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Add CWLFloatInput to the available annotations #34

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Add CWLFloatInput to the available annotations #34

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8 changes: 6 additions & 2 deletions ipython2cwl/cwltoolextractor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@
import yaml
from nbformat.notebooknode import NotebookNode # type: ignore

from .iotypes import CWLFilePathInput, CWLBooleanInput, CWLIntInput, CWLStringInput, CWLFilePathOutput, \
CWLDumpableFile, CWLDumpableBinaryFile, CWLDumpable, CWLPNGPlot, CWLPNGFigure
from .iotypes import CWLFilePathInput, CWLBooleanInput, CWLIntInput, CWLFloatInput, CWLStringInput, \
CWLFilePathOutput, CWLDumpableFile, CWLDumpableBinaryFile, CWLDumpable, CWLPNGPlot, CWLPNGFigure
from .requirements_manager import RequirementsManager

with open(os.sep.join([os.path.abspath(os.path.dirname(__file__)), 'templates', 'template.dockerfile'])) as f:
Expand Down Expand Up @@ -46,6 +46,10 @@ class AnnotatedVariablesExtractor(ast.NodeTransformer):
'int',
'int',
),
(CWLFloatInput.__name__,): (
'float',
'float',
),
(CWLStringInput.__name__,): (
'string',
'str',
Expand Down
13 changes: 13 additions & 0 deletions ipython2cwl/iotypes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,8 @@

* CWLIntInput

* CWLFloatInput

* Outputs:

* CWLFilePathOutput
Expand Down Expand Up @@ -86,6 +88,17 @@ class CWLIntInput(_CWLInput):
"""
pass

class CWLFloatInput(_CWLInput):
"""Use that hint to annotate that a variable is a float input. You can use the typing annotation
as a string by importing it. At the generated script a command line argument with the name of the variable
will be created and the assignment of value will be generalised.

>>> dataset1: CWLFloatInput = 1.0
>>> dataset2: 'CWLFloatInput' = 2.0

"""
pass


class _CWLOutput:
pass
Expand Down
13 changes: 10 additions & 3 deletions tests/test_cwltoolextractor.py
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Expand Up @@ -18,7 +18,8 @@ def test_AnnotatedIPython2CWLToolConverter_cwl_command_line_tool(self):
"import csv",
"input_filename: CWLFilePathInput = 'data.csv'",
"flag: CWLBooleanInput = true",
"num: CWLIntInput = 1",
"num_int: CWLIntInput = 1",
"num_float: CWLFloatInput = 1.0",
"msg: CWLStringInput = 'hello world'",
"with open(input_filename) as f:",
"\tcsv_reader = csv.reader(f)",
Expand Down Expand Up @@ -50,10 +51,16 @@ def test_AnnotatedIPython2CWLToolConverter_cwl_command_line_tool(self):
'prefix': '--flag'
}
},
'num': {
'num_int': {
'type': 'int',
'inputBinding': {
'prefix': '--num'
'prefix': '--num_int'
}
},
'num_float': {
'type': 'float',
'inputBinding': {
'prefix': '--num_float'
}
},
'msg': {
Expand Down