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illusionalillusional
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Migrate command building in Task.CommandInput to .from_fields
1 parent 90c228d commit f9df32e

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2 files changed

+57
-63
lines changed

2 files changed

+57
-63
lines changed

‎tests/test_task_generation.py‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,7 @@ def test_readme_task(self):
6262

6363
command = Task.Command("echo")
6464
command.inputs.append(
65-
Task.Command.CommandInput(
65+
Task.Command.CommandInput.from_fields(
6666
"taskGreeting",
6767
optional=False,
6868
position=None,
@@ -72,7 +72,7 @@ def test_readme_task(self):
7272
)
7373
)
7474
command.inputs.append(
75-
Task.Command.CommandInput(
75+
Task.Command.CommandInput.from_fields(
7676
"otherInput",
7777
optional=True,
7878
position=2,
@@ -83,7 +83,7 @@ def test_readme_task(self):
8383
)
8484
command = Task.Command("echo")
8585
command.inputs.append(
86-
Task.Command.CommandInput(
86+
Task.Command.CommandInput.from_fields(
8787
"taskGreeting",
8888
optional=False,
8989
position=None,
@@ -93,7 +93,7 @@ def test_readme_task(self):
9393
)
9494
)
9595
command.inputs.append(
96-
Task.Command.CommandInput(
96+
Task.Command.CommandInput.from_fields(
9797
"otherInput",
9898
optional=True,
9999
position=2,
@@ -132,8 +132,8 @@ def test_hello_tasks():
132132
class TestCommandGeneration(unittest.TestCase):
133133
def test_simple_command(self):
134134
command = Task.Command("egrep")
135-
command.inputs.append(Task.Command.CommandInput("pattern"))
136-
command.inputs.append(Task.Command.CommandInput("in"))
135+
command.inputs.append(Task.Command.CommandInput("~{pattern}"))
136+
command.inputs.append(Task.Command.CommandInput("~{in}"))
137137

138138
expected = """\
139139
egrep \\
@@ -145,7 +145,7 @@ def test_simple_command(self):
145145
def test_readme_example(self):
146146
command = Task.Command("echo")
147147
command.inputs.append(
148-
Task.Command.CommandInput(
148+
Task.Command.CommandInput.from_fields(
149149
"taskGreeting",
150150
optional=False,
151151
position=None,
@@ -155,7 +155,7 @@ def test_readme_example(self):
155155
)
156156
)
157157
command.inputs.append(
158-
Task.Command.CommandInput(
158+
Task.Command.CommandInput.from_fields(
159159
"otherInput",
160160
optional=True,
161161
position=2,
@@ -172,7 +172,7 @@ def test_readme_example(self):
172172
self.assertEqual(expected, command.get_string())
173173

174174
def test_commandinput_space(self):
175-
t = Task.Command.CommandInput(
175+
t = Task.Command.CommandInput.from_fields(
176176
"taskGreeting",
177177
optional=False,
178178
position=None,
@@ -183,7 +183,7 @@ def test_commandinput_space(self):
183183
self.assertEqual("-a ~{taskGreeting}", t.get_string())
184184

185185
def test_commandinput_nospace(self):
186-
t = Task.Command.CommandInput(
186+
t = Task.Command.CommandInput.from_fields(
187187
"taskGreeting",
188188
optional=False,
189189
position=None,
@@ -194,13 +194,13 @@ def test_commandinput_nospace(self):
194194
self.assertEqual("val=~{taskGreeting}", t.get_string())
195195

196196
def test_commandarg_space(self):
197-
t = Task.Command.CommandInput(
197+
t = Task.Command.CommandInput.from_fields(
198198
"argVal", position=None, prefix="-p", separate_value_from_prefix=True
199199
)
200200
self.assertEqual("-p ~{argVal}", t.get_string())
201201

202202
def test_commandarg_nospace(self):
203-
t = Task.Command.CommandArgument(
203+
t = Task.Command.CommandArgument.from_fields(
204204
prefix="arg=",
205205
value="argVal",
206206
position=None,

‎wdlgen/task.py‎

Lines changed: 45 additions & 51 deletions
Original file line numberDiff line numberDiff line change
@@ -58,84 +58,78 @@ class Command(WdlBase):
5858
class CommandArgument(WdlBase):
5959
def __init__(
6060
self,
61-
prefix: str = None,
62-
value: str = None,
63-
position: int = None,
64-
separate_value_from_prefix: bool = True,
61+
value,
62+
position=None
6563
):
66-
self.prefix: Optional[str] = prefix
67-
self.position: Optional[int] = position
6864
self.value = value
69-
self.separate = separate_value_from_prefix
65+
self.position = position
66+
67+
@staticmethod
68+
def from_fields(prefix: str = None, value: str = None, position: int = None, separate_value_from_prefix: bool = True,):
69+
pre = prefix if prefix else ""
70+
sp = " " if separate_value_from_prefix else ""
71+
val = value if value else ""
72+
return Task.Command.CommandArgument((pre + sp + val).strip(), position=position)
7073

7174
def get_string(self):
72-
pre = self.prefix if self.prefix else ""
73-
sp = " " if self.separate else ""
74-
val = self.value if self.value else ""
75-
return (pre + sp + val).strip()
75+
return self.value
7676

7777
class CommandInput(CommandArgument):
7878
def __init__(
7979
self,
80-
name: str,
81-
optional: bool = False,
82-
prefix: str = None,
83-
position: int = None,
84-
separate_value_from_prefix: bool = True,
85-
default=None,
86-
separator=None,
87-
true=None,
88-
false=None,
89-
separate_arrays=None,
80+
value,
81+
position=None,
9082
):
9183
super().__init__(
92-
prefix=prefix,
93-
value=None,
84+
value=value,
9485
position=position,
95-
separate_value_from_prefix=separate_value_from_prefix,
9686
)
97-
self.name = name
98-
self.optional = optional
99-
self.default = default
100-
self.separator = separator
101-
self.true = true
102-
self.false = false
103-
self.separate_arrays = separate_arrays
10487

10588
@staticmethod
10689
def from_input(inp: Input, prefix: str = None, position: int = None):
107-
return Task.Command.CommandInput(
90+
return Task.Command.CommandInput.from_fields(
10891
inp.name, inp.type.optional, prefix, position
10992
)
11093

111-
def get_string(self):
94+
@staticmethod
95+
def from_fields(name: str,
96+
optional: bool = False,
97+
prefix: str = None,
98+
position: int = None,
99+
separate_value_from_prefix: bool = True,
100+
default=None,
101+
separator=None,
102+
true=None,
103+
false=None,
104+
separate_arrays=None):
105+
112106
name, array_sep, default, true, false = (
113-
self.name,
114-
self.separator,
115-
self.default,
116-
self.true,
117-
self.false,
107+
name,
108+
separator,
109+
default,
110+
true,
111+
false,
118112
)
119113

120-
pr = self.prefix if self.prefix else ""
121-
bc = pr + (" " if self.separate and self.prefix else "")
114+
pr = prefix if prefix else ""
115+
bc = pr + (" " if separate_value_from_prefix and prefix else "")
122116

123-
if self.separate_arrays:
124-
if array_sep or default or true or false:
117+
if separate_arrays:
118+
if separate_arrays or default or true or false:
125119
print(
126120
"separate_array take preferences over: separator, default, true, false"
127121
)
128-
if self.optional:
122+
if optional:
129123
# Ugly optional workaround: https://github.com/openwdl/wdl/issues/25#issuecomment-315424063
130124
# Additional workaround for 'length(select_first({name}, [])' as length requires a non-optional array
131125
internal_pref = f'if defined({name}) && length(select_first([{name}, []])) > 0 then "{bc}" else ""'
132-
return f'~{{{internal_pref}}}~{{sep=" {bc}" {name}}}'
133-
return f'~{{sep=" " prefix("{bc}", {name})}}'
126+
return Task.Command.CommandInput(f'~{{{internal_pref}}}~{{sep=" {bc}" {name}}}', position=position)
127+
return Task.Command.CommandInput(f'~{{sep=" " prefix("{bc}", {name})}}', position=position)
134128

135-
if array_sep and self.optional:
129+
if array_sep and optional:
136130
# optional array with separator
137131
# ifdefname = f'(if defined({name}) then {name} else [])'
138-
return f'~{{true="{bc}" false="" defined({name})}}~{{sep="{array_sep}" {name}}}'
132+
return Task.Command.CommandInput(f'~{{true="{bc}" false="" defined({name})}}~{{sep="{array_sep}" {name}}}', position=position)
139133

140134
options = []
141135
if default:
@@ -156,16 +150,16 @@ def get_string(self):
156150
stroptions = "".join(o + " " for o in options)
157151

158152
prewithquotes = f'"{bc}" + ' if bc.strip() else ""
159-
if self.optional and not default and not is_flag and prewithquotes:
153+
if optional and not default and not is_flag and prewithquotes:
160154
# Option 1: We apply quotes are value, Option 2: We quote whole "prefix + name" combo
161155
full_token = (
162156
f"{prewithquotes} '\"' + {name} + '\"'"
163-
if (self.separate and self.prefix and prewithquotes)
157+
if (separate_value_from_prefix and prefix and prewithquotes)
164158
else f"'\"' + {prewithquotes}{name} + '\"'"
165159
)
166-
return f'~{{{stroptions}if defined({name}) then ({full_token}) else ""}}'
160+
return Task.Command.CommandInput(f'~{{{stroptions}if defined({name}) then ({full_token}) else ""}}', position=position)
167161
else:
168-
return bc + f"~{{{stroptions}{name}}}"
162+
return Task.Command.CommandInput(bc + f"~{{{stroptions}{name}}}", position=position)
169163

170164
def __init__(
171165
self,

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