Add to_python for all operators

janis_core/operators/logical.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 +179,12 @@ 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 +195,7 @@ def friendly_signature():
 
     @staticmethod
     def symbol():
-        return "&&"
+        return "and"
 
     @staticmethod
     def wdl_symbol():
@@ -206,7 +223,7 @@ def friendly_signature():
 
     @staticmethod
     def symbol():
-        return "||"
+        return "or"
 
     @staticmethod
     def wdl_symbol():
@@ -559,6 +576,10 @@ 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 +598,7 @@ 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 +613,10 @@ 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 +650,10 @@ 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/operator.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 +179,9 @@ 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 +229,10 @@ 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/selectors.py

@@ -308,6 +308,14 @@ 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
 
@@ -412,6 +420,9 @@ def __init__(self, inner: Selector, dt: ParseableType):
     def returntype(self) -> DataType:
         return self.data_type
 
+    def __repr__(self):
+        return f"({self.inner_selector} as {self.data_type})"
+
     def to_string_formatter(self):
         from janis_core.operators.stringformatter import StringFormatter
 

janis_core/operators/standard.py

@@ -1,5 +1,7 @@
 from copy import copy
 from typing import List
+
+from janis_core.utils.logger import Logger
 from janis_core.types import (
     DataType,
     UnionType,
@@ -22,6 +24,9 @@ def friendly_signature():
     def argtypes(self) -> List[DataType]:
         return [File()]
 
+    def to_python(self, unwrap_operator, *args):
+        raise NotImplementedError("Determine _safe_ one line solution for ReadContents")
+
     def to_wdl(self, unwrap_operator, *args):
         arg = unwrap_operator(args[0])
         return f"read_string({arg})"
@@ -56,6 +61,10 @@ def evaluate(self, inputs):
         with open(file) as f:
             return load(f)
 
+    def to_python(self, unwrap_operator, *args):
+        raise NotImplementedError("Determine _safe_ one line solution for ReadContents")
+
+
     def to_wdl(self, unwrap_operator, *args):
         f = unwrap_operator(self.args[0])
         return f"read_json({f})"
@@ -91,6 +100,10 @@ def argtypes(self):
     def returntype(self):
         return String()
 
+    def to_python(self, unwrap_operator, *args):
+        iterable, separator = [unwrap_operator(a) for a in self.args]
+        return f"{separator}.join({iterable})"
+
     def to_wdl(self, unwrap_operator, *args):
         iterable, separator = [unwrap_operator(a) for a in self.args]
         iterable_arg = self.args[0]
@@ -124,8 +137,12 @@ class BasenameOperator(Operator):
     def friendly_signature():
         return "Union[File, Directory] -> String"
 
+    def to_python(self, unwrap_operator, *args):
+        arg = unwrap_operator(args[0])
+        return f"os.path.basename({arg})"
+
     def to_wdl(self, unwrap_operator, *args):
-        arg = args[0]
+        arg = unwrap_operator(args[0])
         return f"basename({unwrap_operator(arg)})"
 
     def to_cwl(self, unwrap_operator, *args):
@@ -169,6 +186,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        iterable = unwrap_operator(self.args[0])
+        return f"[[{iterable}[j][i] for j in range(len({iterable}))] for i in range(len({iterable}[0]))]"
+
     def to_wdl(self, unwrap_operator, *args):
         return f"transform({unwrap_operator(args[0])})"
 
@@ -200,6 +221,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"len({arg})"
+
     def to_wdl(self, unwrap_operator, *args):
         arg = unwrap_operator(self.args[0])
         return f"length({arg})"
@@ -213,6 +238,41 @@ def evaluate(self, inputs):
         return len(ar)
 
 
+class RangeOperator(Operator):
+    @staticmethod
+    def friendly_signature():
+        return "Int -> Array[Int]"
+
+    def argtypes(self):
+        return [Int]
+
+    def returntype(self):
+        return Array(Int())
+
+    def __str__(self):
+        return f"0...{self.args[0]}"
+
+    def __repr__(self):
+        return str(self)
+
+    def to_python(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"range({arg})"
+
+    def to_wdl(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"range({arg})"
+
+    def to_cwl(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"Array.from({{ length: {arg} + 1 }}, (_, i) => i)"
+        # return f"{arg}.length"
+
+    def evaluate(self, inputs):
+        ar = self.evaluate_arg(self.args[0], inputs)
+        return list(range(ar))
+
+
 class FlattenOperator(Operator):
     @staticmethod
     def friendly_signature():
@@ -230,6 +290,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        arg = unwrap_operator(self.args[0])
+        return f"[el for sublist in {arg} for el in sublist]"
+
     def to_wdl(self, unwrap_operator, *args):
         arg = unwrap_operator(self.args[0])
         return f"flatten({arg})"
@@ -261,6 +325,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        prefix, iterable = [unwrap_operator(a) for a in self.args]
+        return f"[{prefix} + i for i in {iterable}]"
+
     def to_wdl(self, unwrap_operator, *args):
         prefix, iterable = [unwrap_operator(a) for a in self.args]
         return f"prefix({prefix}, {iterable})"
@@ -278,6 +346,30 @@ class FileSizeOperator(Operator):
     """
     Returned in MB: Note that this does NOT include the reference files (yet)
     """
+    def __new__(cls, *args, **kwargs):
+        multiplier = None
+        src, *otherargs = args
+
+        if len(otherargs) == 1:
+            f = otherargs[0].lower()
+            multiplier_heirarchy = [
+                ("ki" in f, 1024),
+                ("k" in f, 1000),
+                ("mi" in f, 1.024),
+                ("gi" in f, 0.001024),
+                ("g" in f, 0.001),
+            ]
+            if not any(m[0] for m in multiplier_heirarchy):
+                Logger.warn(f"Couldn't determine prefix {f} for FileSizeOperator, defaulting to MB")
+            else:
+                multiplier = [m[1] for m in multiplier_heirarchy if m[0] is True][0]
+
+        instance = super(FileSizeOperator, cls).__new__(cls)
+        instance.__init__(args[0])
+
+        if multiplier is not None and multiplier != 1:
+            return instance * multiplier
+        return instance
 
     @staticmethod
     def friendly_signature():
@@ -296,6 +388,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        f = unwrap_operator(self.args[0])
+        return f"os.stat({f}).st_size / 1000"
+
     def to_wdl(self, unwrap_operator, *args):
         f = unwrap_operator(self.args[0])
         return f'size({f}, "MB")'
@@ -338,6 +434,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        iterable = unwrap_operator(self.args[0])
+        return f"[a for a in {iterable} if a is not None][0]"
+
     def to_wdl(self, unwrap_operator, *args):
         iterable = unwrap_operator(self.args[0])
         return f"select_first({iterable})"
@@ -376,6 +476,10 @@ def __str__(self):
     def __repr__(self):
         return str(self)
 
+    def to_python(self, unwrap_operator, *args):
+        iterable = unwrap_operator(self.args[0])
+        return f"[a for a in {iterable} if a is not None]"
+
     def to_wdl(self, unwrap_operator, *args):
         iterable = unwrap_operator(self.args[0])
         return f"select_all({iterable})"