Merge pull request #69 from PMCC-BioinformaticsCore/add-from-wdl

Add WDL parser to Janis

Author: junyk

janis_core/ingestion/fromwdl.py

@@ -53,6 +53,10 @@ def __repr__(self):
     def evaluate(self, inputs):
         return self.evaluate_arg(self.args[0], inputs) is not None
 
+    def to_python(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"{arg} is not None"
+
     def to_cwl(self, unwrap_operator, *args):
         arg = unwrap_operator(self.args[0])
         # 2 equals (!=) in javascript will coerce undefined to equal null
@@ -103,6 +107,10 @@ def to_cwl(self, unwrap_operator, *args):
         cond, v1, v2 = [unwrap_operator(a) for a in self.args]
         return f"{cond} ? {v1} : {v2}"
 
+    def to_python(self, unwrap_operator, *args):
+        condition, iftrue, iffalse = [unwrap_operator(a) for a in self.args]
+        return f"({iftrue} if {condition} else {iffalse})"
+
 
 class AssertNotNull(Operator):
     @staticmethod
@@ -117,6 +125,9 @@ def evaluate(self, inputs):
         assert result is not None
         return result
 
+    def to_python(self, unwrap_operator, *args):
+        return unwrap_operator(unwrap_operator(args[0]))
+
     def to_wdl(self, unwrap_operator, *args):
         arg = unwrap_operator(self.args[0])
         return f"select_first([{arg}])"
@@ -168,6 +179,10 @@ def returntype(self):
     def apply_to(value):
         return not value
 
+    def to_python(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"not {arg}"
+
     # Two value operators
 
 
@@ -178,7 +193,7 @@ def friendly_signature():
 
     @staticmethod
     def symbol():
-        return "&&"
+        return "and"
 
     @staticmethod
     def wdl_symbol():
@@ -206,7 +221,7 @@ def friendly_signature():
 
     @staticmethod
     def symbol():
-        return "||"
+        return "or"
 
     @staticmethod
     def wdl_symbol():
@@ -559,6 +574,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"math.floor({arg})"
+
     def to_wdl(self, unwrap_operator, *args):
         arg = unwrap_operator(self.args[0])
         return f"floor({arg})"
@@ -577,7 +596,7 @@ def evaluate(self, inputs):
 class CeilOperator(Operator):
     @staticmethod
     def friendly_signature():
-        return "Numeric, NumericType -> Int"
+        return "Numeric -> Int"
 
     def argtypes(self) -> List[DataType]:
         return [NumericType]
@@ -592,6 +611,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"math.ceil({arg})"
+
     def to_wdl(self, unwrap_operator, *args):
         arg = unwrap_operator(self.args[0])
         return f"ceil({arg})"
@@ -625,6 +648,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"math.round({arg})"
+
     def to_wdl(self, unwrap_operator, *args):
         arg = unwrap_operator(self.args[0])
         return f"round({arg})"

janis_core/operators/logical.py

@@ -134,6 +134,10 @@ def to_wdl(self, unwrap_operator, *args):
     def to_cwl(self, unwrap_operator, *args):
         pass
 
+    @abstractmethod
+    def to_python(self, unwrap_operator, *args):
+        pass
+
     def to_string_formatter(self):
         import re
         from janis_core.operators.stringformatter import StringFormatter
@@ -158,7 +162,10 @@ def argtypes(self):
         return [Array(AnyType), Int]
 
     def returntype(self):
-        return self.args[0].returntype().subtype()
+        inner = get_instantiated_type(self.args[0].returntype())
+        if isinstance(inner, Array):
+            return inner.subtype()
+        return inner
 
     def __str__(self):
         base, index = self.args
@@ -172,6 +179,10 @@ def evaluate(self, inputs):
 
         return iterable[idx]
 
+    def to_python(self, unwrap_operator, *args):
+        base, index = [unwrap_operator(a) for a in self.args]
+        return f"{base}[{index}]"
+
     def to_wdl(self, unwrap_operator, *args):
         base, index = [unwrap_operator(a) for a in self.args]
         return f"{base}[{index}]"
@@ -219,6 +230,9 @@ def to_wdl(self, unwrap_operator, *args):
     def to_cwl(self, unwrap_operator, *args):
         return f"{self.cwl_symbol()}({unwrap_operator(*args)})"
 
+    def to_python(self, unwrap_operator, *args):
+        return f"{self.symbol()}({unwrap_operator(*args)})"
+
 
 class TwoValueOperator(Operator, ABC):
     @staticmethod
@@ -253,6 +267,10 @@ def to_cwl(self, unwrap_operator, *args):
         arg1, arg2 = [unwrap_operator(a) for a in self.args]
         return f"({arg1} {self.cwl_symbol()} {arg2})"
 
+    def to_python(self, unwrap_operator, *args):
+        arg1, arg2 = [unwrap_operator(a) for a in self.args]
+        return f"({arg1} {self.symbol()} {arg2})"
+
     def __str__(self):
         args = self.args
         return f"({args[0]} {self.symbol()} {args[1]})"

janis_core/operators/operator.py

@@ -245,6 +245,10 @@ def basename(self):
 
         return BasenameOperator(self)
 
+    def replace(self, pattern, replacement):
+        from .standard import ReplaceOperator
+        return ReplaceOperator(self, pattern, replacement)
+
     def file_size(self):
         from .standard import FileSizeOperator
 
@@ -308,6 +312,14 @@ def to_string_formatter(self):
 
         return StringFormatter(f"{{{self.input_to_select}}}", **kwarg)
 
+    def init_dictionary(self):
+        d = {"input_to_select": self.input_to_select}
+        if self.remove_file_extension is not None:
+            d["remove_file_extension"] = self.remove_file_extension
+        if not isinstance(self.type_hint, File):
+            d["type_hint"] = self.type_hint
+        return d
+
     def __str__(self):
         return "inputs." + self.input_to_select
 
@@ -332,7 +344,7 @@ def id(self):
     def returntype(self):
         out = first_value(self.input_node.outputs()).outtype
 
-        if self.input_node is not None:
+        if self.input_node is not None and self.input_node.default is not None:
             import copy
 
             out = copy.copy(out)
@@ -367,8 +379,14 @@ def __init__(self, node, tag):
     def returntype(self):
         retval = self.node.outputs()[self.tag].outtype
 
-        if hasattr(self.node, "scatter") and self.node.scatter:
+        if self.node.node_type != NodeType.STEP:
+            return retval
+
+        if hasattr(self.node, "scatter") and self.node.scatter is not None:
             retval = Array(retval)
+        elif hasattr(self.node, "foreach") and self.node.foreach is not None:
+            retval = Array(retval)
+
         return retval
 
     @staticmethod
@@ -412,9 +430,24 @@ def __init__(self, inner: Selector, dt: ParseableType):
     def returntype(self) -> DataType:
         return self.data_type
 
-    def to_string_formatter(self):
+    def __repr__(self):
         return f"({self.inner_selector} as {self.data_type})"
 
+    def to_string_formatter(self):
+        from janis_core.operators.stringformatter import StringFormatter
+
+        return StringFormatter("{value}", value=self.inner_selector)
+
+
+class ForEachSelector(Selector):
+    def returntype(self) -> DataType:
+        return File()
+
+    def to_string_formatter(self):
+        from janis_core.operators.stringformatter import StringFormatter
+
+        return StringFormatter("{inp}", inp=self)
+
 
 class ResourceSelector(InputSelector):
     def __init__(