any]
+ ): # type: (...) -> None
+ self.idx = {} # type: Dict[Text, Dict[Text, Any]]
+ self.fileuri = fileuri # type: Optional[Text]
+ self.namespaces = namespaces
+ self.original_doc = original_doc
+ if copyfrom is not None:
+ self.idx = copyfrom.idx
+ if fetcher is None:
+ fetcher = copyfrom.fetcher
+ if fileuri is None:
+ self.fileuri = copyfrom.fileuri
+ if namespaces is None:
+ self.namespaces = copyfrom.namespaces
+
+ if fetcher is None:
+ import requests
+ from cachecontrol.wrapper import CacheControl
+ from cachecontrol.caches import FileCache
+ from schema_salad.ref_resolver import DefaultFetcher
+
+ if "HOME" in os.environ:
+ session = CacheControl(
+ requests.Session(),
+ cache=FileCache(
+ os.path.join(os.environ["HOME"], ".cache", "salad")
+ ),
+ )
+ elif "TMPDIR" in os.environ:
+ session = CacheControl(
+ requests.Session(),
+ cache=FileCache(
+ os.path.join(os.environ["TMPDIR"], ".cache", "salad")
+ ),
+ )
+ else:
+ session = CacheControl(
+ requests.Session(), cache=FileCache("/tmp", ".cache", "salad")
+ )
+ self.fetcher = DefaultFetcher({}, session) # type: Fetcher
+ else:
+ self.fetcher = fetcher
+
+ self.vocab = _vocab
+ self.rvocab = _rvocab
+
+ if namespaces is not None:
+ self.vocab = self.vocab.copy()
+ self.rvocab = self.rvocab.copy()
+ for k, v in iteritems(namespaces):
+ self.vocab[k] = v
+ self.rvocab[v] = k
+
+
+def load_field(val, fieldtype, baseuri, loadingOptions):
+ # type: (Union[Text, Dict[Text, Text]], _Loader, Text, LoadingOptions) -> Any
+ if isinstance(val, MutableMapping):
+ if "$import" in val:
+ if loadingOptions.fileuri is None:
+ raise SchemaSaladException("Cannot load $import without fileuri")
+ return _document_load_by_url(
+ fieldtype,
+ loadingOptions.fetcher.urljoin(loadingOptions.fileuri, val["$import"]),
+ loadingOptions,
+ )
+ elif "$include" in val:
+ if loadingOptions.fileuri is None:
+ raise SchemaSaladException("Cannot load $import without fileuri")
+ val = loadingOptions.fetcher.fetch_text(
+ loadingOptions.fetcher.urljoin(loadingOptions.fileuri, val["$include"])
+ )
+ return fieldtype.load(val, baseuri, loadingOptions)
+
+
+save_type = Union[
+ Dict[Text, Text], List[Union[Dict[Text, Text], List[Any], None]], None
+]
+
+
+def save(
+ val, # type: Optional[Union[Savable, MutableSequence[Savable]]]
+ top=True, # type: bool
+ base_url="", # type: Text
+ relative_uris=True, # type: bool
+): # type: (...) -> save_type
+
+ if isinstance(val, Savable):
+ return val.save(top=top, base_url=base_url, relative_uris=relative_uris)
+ if isinstance(val, MutableSequence):
+ return [
+ save(v, top=False, base_url=base_url, relative_uris=relative_uris)
+ for v in val
+ ]
+ if isinstance(val, MutableMapping):
+ newdict = {}
+ for key in val:
+ newdict[key] = save(
+ val[key], top=False, base_url=base_url, relative_uris=relative_uris
+ )
+ return newdict
+ return val
+
+
+def expand_url(
+ url, # type: Union[str, Text]
+ base_url, # type: Union[str, Text]
+ loadingOptions, # type: LoadingOptions
+ scoped_id=False, # type: bool
+ vocab_term=False, # type: bool
+ scoped_ref=None, # type: Optional[int]
+):
+ # type: (...) -> Text
+ url = Text(url)
+
+ if url in (u"@id", u"@type"):
+ return url
+
+ if vocab_term and url in loadingOptions.vocab:
+ return url
+
+ if bool(loadingOptions.vocab) and u":" in url:
+ prefix = url.split(u":")[0]
+ if prefix in loadingOptions.vocab:
+ url = loadingOptions.vocab[prefix] + url[len(prefix) + 1 :]
+
+ split = urllib.parse.urlsplit(url)
+
+ if (
+ (bool(split.scheme) and split.scheme in [u"http", u"https", u"file"])
+ or url.startswith(u"$(")
+ or url.startswith(u"${")
+ ):
+ pass
+ elif scoped_id and not bool(split.fragment):
+ splitbase = urllib.parse.urlsplit(base_url)
+ frg = u""
+ if bool(splitbase.fragment):
+ frg = splitbase.fragment + u"/" + split.path
+ else:
+ frg = split.path
+ pt = splitbase.path if splitbase.path != "" else "/"
+ url = urllib.parse.urlunsplit(
+ (splitbase.scheme, splitbase.netloc, pt, splitbase.query, frg)
+ )
+ elif scoped_ref is not None and not bool(split.fragment):
+ splitbase = urllib.parse.urlsplit(base_url)
+ sp = splitbase.fragment.split(u"/")
+ n = scoped_ref
+ while n > 0 and len(sp) > 0:
+ sp.pop()
+ n -= 1
+ sp.append(url)
+ url = urllib.parse.urlunsplit(
+ (
+ splitbase.scheme,
+ splitbase.netloc,
+ splitbase.path,
+ splitbase.query,
+ u"/".join(sp),
+ )
+ )
+ else:
+ url = loadingOptions.fetcher.urljoin(base_url, url)
+
+ if vocab_term:
+ split = urllib.parse.urlsplit(url)
+ if bool(split.scheme):
+ if url in loadingOptions.rvocab:
+ return loadingOptions.rvocab[url]
+ else:
+ raise ValidationException("Term '{}' not in vocabulary".format(url))
+
+ return url
+
+
+class _Loader(object):
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ pass
+
+
+class _AnyLoader(_Loader):
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ if doc is not None:
+ return doc
+ raise ValidationException("Expected non-null")
+
+
+class _PrimitiveLoader(_Loader):
+ def __init__(self, tp):
+ # type: (Union[type, Tuple[Type[Text], Type[Text]]]) -> None
+ self.tp = tp
+
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ if not isinstance(doc, self.tp):
+ raise ValidationException(
+ "Expected a {} but got {}".format(
+ self.tp.__class__.__name__, doc.__class__.__name__
+ )
+ )
+ return doc
+
+ def __repr__(self): # type: () -> str
+ return str(self.tp)
+
+
+class _ArrayLoader(_Loader):
+ def __init__(self, items):
+ # type: (_Loader) -> None
+ self.items = items
+
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ if not isinstance(doc, MutableSequence):
+ raise ValidationException("Expected a list")
+ r = [] # type: List[Any]
+ errors = [] # type: List[SchemaSaladException]
+ for i in range(0, len(doc)):
+ try:
+ lf = load_field(
+ doc[i], _UnionLoader((self, self.items)), baseuri, loadingOptions
+ )
+ if isinstance(lf, MutableSequence):
+ r.extend(lf)
+ else:
+ r.append(lf)
+ except ValidationException as e:
+ errors.append(ValidationException(
+ str(e),
+ SourceLine(doc, i, str),
+ [e]
+ ))
+ if errors:
+ raise ValidationException("", None, errors)
+ return r
+
+ def __repr__(self): # type: () -> str
+ return "array<{}>".format(self.items)
+
+
+class _EnumLoader(_Loader):
+ def __init__(self, symbols):
+ # type: (Sequence[Text]) -> None
+ self.symbols = symbols
+
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ if doc in self.symbols:
+ return doc
+ else:
+ raise ValidationException("Expected one of {}".format(self.symbols))
+
+
+class _RecordLoader(_Loader):
+ def __init__(self, classtype):
+ # type: (Type[Savable]) -> None
+ self.classtype = classtype
+
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ if not isinstance(doc, MutableMapping):
+ raise ValidationException("Expected a dict")
+ return self.classtype.fromDoc(doc, baseuri, loadingOptions, docRoot=docRoot)
+
+ def __repr__(self): # type: () -> str
+ return str(self.classtype)
+
+
+class _UnionLoader(_Loader):
+ def __init__(self, alternates):
+ # type: (Sequence[_Loader]) -> None
+ self.alternates = alternates
+
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ errors = []
+ for t in self.alternates:
+ try:
+ return t.load(doc, baseuri, loadingOptions, docRoot=docRoot)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ u"tried {} but".format(t.__class__.__name__), None, [e]
+ )
+ )
+ raise ValidationException("", None, errors, u"-")
+
+ def __repr__(self): # type: () -> str
+ return " | ".join(str(a) for a in self.alternates)
+
+
+class _URILoader(_Loader):
+ def __init__(self, inner, scoped_id, vocab_term, scoped_ref):
+ # type: (_Loader, bool, bool, Union[int, None]) -> None
+ self.inner = inner
+ self.scoped_id = scoped_id
+ self.vocab_term = vocab_term
+ self.scoped_ref = scoped_ref
+
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ if isinstance(doc, MutableSequence):
+ doc = [
+ expand_url(
+ i,
+ baseuri,
+ loadingOptions,
+ self.scoped_id,
+ self.vocab_term,
+ self.scoped_ref,
+ )
+ for i in doc
+ ]
+ if isinstance(doc, string_types):
+ doc = expand_url(
+ doc,
+ baseuri,
+ loadingOptions,
+ self.scoped_id,
+ self.vocab_term,
+ self.scoped_ref,
+ )
+ return self.inner.load(doc, baseuri, loadingOptions)
+
+
+class _TypeDSLLoader(_Loader):
+ typeDSLregex = re.compile(r"^([^[?]+)(\[\])?(\?)?$")
+
+ def __init__(self, inner, refScope):
+ # type: (_Loader, Union[int, None]) -> None
+ self.inner = inner
+ self.refScope = refScope
+
+ def resolve(
+ self,
+ doc, # type: Text
+ baseuri, # type: Text
+ loadingOptions, # type: LoadingOptions
+ ):
+ # type: (...) -> Union[List[Union[Dict[Text, Text], Text]], Dict[Text, Text], Text]
+ m = self.typeDSLregex.match(doc)
+ if m:
+ first = expand_url(
+ m.group(1), baseuri, loadingOptions, False, True, self.refScope
+ )
+ second = third = None
+ if bool(m.group(2)):
+ second = {u"type": u"array", u"items": first}
+ # second = CommentedMap((("type", "array"),
+ # ("items", first)))
+ # second.lc.add_kv_line_col("type", lc)
+ # second.lc.add_kv_line_col("items", lc)
+ # second.lc.filename = filename
+ if bool(m.group(3)):
+ third = [u"null", second or first]
+ # third = CommentedSeq([u"null", second or first])
+ # third.lc.add_kv_line_col(0, lc)
+ # third.lc.add_kv_line_col(1, lc)
+ # third.lc.filename = filename
+ return third or second or first
+ return doc
+
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ if isinstance(doc, MutableSequence):
+ r = [] # type: List[Any]
+ for d in doc:
+ if isinstance(d, string_types):
+ resolved = self.resolve(d, baseuri, loadingOptions)
+ if isinstance(resolved, MutableSequence):
+ for i in resolved:
+ if i not in r:
+ r.append(i)
+ else:
+ if resolved not in r:
+ r.append(resolved)
+ else:
+ r.append(d)
+ doc = r
+ elif isinstance(doc, string_types):
+ doc = self.resolve(doc, baseuri, loadingOptions)
+
+ return self.inner.load(doc, baseuri, loadingOptions)
+
+
+class _IdMapLoader(_Loader):
+ def __init__(self, inner, mapSubject, mapPredicate):
+ # type: (_Loader, Text, Union[Text, None]) -> None
+ self.inner = inner
+ self.mapSubject = mapSubject
+ self.mapPredicate = mapPredicate
+
+ def load(self, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> Any
+ if isinstance(doc, MutableMapping):
+ r = [] # type: List[Any]
+ for k in sorted(doc.keys()):
+ val = doc[k]
+ if isinstance(val, CommentedMap):
+ v = copy.copy(val)
+ v.lc.data = val.lc.data
+ v.lc.filename = val.lc.filename
+ v[self.mapSubject] = k
+ r.append(v)
+ elif isinstance(val, MutableMapping):
+ v2 = copy.copy(val)
+ v2[self.mapSubject] = k
+ r.append(v2)
+ else:
+ if self.mapPredicate:
+ v3 = {self.mapPredicate: val}
+ v3[self.mapSubject] = k
+ r.append(v3)
+ else:
+ raise ValidationException("No mapPredicate")
+ doc = r
+ return self.inner.load(doc, baseuri, loadingOptions)
+
+
+def _document_load(loader, doc, baseuri, loadingOptions):
+ # type: (_Loader, Any, Text, LoadingOptions) -> Any
+ if isinstance(doc, string_types):
+ return _document_load_by_url(
+ loader, loadingOptions.fetcher.urljoin(baseuri, doc), loadingOptions
+ )
+
+ if isinstance(doc, MutableMapping):
+ if "$namespaces" in doc:
+ loadingOptions = LoadingOptions(
+ copyfrom=loadingOptions, namespaces=doc["$namespaces"]
+ )
+ doc = {k: v for k, v in doc.items() if k != "$namespaces"}
+
+ if "$base" in doc:
+ baseuri = doc["$base"]
+
+ if "$graph" in doc:
+ return loader.load(doc["$graph"], baseuri, loadingOptions)
+ else:
+ return loader.load(doc, baseuri, loadingOptions, docRoot=baseuri)
+
+ if isinstance(doc, MutableSequence):
+ return loader.load(doc, baseuri, loadingOptions)
+
+ raise ValidationException("Oops, we shouldn't be here!")
+
+
+def _document_load_by_url(loader, url, loadingOptions):
+ # type: (_Loader, Text, LoadingOptions) -> Any
+ if url in loadingOptions.idx:
+ return _document_load(loader, loadingOptions.idx[url], url, loadingOptions)
+
+ text = loadingOptions.fetcher.fetch_text(url)
+ if isinstance(text, bytes):
+ textIO = StringIO(text.decode("utf-8"))
+ else:
+ textIO = StringIO(text)
+ textIO.name = str(url)
+ result = yaml.round_trip_load(textIO, preserve_quotes=True)
+ add_lc_filename(result, url)
+
+ loadingOptions.idx[url] = result
+
+ loadingOptions = LoadingOptions(copyfrom=loadingOptions, fileuri=url)
+
+ return _document_load(loader, result, url, loadingOptions)
+
+
+def file_uri(path, split_frag=False): # type: (str, bool) -> str
+ if path.startswith("file://"):
+ return path
+ if split_frag:
+ pathsp = path.split("#", 2)
+ frag = "#" + urllib.parse.quote(str(pathsp[1])) if len(pathsp) == 2 else ""
+ urlpath = urllib.request.pathname2url(str(pathsp[0]))
+ else:
+ urlpath = urllib.request.pathname2url(path)
+ frag = ""
+ if urlpath.startswith("//"):
+ return "file:{}{}".format(urlpath, frag)
+ else:
+ return "file://{}{}".format(urlpath, frag)
+
+
+def prefix_url(url, namespaces): # type: (Text, Dict[Text, Text]) -> Text
+ for k, v in namespaces.items():
+ if url.startswith(v):
+ return k + ":" + url[len(v) :]
+ return url
+
+
+def save_relative_uri(uri, base_url, scoped_id, ref_scope, relative_uris):
+ # type: (Text, Text, bool, Optional[int], bool) -> Union[Text, List[Text]]
+ if not relative_uris or uri == base_url:
+ return uri
+ if isinstance(uri, MutableSequence):
+ return [
+ save_relative_uri(u, base_url, scoped_id, ref_scope, relative_uris)
+ for u in uri
+ ]
+ elif isinstance(uri, text_type):
+ urisplit = urllib.parse.urlsplit(uri)
+ basesplit = urllib.parse.urlsplit(base_url)
+ if urisplit.scheme == basesplit.scheme and urisplit.netloc == basesplit.netloc:
+ if urisplit.path != basesplit.path:
+ p = os.path.relpath(urisplit.path, os.path.dirname(basesplit.path))
+ if urisplit.fragment:
+ p = p + "#" + urisplit.fragment
+ return p
+
+ basefrag = basesplit.fragment + "/"
+ if ref_scope:
+ sp = basefrag.split("/")
+ i = 0
+ while i < ref_scope:
+ sp.pop()
+ i += 1
+ basefrag = "/".join(sp)
+
+ if urisplit.fragment.startswith(basefrag):
+ return urisplit.fragment[len(basefrag) :]
+ else:
+ return urisplit.fragment
+ return uri
+ else:
+ return save(uri, top=False, base_url=base_url)
+
+
+class Documented(Savable):
+ pass
+
+
+class RecordField(Documented):
+ """
+A field of a record.
+ """
+ def __init__(
+ self,
+ doc, # type: Any
+ type, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.doc = doc
+ self.type = type
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> RecordField
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+
+ if name is None:
+ if docRoot is not None:
+ name = docRoot
+ else:
+ raise ValidationException("Missing name")
+ baseuri = name
+ if 'doc' in _doc:
+ try:
+ doc = load_field(_doc.get(
+ 'doc'), union_of_None_type_or_strtype_or_array_of_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `doc` field is not valid because:",
+ SourceLine(_doc, 'doc', str),
+ [e]
+ )
+ )
+ else:
+ doc = None
+ try:
+ type = load_field(_doc.get(
+ 'type'), typedsl_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_2, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `type` field is not valid because:",
+ SourceLine(_doc, 'type', str),
+ [e]
+ )
+ )
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `doc`, `name`, `type`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'RecordField'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(doc, type, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.doc is not None:
+ r['doc'] = save(
+ self.doc,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if self.type is not None:
+ r['type'] = save(
+ self.type,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'doc', u'name', u'type'])
+
+
+class RecordSchema(Savable):
+ def __init__(
+ self,
+ fields, # type: Any
+ type, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.fields = fields
+ self.type = type
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> RecordSchema
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+ if 'fields' in _doc:
+ try:
+ fields = load_field(_doc.get(
+ 'fields'), idmap_fields_union_of_None_type_or_array_of_RecordFieldLoader, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `fields` field is not valid because:",
+ SourceLine(_doc, 'fields', str),
+ [e]
+ )
+ )
+ else:
+ fields = None
+ try:
+ type = load_field(_doc.get(
+ 'type'), typedsl_enum_d9cba076fca539106791a4f46d198c7fcfbdb779Loader_2, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `type` field is not valid because:",
+ SourceLine(_doc, 'type', str),
+ [e]
+ )
+ )
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `fields`, `type`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'RecordSchema'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(fields, type, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.fields is not None:
+ r['fields'] = save(
+ self.fields,
+ top=False,
+ base_url=base_url,
+ relative_uris=relative_uris)
+
+ if self.type is not None:
+ r['type'] = save(
+ self.type,
+ top=False,
+ base_url=base_url,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'fields', u'type'])
+
+
+class EnumSchema(Savable):
+ """
+Define an enumerated type.
+
+ """
+ def __init__(
+ self,
+ symbols, # type: Any
+ type, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.symbols = symbols
+ self.type = type
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> EnumSchema
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+ try:
+ symbols = load_field(_doc.get(
+ 'symbols'), uri_array_of_strtype_True_False_None, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `symbols` field is not valid because:",
+ SourceLine(_doc, 'symbols', str),
+ [e]
+ )
+ )
+ try:
+ type = load_field(_doc.get(
+ 'type'), typedsl_enum_d961d79c225752b9fadb617367615ab176b47d77Loader_2, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `type` field is not valid because:",
+ SourceLine(_doc, 'type', str),
+ [e]
+ )
+ )
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `symbols`, `type`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'EnumSchema'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(symbols, type, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.symbols is not None:
+ u = save_relative_uri(
+ self.symbols,
+ base_url,
+ True,
+ None,
+ relative_uris)
+ if u:
+ r['symbols'] = u
+
+ if self.type is not None:
+ r['type'] = save(
+ self.type,
+ top=False,
+ base_url=base_url,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'symbols', u'type'])
+
+
+class ArraySchema(Savable):
+ def __init__(
+ self,
+ items, # type: Any
+ type, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.items = items
+ self.type = type
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> ArraySchema
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+ try:
+ items = load_field(_doc.get(
+ 'items'), uri_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_False_True_2, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `items` field is not valid because:",
+ SourceLine(_doc, 'items', str),
+ [e]
+ )
+ )
+ try:
+ type = load_field(_doc.get(
+ 'type'), typedsl_enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader_2, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `type` field is not valid because:",
+ SourceLine(_doc, 'type', str),
+ [e]
+ )
+ )
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `items`, `type`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'ArraySchema'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(items, type, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.items is not None:
+ u = save_relative_uri(
+ self.items,
+ base_url,
+ False,
+ 2,
+ relative_uris)
+ if u:
+ r['items'] = u
+
+ if self.type is not None:
+ r['type'] = save(
+ self.type,
+ top=False,
+ base_url=base_url,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'items', u'type'])
+
+
+class Labeled(Savable):
+ pass
+
+
+class Identified(Savable):
+ pass
+
+
+class Parameter(Documented, Identified):
+ """
+Define an input or output parameter to a process.
+
+ """
+ pass
+
+
+class InputParameter(Parameter):
+ pass
+
+
+class OutputParameter(Parameter):
+ pass
+
+
+class Process(Identified, Labeled, Documented):
+ """
+
+The base executable type in CWL is the `Process` object defined by the
+document. Note that the `Process` object is abstract and cannot be
+directly executed.
+
+ """
+ pass
+
+
+class HasStepPosition(Savable):
+ pass
+
+
+class StepPosition(Savable):
+ """
+This field specifies the location of the step's node when rendered in the workflow editor.
+ """
+ def __init__(
+ self,
+ top, # type: Any
+ left, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.top = top
+ self.left = left
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> StepPosition
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+ try:
+ top = load_field(_doc.get(
+ 'top'), floattype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `top` field is not valid because:",
+ SourceLine(_doc, 'top', str),
+ [e]
+ )
+ )
+ try:
+ left = load_field(_doc.get(
+ 'left'), floattype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `left` field is not valid because:",
+ SourceLine(_doc, 'left', str),
+ [e]
+ )
+ )
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `top`, `left`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'StepPosition'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(top, left, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.top is not None:
+ r['top'] = save(
+ self.top,
+ top=False,
+ base_url=base_url,
+ relative_uris=relative_uris)
+
+ if self.left is not None:
+ r['left'] = save(
+ self.left,
+ top=False,
+ base_url=base_url,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'top', u'left'])
+
+
+class ReferencesTool(Savable):
+ pass
+
+
+class ToolShedRepository(Savable):
+ def __init__(
+ self,
+ changeset_revision, # type: Any
+ owner, # type: Any
+ tool_shed, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.changeset_revision = changeset_revision
+ self.owner = owner
+ self.tool_shed = tool_shed
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> ToolShedRepository
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+
+ if name is None:
+ if docRoot is not None:
+ name = docRoot
+ else:
+ raise ValidationException("Missing name")
+ baseuri = name
+ try:
+ changeset_revision = load_field(_doc.get(
+ 'changeset_revision'), strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `changeset_revision` field is not valid because:",
+ SourceLine(_doc, 'changeset_revision', str),
+ [e]
+ )
+ )
+ try:
+ owner = load_field(_doc.get(
+ 'owner'), strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `owner` field is not valid because:",
+ SourceLine(_doc, 'owner', str),
+ [e]
+ )
+ )
+ try:
+ tool_shed = load_field(_doc.get(
+ 'tool_shed'), strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `tool_shed` field is not valid because:",
+ SourceLine(_doc, 'tool_shed', str),
+ [e]
+ )
+ )
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `changeset_revision`, `name`, `owner`, `tool_shed`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'ToolShedRepository'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(changeset_revision, owner, tool_shed, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.changeset_revision is not None:
+ r['changeset_revision'] = save(
+ self.changeset_revision,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if self.owner is not None:
+ r['owner'] = save(
+ self.owner,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if self.tool_shed is not None:
+ r['tool_shed'] = save(
+ self.tool_shed,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'changeset_revision', u'name', u'owner', u'tool_shed'])
+
+
+class WorkflowInputParameter(InputParameter):
+ def __init__(
+ self,
+ doc, # type: Any
+ id, # type: Any
+ default, # type: Any
+ type, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.doc = doc
+ self.id = id
+ self.default = default
+ self.type = type
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> WorkflowInputParameter
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+ if 'id' in _doc:
+ try:
+ id = load_field(_doc.get(
+ 'id'), uri_union_of_None_type_or_strtype_True_False_None, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `id` field is not valid because:",
+ SourceLine(_doc, 'id', str),
+ [e]
+ )
+ )
+ else:
+ id = None
+
+ if id is None:
+ if docRoot is not None:
+ id = docRoot
+ else:
+ id = "_:" + str(uuid.uuid4())
+ baseuri = id
+ if 'doc' in _doc:
+ try:
+ doc = load_field(_doc.get(
+ 'doc'), union_of_None_type_or_strtype_or_array_of_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `doc` field is not valid because:",
+ SourceLine(_doc, 'doc', str),
+ [e]
+ )
+ )
+ else:
+ doc = None
+ if 'default' in _doc:
+ try:
+ default = load_field(_doc.get(
+ 'default'), union_of_None_type_or_Any_type, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `default` field is not valid because:",
+ SourceLine(_doc, 'default', str),
+ [e]
+ )
+ )
+ else:
+ default = None
+ if 'type' in _doc:
+ try:
+ type = load_field(_doc.get(
+ 'type'), typedsl_union_of_None_type_or_GalaxyTypeLoader_2, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `type` field is not valid because:",
+ SourceLine(_doc, 'type', str),
+ [e]
+ )
+ )
+ else:
+ type = None
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `doc`, `id`, `default`, `type`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'WorkflowInputParameter'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(doc, id, default, type, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.id is not None:
+ u = save_relative_uri(
+ self.id,
+ base_url,
+ True,
+ None,
+ relative_uris)
+ if u:
+ r['id'] = u
+
+ if self.doc is not None:
+ r['doc'] = save(
+ self.doc,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.default is not None:
+ r['default'] = save(
+ self.default,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.type is not None:
+ r['type'] = save(
+ self.type,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'doc', u'id', u'default', u'type'])
+
+
+class WorkflowOutputParameter(OutputParameter):
+ """
+Describe an output parameter of a workflow. The parameter must be
+connected to one parameter defined in the workflow that
+will provide the value of the output parameter. It is legal to
+connect a WorkflowInputParameter to a WorkflowOutputParameter.
+
+ """
+ def __init__(
+ self,
+ doc, # type: Any
+ id, # type: Any
+ outputSource, # type: Any
+ type, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.doc = doc
+ self.id = id
+ self.outputSource = outputSource
+ self.type = type
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> WorkflowOutputParameter
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+ if 'id' in _doc:
+ try:
+ id = load_field(_doc.get(
+ 'id'), uri_union_of_None_type_or_strtype_True_False_None, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `id` field is not valid because:",
+ SourceLine(_doc, 'id', str),
+ [e]
+ )
+ )
+ else:
+ id = None
+
+ if id is None:
+ if docRoot is not None:
+ id = docRoot
+ else:
+ id = "_:" + str(uuid.uuid4())
+ baseuri = id
+ if 'doc' in _doc:
+ try:
+ doc = load_field(_doc.get(
+ 'doc'), union_of_None_type_or_strtype_or_array_of_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `doc` field is not valid because:",
+ SourceLine(_doc, 'doc', str),
+ [e]
+ )
+ )
+ else:
+ doc = None
+ if 'outputSource' in _doc:
+ try:
+ outputSource = load_field(_doc.get(
+ 'outputSource'), union_of_None_type_or_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `outputSource` field is not valid because:",
+ SourceLine(_doc, 'outputSource', str),
+ [e]
+ )
+ )
+ else:
+ outputSource = None
+ if 'type' in _doc:
+ try:
+ type = load_field(_doc.get(
+ 'type'), typedsl_union_of_None_type_or_GalaxyTypeLoader_2, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `type` field is not valid because:",
+ SourceLine(_doc, 'type', str),
+ [e]
+ )
+ )
+ else:
+ type = None
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `doc`, `id`, `outputSource`, `type`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'WorkflowOutputParameter'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(doc, id, outputSource, type, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.id is not None:
+ u = save_relative_uri(
+ self.id,
+ base_url,
+ True,
+ None,
+ relative_uris)
+ if u:
+ r['id'] = u
+
+ if self.doc is not None:
+ r['doc'] = save(
+ self.doc,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.outputSource is not None:
+ r['outputSource'] = save(
+ self.outputSource,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.type is not None:
+ r['type'] = save(
+ self.type,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'doc', u'id', u'outputSource', u'type'])
+
+
+class WorkflowStep(Identified, Labeled, Documented, HasStepPosition, ReferencesTool):
+ """
+Workflow step.
+
+ """
+ def __init__(
+ self,
+ id, # type: Any
+ label, # type: Any
+ doc, # type: Any
+ position, # type: Any
+ tool_id, # type: Any
+ tool_shed_repository, # type: Any
+ tool_version, # type: Any
+ in_, # type: Any
+ out, # type: Any
+ state, # type: Any
+ type, # type: Any
+ run, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.id = id
+ self.label = label
+ self.doc = doc
+ self.position = position
+ self.tool_id = tool_id
+ self.tool_shed_repository = tool_shed_repository
+ self.tool_version = tool_version
+ self.in_ = in_
+ self.out = out
+ self.state = state
+ self.type = type
+ self.run = run
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> WorkflowStep
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+ if 'id' in _doc:
+ try:
+ id = load_field(_doc.get(
+ 'id'), uri_union_of_None_type_or_strtype_True_False_None, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `id` field is not valid because:",
+ SourceLine(_doc, 'id', str),
+ [e]
+ )
+ )
+ else:
+ id = None
+
+ if id is None:
+ if docRoot is not None:
+ id = docRoot
+ else:
+ id = "_:" + str(uuid.uuid4())
+ baseuri = id
+ if 'label' in _doc:
+ try:
+ label = load_field(_doc.get(
+ 'label'), union_of_None_type_or_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `label` field is not valid because:",
+ SourceLine(_doc, 'label', str),
+ [e]
+ )
+ )
+ else:
+ label = None
+ if 'doc' in _doc:
+ try:
+ doc = load_field(_doc.get(
+ 'doc'), union_of_None_type_or_strtype_or_array_of_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `doc` field is not valid because:",
+ SourceLine(_doc, 'doc', str),
+ [e]
+ )
+ )
+ else:
+ doc = None
+ if 'position' in _doc:
+ try:
+ position = load_field(_doc.get(
+ 'position'), union_of_None_type_or_StepPositionLoader, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `position` field is not valid because:",
+ SourceLine(_doc, 'position', str),
+ [e]
+ )
+ )
+ else:
+ position = None
+ if 'tool_id' in _doc:
+ try:
+ tool_id = load_field(_doc.get(
+ 'tool_id'), union_of_None_type_or_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `tool_id` field is not valid because:",
+ SourceLine(_doc, 'tool_id', str),
+ [e]
+ )
+ )
+ else:
+ tool_id = None
+ if 'tool_shed_repository' in _doc:
+ try:
+ tool_shed_repository = load_field(_doc.get(
+ 'tool_shed_repository'), union_of_None_type_or_ToolShedRepositoryLoader, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `tool_shed_repository` field is not valid because:",
+ SourceLine(_doc, 'tool_shed_repository', str),
+ [e]
+ )
+ )
+ else:
+ tool_shed_repository = None
+ if 'tool_version' in _doc:
+ try:
+ tool_version = load_field(_doc.get(
+ 'tool_version'), union_of_None_type_or_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `tool_version` field is not valid because:",
+ SourceLine(_doc, 'tool_version', str),
+ [e]
+ )
+ )
+ else:
+ tool_version = None
+ if 'in' in _doc:
+ try:
+ in_ = load_field(_doc.get(
+ 'in'), idmap_in__union_of_None_type_or_array_of_WorkflowStepInputLoader, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `in` field is not valid because:",
+ SourceLine(_doc, 'in', str),
+ [e]
+ )
+ )
+ else:
+ in_ = None
+ if 'out' in _doc:
+ try:
+ out = load_field(_doc.get(
+ 'out'), uri_union_of_array_of_union_of_strtype_or_WorkflowStepOutputLoader_or_None_type_True_False_None, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `out` field is not valid because:",
+ SourceLine(_doc, 'out', str),
+ [e]
+ )
+ )
+ else:
+ out = None
+ if 'state' in _doc:
+ try:
+ state = load_field(_doc.get(
+ 'state'), union_of_None_type_or_Any_type, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `state` field is not valid because:",
+ SourceLine(_doc, 'state', str),
+ [e]
+ )
+ )
+ else:
+ state = None
+ if 'type' in _doc:
+ try:
+ type = load_field(_doc.get(
+ 'type'), typedsl_union_of_None_type_or_WorkflowStepTypeLoader_2, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `type` field is not valid because:",
+ SourceLine(_doc, 'type', str),
+ [e]
+ )
+ )
+ else:
+ type = None
+ if 'run' in _doc:
+ try:
+ run = load_field(_doc.get(
+ 'run'), uri_union_of_None_type_or_GalaxyWorkflowLoader_False_False_None, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `run` field is not valid because:",
+ SourceLine(_doc, 'run', str),
+ [e]
+ )
+ )
+ else:
+ run = None
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `id`, `label`, `doc`, `position`, `tool_id`, `tool_shed_repository`, `tool_version`, `in`, `out`, `state`, `type`, `run`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'WorkflowStep'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(id, label, doc, position, tool_id, tool_shed_repository, tool_version, in_, out, state, type, run, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.id is not None:
+ u = save_relative_uri(
+ self.id,
+ base_url,
+ True,
+ None,
+ relative_uris)
+ if u:
+ r['id'] = u
+
+ if self.label is not None:
+ r['label'] = save(
+ self.label,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.doc is not None:
+ r['doc'] = save(
+ self.doc,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.position is not None:
+ r['position'] = save(
+ self.position,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.tool_id is not None:
+ r['tool_id'] = save(
+ self.tool_id,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.tool_shed_repository is not None:
+ r['tool_shed_repository'] = save(
+ self.tool_shed_repository,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.tool_version is not None:
+ r['tool_version'] = save(
+ self.tool_version,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.in_ is not None:
+ r['in'] = save(
+ self.in_,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.out is not None:
+ u = save_relative_uri(
+ self.out,
+ self.id,
+ True,
+ None,
+ relative_uris)
+ if u:
+ r['out'] = u
+
+ if self.state is not None:
+ r['state'] = save(
+ self.state,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.type is not None:
+ r['type'] = save(
+ self.type,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.run is not None:
+ u = save_relative_uri(
+ self.run,
+ self.id,
+ False,
+ None,
+ relative_uris)
+ if u:
+ r['run'] = u
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'id', u'label', u'doc', u'position', u'tool_id', u'tool_shed_repository', u'tool_version', u'in', u'out', u'state', u'type', u'run'])
+
+
+class Sink(Savable):
+ pass
+
+
+class WorkflowStepInput(Identified, Sink, Labeled):
+ """
+TODO:
+
+ """
+ def __init__(
+ self,
+ id, # type: Any
+ source, # type: Any
+ label, # type: Any
+ default, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.id = id
+ self.source = source
+ self.label = label
+ self.default = default
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> WorkflowStepInput
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+ if 'id' in _doc:
+ try:
+ id = load_field(_doc.get(
+ 'id'), uri_union_of_None_type_or_strtype_True_False_None, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `id` field is not valid because:",
+ SourceLine(_doc, 'id', str),
+ [e]
+ )
+ )
+ else:
+ id = None
+
+ if id is None:
+ if docRoot is not None:
+ id = docRoot
+ else:
+ id = "_:" + str(uuid.uuid4())
+ baseuri = id
+ if 'source' in _doc:
+ try:
+ source = load_field(_doc.get(
+ 'source'), uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_2, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `source` field is not valid because:",
+ SourceLine(_doc, 'source', str),
+ [e]
+ )
+ )
+ else:
+ source = None
+ if 'label' in _doc:
+ try:
+ label = load_field(_doc.get(
+ 'label'), union_of_None_type_or_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `label` field is not valid because:",
+ SourceLine(_doc, 'label', str),
+ [e]
+ )
+ )
+ else:
+ label = None
+ if 'default' in _doc:
+ try:
+ default = load_field(_doc.get(
+ 'default'), union_of_None_type_or_Any_type, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `default` field is not valid because:",
+ SourceLine(_doc, 'default', str),
+ [e]
+ )
+ )
+ else:
+ default = None
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `id`, `source`, `label`, `default`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'WorkflowStepInput'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(id, source, label, default, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.id is not None:
+ u = save_relative_uri(
+ self.id,
+ base_url,
+ True,
+ None,
+ relative_uris)
+ if u:
+ r['id'] = u
+
+ if self.source is not None:
+ u = save_relative_uri(
+ self.source,
+ self.id,
+ False,
+ 2,
+ relative_uris)
+ if u:
+ r['source'] = u
+
+ if self.label is not None:
+ r['label'] = save(
+ self.label,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if self.default is not None:
+ r['default'] = save(
+ self.default,
+ top=False,
+ base_url=self.id,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'id', u'source', u'label', u'default'])
+
+
+class WorkflowStepOutput(Identified):
+ """
+Associate an output parameter of the underlying process with a workflow
+parameter. The workflow parameter (given in the `id` field) be may be used
+as a `source` to connect with input parameters of other workflow steps, or
+with an output parameter of the process.
+
+A unique identifier for this workflow output parameter. This is
+the identifier to use in the `source` field of `WorkflowStepInput`
+to connect the output value to downstream parameters.
+
+ """
+ def __init__(
+ self,
+ id, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.id = id
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> WorkflowStepOutput
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+ if 'id' in _doc:
+ try:
+ id = load_field(_doc.get(
+ 'id'), uri_union_of_None_type_or_strtype_True_False_None, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `id` field is not valid because:",
+ SourceLine(_doc, 'id', str),
+ [e]
+ )
+ )
+ else:
+ id = None
+
+ if id is None:
+ if docRoot is not None:
+ id = docRoot
+ else:
+ id = "_:" + str(uuid.uuid4())
+ baseuri = id
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `id`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'WorkflowStepOutput'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(id, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ if self.id is not None:
+ u = save_relative_uri(
+ self.id,
+ base_url,
+ True,
+ None,
+ relative_uris)
+ if u:
+ r['id'] = u
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'id'])
+
+
+class GalaxyWorkflow(Process):
+ """
+This is documentation for a workflow!
+ """
+ def __init__(
+ self,
+ id, # type: Any
+ label, # type: Any
+ doc, # type: Any
+ inputs, # type: Any
+ outputs, # type: Any
+ steps, # type: Any
+ extension_fields=None, # type: Optional[Dict[Text, Any]]
+ loadingOptions=None # type: Optional[LoadingOptions]
+ ): # type: (...) -> None
+
+ if extension_fields:
+ self.extension_fields = extension_fields
+ else:
+ self.extension_fields = yaml.comments.CommentedMap()
+ if loadingOptions:
+ self.loadingOptions = loadingOptions
+ else:
+ self.loadingOptions = LoadingOptions()
+ self.id = id
+ self.label = label
+ self.doc = doc
+ self.inputs = inputs
+ self.outputs = outputs
+ self.class_ = "GalaxyWorkflow"
+ self.steps = steps
+
+ @classmethod
+ def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
+ # type: (Any, Text, LoadingOptions, Optional[Text]) -> GalaxyWorkflow
+
+ _doc = copy.copy(doc)
+ if hasattr(doc, 'lc'):
+ _doc.lc.data = doc.lc.data
+ _doc.lc.filename = doc.lc.filename
+ errors = []
+
+ if _doc.get('class') != 'GalaxyWorkflow':
+ raise ValidationException("Not a GalaxyWorkflow")
+
+ if 'id' in _doc:
+ try:
+ id = load_field(_doc.get(
+ 'id'), uri_union_of_None_type_or_strtype_True_False_None, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `id` field is not valid because:",
+ SourceLine(_doc, 'id', str),
+ [e]
+ )
+ )
+ else:
+ id = None
+
+ if id is None:
+ if docRoot is not None:
+ id = docRoot
+ else:
+ id = "_:" + str(uuid.uuid4())
+ baseuri = id
+ if 'label' in _doc:
+ try:
+ label = load_field(_doc.get(
+ 'label'), union_of_None_type_or_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `label` field is not valid because:",
+ SourceLine(_doc, 'label', str),
+ [e]
+ )
+ )
+ else:
+ label = None
+ if 'doc' in _doc:
+ try:
+ doc = load_field(_doc.get(
+ 'doc'), union_of_None_type_or_strtype_or_array_of_strtype, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `doc` field is not valid because:",
+ SourceLine(_doc, 'doc', str),
+ [e]
+ )
+ )
+ else:
+ doc = None
+ try:
+ inputs = load_field(_doc.get(
+ 'inputs'), idmap_inputs_array_of_WorkflowInputParameterLoader, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `inputs` field is not valid because:",
+ SourceLine(_doc, 'inputs', str),
+ [e]
+ )
+ )
+ try:
+ outputs = load_field(_doc.get(
+ 'outputs'), idmap_outputs_array_of_WorkflowOutputParameterLoader, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `outputs` field is not valid because:",
+ SourceLine(_doc, 'outputs', str),
+ [e]
+ )
+ )
+ try:
+ steps = load_field(_doc.get(
+ 'steps'), idmap_steps_union_of_array_of_WorkflowStepLoader, baseuri, loadingOptions)
+ except ValidationException as e:
+ errors.append(
+ ValidationException(
+ "the `steps` field is not valid because:",
+ SourceLine(_doc, 'steps', str),
+ [e]
+ )
+ )
+
+ extension_fields = yaml.comments.CommentedMap()
+ for k in _doc.keys():
+ if k not in cls.attrs:
+ if ":" in k:
+ ex = expand_url(k,
+ u"",
+ loadingOptions,
+ scoped_id=False,
+ vocab_term=False)
+ extension_fields[ex] = _doc[k]
+ else:
+ errors.append(
+ ValidationException(
+ "invalid field `%s`, expected one of: `id`, `label`, `doc`, `inputs`, `outputs`, `name`, `class`, `steps`" % (k),
+ SourceLine(_doc, k, str)
+ )
+ )
+ break
+
+ if errors:
+ raise ValidationException("Trying 'GalaxyWorkflow'", None, errors)
+ loadingOptions = copy.deepcopy(loadingOptions)
+ loadingOptions.original_doc = _doc
+ return cls(id, label, doc, inputs, outputs, steps, extension_fields=extension_fields, loadingOptions=loadingOptions)
+
+ def save(self, top=False, base_url="", relative_uris=True):
+ # type: (bool, Text, bool) -> Dict[Text, Any]
+ r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
+ for ef in self.extension_fields:
+ r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
+
+ r['class'] = 'GalaxyWorkflow'
+
+ if self.id is not None:
+ u = save_relative_uri(
+ self.id,
+ self.name,
+ True,
+ None,
+ relative_uris)
+ if u:
+ r['id'] = u
+
+ if self.label is not None:
+ r['label'] = save(
+ self.label,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if self.doc is not None:
+ r['doc'] = save(
+ self.doc,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if self.inputs is not None:
+ r['inputs'] = save(
+ self.inputs,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if self.outputs is not None:
+ r['outputs'] = save(
+ self.outputs,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if self.steps is not None:
+ r['steps'] = save(
+ self.steps,
+ top=False,
+ base_url=self.name,
+ relative_uris=relative_uris)
+
+ if top and self.loadingOptions.namespaces:
+ r["$namespaces"] = self.loadingOptions.namespaces
+
+ return r
+
+ attrs = frozenset([u'id', u'label', u'doc', u'inputs', u'outputs', u'name', u'class', u'steps'])
+
+
+_vocab = {
+ "Any": "https://w3id.org/cwl/salad#Any",
+ "ArraySchema": "https://w3id.org/cwl/salad#ArraySchema",
+ "Documented": "https://w3id.org/cwl/salad#Documented",
+ "EnumSchema": "https://w3id.org/cwl/salad#EnumSchema",
+ "File": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/File",
+ "GalaxyType": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType",
+ "GalaxyWorkflow": "https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow",
+ "HasStepPosition": "https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition",
+ "Identified": "https://w3id.org/cwl/cwl#Identified",
+ "InputParameter": "https://w3id.org/cwl/cwl#InputParameter",
+ "Labeled": "https://w3id.org/cwl/cwl#Labeled",
+ "OutputParameter": "https://w3id.org/cwl/cwl#OutputParameter",
+ "Parameter": "https://w3id.org/cwl/cwl#Parameter",
+ "PrimitiveType": "https://w3id.org/cwl/salad#PrimitiveType",
+ "Process": "https://w3id.org/cwl/cwl#Process",
+ "RecordField": "https://w3id.org/cwl/salad#RecordField",
+ "RecordSchema": "https://w3id.org/cwl/salad#RecordSchema",
+ "ReferencesTool": "https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool",
+ "Sink": "https://galaxyproject.org/gxformat2/v19_09#Sink",
+ "StepPosition": "https://galaxyproject.org/gxformat2/gxformat2common#StepPosition",
+ "ToolShedRepository": "https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository",
+ "WorkflowInputParameter": "https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter",
+ "WorkflowOutputParameter": "https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter",
+ "WorkflowStep": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStep",
+ "WorkflowStepInput": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput",
+ "WorkflowStepOutput": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput",
+ "WorkflowStepType": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType",
+ "array": "https://w3id.org/cwl/salad#array",
+ "boolean": "http://www.w3.org/2001/XMLSchema#boolean",
+ "collection": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/collection",
+ "data": "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/data",
+ "double": "http://www.w3.org/2001/XMLSchema#double",
+ "enum": "https://w3id.org/cwl/salad#enum",
+ "float": "http://www.w3.org/2001/XMLSchema#float",
+ "int": "http://www.w3.org/2001/XMLSchema#int",
+ "long": "http://www.w3.org/2001/XMLSchema#long",
+ "null": "https://w3id.org/cwl/salad#null",
+ "pause": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/pause",
+ "record": "https://w3id.org/cwl/salad#record",
+ "string": "http://www.w3.org/2001/XMLSchema#string",
+ "subworkflow": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/subworkflow",
+ "tool": "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/tool",
+}
+_rvocab = {
+ "https://w3id.org/cwl/salad#Any": "Any",
+ "https://w3id.org/cwl/salad#ArraySchema": "ArraySchema",
+ "https://w3id.org/cwl/salad#Documented": "Documented",
+ "https://w3id.org/cwl/salad#EnumSchema": "EnumSchema",
+ "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/File": "File",
+ "https://galaxyproject.org/gxformat2/v19_09#GalaxyType": "GalaxyType",
+ "https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow": "GalaxyWorkflow",
+ "https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition": "HasStepPosition",
+ "https://w3id.org/cwl/cwl#Identified": "Identified",
+ "https://w3id.org/cwl/cwl#InputParameter": "InputParameter",
+ "https://w3id.org/cwl/cwl#Labeled": "Labeled",
+ "https://w3id.org/cwl/cwl#OutputParameter": "OutputParameter",
+ "https://w3id.org/cwl/cwl#Parameter": "Parameter",
+ "https://w3id.org/cwl/salad#PrimitiveType": "PrimitiveType",
+ "https://w3id.org/cwl/cwl#Process": "Process",
+ "https://w3id.org/cwl/salad#RecordField": "RecordField",
+ "https://w3id.org/cwl/salad#RecordSchema": "RecordSchema",
+ "https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool": "ReferencesTool",
+ "https://galaxyproject.org/gxformat2/v19_09#Sink": "Sink",
+ "https://galaxyproject.org/gxformat2/gxformat2common#StepPosition": "StepPosition",
+ "https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository": "ToolShedRepository",
+ "https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter": "WorkflowInputParameter",
+ "https://galaxyproject.org/gxformat2/v19_09#WorkflowOutputParameter": "WorkflowOutputParameter",
+ "https://galaxyproject.org/gxformat2/v19_09#WorkflowStep": "WorkflowStep",
+ "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput": "WorkflowStepInput",
+ "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepOutput": "WorkflowStepOutput",
+ "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType": "WorkflowStepType",
+ "https://w3id.org/cwl/salad#array": "array",
+ "http://www.w3.org/2001/XMLSchema#boolean": "boolean",
+ "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/collection": "collection",
+ "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/data": "data",
+ "http://www.w3.org/2001/XMLSchema#double": "double",
+ "https://w3id.org/cwl/salad#enum": "enum",
+ "http://www.w3.org/2001/XMLSchema#float": "float",
+ "http://www.w3.org/2001/XMLSchema#int": "int",
+ "http://www.w3.org/2001/XMLSchema#long": "long",
+ "https://w3id.org/cwl/salad#null": "null",
+ "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/pause": "pause",
+ "https://w3id.org/cwl/salad#record": "record",
+ "http://www.w3.org/2001/XMLSchema#string": "string",
+ "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/subworkflow": "subworkflow",
+ "https://galaxyproject.org/gxformat2/v19_09#WorkflowStepType/tool": "tool",
+}
+
+inttype = _PrimitiveLoader(int)
+booltype = _PrimitiveLoader(bool)
+strtype = _PrimitiveLoader((str, text_type))
+Any_type = _AnyLoader()
+floattype = _PrimitiveLoader(float)
+None_type = _PrimitiveLoader(type(None))
+DocumentedLoader = _RecordLoader(Documented)
+PrimitiveTypeLoader = _EnumLoader(("null", "boolean", "int", "long", "float", "double", "string",))
+AnyLoader = _EnumLoader(("Any",))
+RecordFieldLoader = _RecordLoader(RecordField)
+RecordSchemaLoader = _RecordLoader(RecordSchema)
+EnumSchemaLoader = _RecordLoader(EnumSchema)
+ArraySchemaLoader = _RecordLoader(ArraySchema)
+LabeledLoader = _RecordLoader(Labeled)
+IdentifiedLoader = _RecordLoader(Identified)
+ParameterLoader = _RecordLoader(Parameter)
+InputParameterLoader = _RecordLoader(InputParameter)
+OutputParameterLoader = _RecordLoader(OutputParameter)
+ProcessLoader = _RecordLoader(Process)
+HasStepPositionLoader = _RecordLoader(HasStepPosition)
+StepPositionLoader = _RecordLoader(StepPosition)
+ReferencesToolLoader = _RecordLoader(ReferencesTool)
+ToolShedRepositoryLoader = _RecordLoader(ToolShedRepository)
+GalaxyTypeLoader = _EnumLoader(("File", "data", "collection",))
+WorkflowStepTypeLoader = _EnumLoader(("tool", "subworkflow", "pause",))
+WorkflowInputParameterLoader = _RecordLoader(WorkflowInputParameter)
+WorkflowOutputParameterLoader = _RecordLoader(WorkflowOutputParameter)
+WorkflowStepLoader = _RecordLoader(WorkflowStep)
+SinkLoader = _RecordLoader(Sink)
+WorkflowStepInputLoader = _RecordLoader(WorkflowStepInput)
+WorkflowStepOutputLoader = _RecordLoader(WorkflowStepOutput)
+GalaxyWorkflowLoader = _RecordLoader(GalaxyWorkflow)
+array_of_strtype = _ArrayLoader(strtype)
+union_of_None_type_or_strtype_or_array_of_strtype = _UnionLoader((None_type, strtype, array_of_strtype,))
+uri_strtype_True_False_None = _URILoader(strtype, True, False, None)
+union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype = _UnionLoader((PrimitiveTypeLoader, RecordSchemaLoader, EnumSchemaLoader, ArraySchemaLoader, strtype,))
+array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype = _ArrayLoader(union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype)
+union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype = _UnionLoader((PrimitiveTypeLoader, RecordSchemaLoader, EnumSchemaLoader, ArraySchemaLoader, strtype, array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype,))
+typedsl_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_2 = _TypeDSLLoader(union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype, 2)
+array_of_RecordFieldLoader = _ArrayLoader(RecordFieldLoader)
+union_of_None_type_or_array_of_RecordFieldLoader = _UnionLoader((None_type, array_of_RecordFieldLoader,))
+idmap_fields_union_of_None_type_or_array_of_RecordFieldLoader = _IdMapLoader(union_of_None_type_or_array_of_RecordFieldLoader, 'name', 'type')
+enum_d9cba076fca539106791a4f46d198c7fcfbdb779Loader = _EnumLoader(("record",))
+typedsl_enum_d9cba076fca539106791a4f46d198c7fcfbdb779Loader_2 = _TypeDSLLoader(enum_d9cba076fca539106791a4f46d198c7fcfbdb779Loader, 2)
+uri_array_of_strtype_True_False_None = _URILoader(array_of_strtype, True, False, None)
+enum_d961d79c225752b9fadb617367615ab176b47d77Loader = _EnumLoader(("enum",))
+typedsl_enum_d961d79c225752b9fadb617367615ab176b47d77Loader_2 = _TypeDSLLoader(enum_d961d79c225752b9fadb617367615ab176b47d77Loader, 2)
+uri_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_False_True_2 = _URILoader(union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype, False, True, 2)
+enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader = _EnumLoader(("array",))
+typedsl_enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader_2 = _TypeDSLLoader(enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader, 2)
+union_of_None_type_or_strtype = _UnionLoader((None_type, strtype,))
+uri_union_of_None_type_or_strtype_True_False_None = _URILoader(union_of_None_type_or_strtype, True, False, None)
+union_of_None_type_or_Any_type = _UnionLoader((None_type, Any_type,))
+union_of_WorkflowInputParameterLoader = _UnionLoader((WorkflowInputParameterLoader,))
+array_of_union_of_WorkflowInputParameterLoader = _ArrayLoader(union_of_WorkflowInputParameterLoader)
+idmap_inputs_array_of_union_of_WorkflowInputParameterLoader = _IdMapLoader(array_of_union_of_WorkflowInputParameterLoader, 'id', 'type')
+union_of_WorkflowOutputParameterLoader = _UnionLoader((WorkflowOutputParameterLoader,))
+array_of_union_of_WorkflowOutputParameterLoader = _ArrayLoader(union_of_WorkflowOutputParameterLoader)
+idmap_outputs_array_of_union_of_WorkflowOutputParameterLoader = _IdMapLoader(array_of_union_of_WorkflowOutputParameterLoader, 'id', 'type')
+union_of_None_type_or_StepPositionLoader = _UnionLoader((None_type, StepPositionLoader,))
+union_of_None_type_or_ToolShedRepositoryLoader = _UnionLoader((None_type, ToolShedRepositoryLoader,))
+union_of_None_type_or_GalaxyTypeLoader = _UnionLoader((None_type, GalaxyTypeLoader,))
+typedsl_union_of_None_type_or_GalaxyTypeLoader_2 = _TypeDSLLoader(union_of_None_type_or_GalaxyTypeLoader, 2)
+array_of_WorkflowStepInputLoader = _ArrayLoader(WorkflowStepInputLoader)
+union_of_None_type_or_array_of_WorkflowStepInputLoader = _UnionLoader((None_type, array_of_WorkflowStepInputLoader,))
+idmap_in__union_of_None_type_or_array_of_WorkflowStepInputLoader = _IdMapLoader(union_of_None_type_or_array_of_WorkflowStepInputLoader, 'id', 'source')
+union_of_strtype_or_WorkflowStepOutputLoader = _UnionLoader((strtype, WorkflowStepOutputLoader,))
+array_of_union_of_strtype_or_WorkflowStepOutputLoader = _ArrayLoader(union_of_strtype_or_WorkflowStepOutputLoader)
+union_of_array_of_union_of_strtype_or_WorkflowStepOutputLoader_or_None_type = _UnionLoader((array_of_union_of_strtype_or_WorkflowStepOutputLoader, None_type,))
+uri_union_of_array_of_union_of_strtype_or_WorkflowStepOutputLoader_or_None_type_True_False_None = _URILoader(union_of_array_of_union_of_strtype_or_WorkflowStepOutputLoader_or_None_type, True, False, None)
+union_of_None_type_or_WorkflowStepTypeLoader = _UnionLoader((None_type, WorkflowStepTypeLoader,))
+typedsl_union_of_None_type_or_WorkflowStepTypeLoader_2 = _TypeDSLLoader(union_of_None_type_or_WorkflowStepTypeLoader, 2)
+union_of_None_type_or_GalaxyWorkflowLoader = _UnionLoader((None_type, GalaxyWorkflowLoader,))
+uri_union_of_None_type_or_GalaxyWorkflowLoader_False_False_None = _URILoader(union_of_None_type_or_GalaxyWorkflowLoader, False, False, None)
+uri_union_of_None_type_or_strtype_or_array_of_strtype_False_False_2 = _URILoader(union_of_None_type_or_strtype_or_array_of_strtype, False, False, 2)
+array_of_WorkflowInputParameterLoader = _ArrayLoader(WorkflowInputParameterLoader)
+idmap_inputs_array_of_WorkflowInputParameterLoader = _IdMapLoader(array_of_WorkflowInputParameterLoader, 'id', 'type')
+array_of_WorkflowOutputParameterLoader = _ArrayLoader(WorkflowOutputParameterLoader)
+idmap_outputs_array_of_WorkflowOutputParameterLoader = _IdMapLoader(array_of_WorkflowOutputParameterLoader, 'id', 'type')
+uri_strtype_False_True_None = _URILoader(strtype, False, True, None)
+array_of_WorkflowStepLoader = _ArrayLoader(WorkflowStepLoader)
+union_of_array_of_WorkflowStepLoader = _UnionLoader((array_of_WorkflowStepLoader,))
+idmap_steps_union_of_array_of_WorkflowStepLoader = _IdMapLoader(union_of_array_of_WorkflowStepLoader, 'id', 'None')
+union_of_GalaxyWorkflowLoader = _UnionLoader((GalaxyWorkflowLoader,))
+array_of_union_of_GalaxyWorkflowLoader = _ArrayLoader(union_of_GalaxyWorkflowLoader)
+union_of_GalaxyWorkflowLoader_or_array_of_union_of_GalaxyWorkflowLoader = _UnionLoader((GalaxyWorkflowLoader, array_of_union_of_GalaxyWorkflowLoader,))
+
+
+def load_document(doc, baseuri=None, loadingOptions=None):
+ # type: (Any, Optional[Text], Optional[LoadingOptions]) -> Any
+ if baseuri is None:
+ baseuri = file_uri(os.getcwd()) + "/"
+ if loadingOptions is None:
+ loadingOptions = LoadingOptions()
+ return _document_load(union_of_GalaxyWorkflowLoader_or_array_of_union_of_GalaxyWorkflowLoader, doc, baseuri, loadingOptions)
+
+
+def load_document_by_string(string, uri, loadingOptions=None):
+ # type: (Any, Text, Optional[LoadingOptions]) -> Any
+ result = yaml.round_trip_load(string, preserve_quotes=True)
+ add_lc_filename(result, uri)
+
+ if loadingOptions is None:
+ loadingOptions = LoadingOptions(fileuri=uri)
+ loadingOptions.idx[uri] = result
+
+ return _document_load(union_of_GalaxyWorkflowLoader_or_array_of_union_of_GalaxyWorkflowLoader, result, uri, loadingOptions)
diff --git a/java/.gitignore b/java/.gitignore
new file mode 100644
index 0000000..2f7896d
--- /dev/null
+++ b/java/.gitignore
@@ -0,0 +1 @@
+target/
diff --git a/java/README.md b/java/README.md
new file mode 100644
index 0000000..106be62
--- /dev/null
+++ b/java/README.md
@@ -0,0 +1,35 @@
+# org.galaxyproject.gxformat2.v19_09
+
+This project contains Java objects and utilities auto-generated by Schema Salad for parsing documents corresponding to the https://galaxyproject.org/gxformat2/v19_09# schema.
+
+## License
+
+This project is licensed under the [Apache License, Version 2.0](https://www.apache.org/licenses/LICENSE-2.0.txt).
+
+## Contributing
+
+This project is auto-generated by [Schema Salad](https://github.com/common-workflow-language/schema_salad)
+and likely should not be modified directly. Instead consider filing an issue or opening
+a pull request against the Schema Salad repository.
+
+## Requirements
+
+This Java library requires Java 8+. Building and testing this project requires
+[Apache Maven](https://maven.apache.org/) (``mvn``).
+
+## Usage
+
+Compile the project, test it, and build a jar
+
+ $ mvn install
+ $ ls target/ # jar file in here
+
+Building a standalone jar with all dependencies included and use it to validate a document
+
+ $ mvn assembly:single
+ $ java -jar target/+ * + * Defines the type of the array elements. * + * + *+ */ + Object getItems(); + /** + * Getter for property https://w3id.org/cwl/salad#type
+ * + * Must be `array` * + * + *+ */ + enum_d062602be0b4b8fd33e69e29a841317b6ab665bc getType(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/ArraySchemaImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/ArraySchemaImpl.java new file mode 100644 index 0000000..31b6708 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/ArraySchemaImpl.java @@ -0,0 +1,102 @@ +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.LoaderInstances; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions; +import org.galaxyproject.gxformat2.v19_09.utils.LoadingOptionsBuilder; +import org.galaxyproject.gxformat2.v19_09.utils.SavableImpl; +import org.galaxyproject.gxformat2.v19_09.utils.ValidationException; + +/** Auto-generated class implementation for https://w3id.org/cwl/salad#ArraySchema
+ * + * Defines the type of the array elements. * + * + *+ */ + public Object getItems() { + return this.items; + } + + private enum_d062602be0b4b8fd33e69e29a841317b6ab665bc type; + + /** + * Getter for property https://w3id.org/cwl/salad#type
+ * + * Must be `array` * + * + *+ */ + public enum_d062602be0b4b8fd33e69e29a841317b6ab665bc getType() { + return this.type; + } + + /** + * Used by {@link org.galaxyproject.gxformat2.v19_09.utils.RootLoader} to construct instances of + * ArraySchemaImpl. + * + * @param __doc_ Document fragment to load this record object from (presumably a {@link + * java.util.Map}). + * @param __baseUri_ Base URI to generate child document IDs against. + * @param __loadingOptions Context for loading URIs and populating objects. + * @param __docRoot_ ID at this position in the document (if available) (maybe?) + * @throws ValidationException If the document fragment is not a {@link java.util.Map} or + * validation of fields fails. + */ + public ArraySchemaImpl( + final Object __doc_, + final String __baseUri_, + LoadingOptions __loadingOptions, + final String __docRoot_) { + super(__doc_, __baseUri_, __loadingOptions, __docRoot_); + // Prefix plumbing variables with '__' to reduce likelihood of collision with + // generated names. + String __baseUri = __baseUri_; + String __docRoot = __docRoot_; + if (!(__doc_ instanceof java.util.Map)) { + throw new ValidationException("ArraySchemaImpl called on non-map"); + } + final java.util.Map
+ * + * A documentation string for this object, or an array of strings which should be concatenated. * + * + *+ */ + Object getDoc(); +} diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/EnumSchema.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/EnumSchema.java new file mode 100644 index 0000000..cba8288 --- /dev/null +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/EnumSchema.java @@ -0,0 +1,36 @@ +package org.galaxyproject.gxformat2.v19_09; + +import org.galaxyproject.gxformat2.v19_09.utils.Savable; + +/** + * Auto-generated interface for https://w3id.org/cwl/salad#EnumSchema
+ * + * Define an enumerated type. + * + *+ */ +public interface EnumSchema extends Savable { + /** + * Getter for property https://w3id.org/cwl/salad#symbols
+ * + * Defines the set of valid symbols. * + * + *+ */ + java.util.List