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Moved param_for_source_id in the utils package
1 parent 13cf533 commit ec82a0a

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7 files changed

+191
-502
lines changed

7 files changed

+191
-502
lines changed

‎cwl_utils/cwl_v1_0_expression_refactor.py‎

Lines changed: 21 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -17,17 +17,7 @@
1717
import cwl_utils.parser.cwl_v1_0_utils as utils
1818
from cwl_utils.errors import JavascriptException, WorkflowException
1919
from cwl_utils.expression import do_eval, interpolate
20-
from cwl_utils.parser.cwl_v1_0_utils import (
21-
AnyTypeSchema,
22-
BasicCommandInputTypeSchemas,
23-
BasicCommandOutputTypeSchemas,
24-
BasicInputTypeSchemas,
25-
BasicOutputTypeSchemas,
26-
CommandInputTypeSchemas,
27-
CommandOutputTypeSchemas,
28-
InputTypeSchemas,
29-
OutputTypeSchemas,
30-
)
20+
from cwl_utils.parser.utils import param_for_source_id
3121
from cwl_utils.types import (
3222
CWLDirectoryType,
3323
CWLFileType,
@@ -68,7 +58,7 @@ def escape_expression_field(contents: str) -> str:
6858

6959

7060
def _clean_type_ids(
71-
cwltype: InputTypeSchemas | CommandOutputTypeSchemas,
61+
cwltype: utils.InputTypeSchemas | utils.CommandOutputTypeSchemas,
7262
) -> None:
7363
if isinstance(cwltype, cwl.ArraySchema):
7464
if is_sequence(cwltype.items):
@@ -94,8 +84,8 @@ def _clean_type_ids(
9484

9585

9686
def clean_type_ids(
97-
cwltype: AnyTypeSchema,
98-
) -> AnyTypeSchema:
87+
cwltype: utils.AnyTypeSchema,
88+
) -> utils.AnyTypeSchema:
9989
"""Simplify type identifiers."""
10090
result = copy.deepcopy(cwltype)
10191
if is_sequence(result):
@@ -180,8 +170,8 @@ def get_expression(
180170

181171

182172
def _plain_input_schema_to_clt_input_schema(
183-
input_type: BasicInputTypeSchemas,
184-
) -> BasicCommandInputTypeSchemas:
173+
input_type: utils.BasicInputTypeSchemas,
174+
) -> utils.BasicCommandInputTypeSchemas:
185175
match input_type:
186176
case cwl.InputArraySchema():
187177
return cwl.CommandInputArraySchema.fromDoc(
@@ -207,8 +197,8 @@ def _plain_input_schema_to_clt_input_schema(
207197

208198

209199
def plain_input_schema_to_clt_input_schema(
210-
input_type: InputTypeSchemas,
211-
) -> CommandInputTypeSchemas:
200+
input_type: utils.InputTypeSchemas,
201+
) -> utils.CommandInputTypeSchemas:
212202
if is_sequence(input_type):
213203
return [
214204
_plain_input_schema_to_clt_input_schema(input_type_item)
@@ -220,8 +210,8 @@ def plain_input_schema_to_clt_input_schema(
220210

221211

222212
def _plain_input_schema_to_plain_output_schema(
223-
input_type: BasicInputTypeSchemas,
224-
) -> BasicOutputTypeSchemas:
213+
input_type: utils.BasicInputTypeSchemas,
214+
) -> utils.BasicOutputTypeSchemas:
225215
match input_type:
226216
case cwl.InputArraySchema():
227217
return cwl.OutputArraySchema.fromDoc(
@@ -247,8 +237,8 @@ def _plain_input_schema_to_plain_output_schema(
247237

248238

249239
def plain_input_schema_to_plain_output_schema(
250-
input_type: InputTypeSchemas,
251-
) -> OutputTypeSchemas:
240+
input_type: utils.InputTypeSchemas,
241+
) -> utils.OutputTypeSchemas:
252242
if is_sequence(input_type):
253243
return [
254244
_plain_input_schema_to_plain_output_schema(input_type_item)
@@ -260,8 +250,8 @@ def plain_input_schema_to_plain_output_schema(
260250

261251

262252
def _plain_output_type_to_clt_output_type(
263-
output_type: BasicOutputTypeSchemas,
264-
) -> BasicCommandOutputTypeSchemas:
253+
output_type: utils.BasicOutputTypeSchemas,
254+
) -> utils.BasicCommandOutputTypeSchemas:
265255
match output_type:
266256
case cwl.OutputArraySchema():
267257
return cwl.CommandOutputArraySchema.fromDoc(
@@ -287,8 +277,8 @@ def _plain_output_type_to_clt_output_type(
287277

288278

289279
def plain_output_type_to_clt_output_type(
290-
output_type: OutputTypeSchemas,
291-
) -> CommandOutputTypeSchemas:
280+
output_type: utils.OutputTypeSchemas,
281+
) -> utils.CommandOutputTypeSchemas:
292282
if is_sequence(output_type):
293283
return [
294284
_plain_output_type_to_clt_output_type(output_type_item)
@@ -529,9 +519,9 @@ def generate_etool_from_expr(
529519
if self_type is None:
530520
self_type = target
531521
assert self_type is not None
532-
new_type: InputTypeSchemas
522+
new_type: utils.InputTypeSchemas
533523
if is_sequence(self_type):
534-
new_type_list: MutableSequence[BasicInputTypeSchemas] = []
524+
new_type_list: MutableSequence[utils.BasicInputTypeSchemas] = []
535525
for entry in self_type:
536526
clean_type = clean_type_ids(entry.type_)
537527
if is_sequence(clean_type):
@@ -1636,7 +1626,7 @@ def traverse_CommandLineTool(
16361626
modified = True
16371627
inp_id = "_{}_glob".format(outp.id.split("#")[-1])
16381628
etool_id = f"_expression_{step_id}{inp_id}"
1639-
glob_target_type: CommandInputTypeSchemas = [
1629+
glob_target_type: utils.CommandInputTypeSchemas = [
16401630
"string",
16411631
cwl.CommandInputArraySchema("string", "array"),
16421632
]
@@ -2178,7 +2168,7 @@ def traverse_step(
21782168
) = None
21792169
if inp.source:
21802170
input_source_id = []
2181-
source_types: list[BasicInputTypeSchemas] = []
2171+
source_types: list[utils.BasicInputTypeSchemas] = []
21822172
for source in inp.source:
21832173
source_id = source.split("#")[-1]
21842174
input_source_id.append(source_id)
@@ -2263,9 +2253,7 @@ def workflow_step_to_InputParameters(
22632253
for inp in step_ins:
22642254
inp_id = inp.id.split("#")[-1].split("/")[-1]
22652255
if inp.source and inp_id != except_in_id:
2266-
param = copy.deepcopy(
2267-
utils.param_for_source_id(parent, sourcenames=inp.source)
2268-
)
2256+
param = copy.deepcopy(param_for_source_id(parent, sourcenames=inp.source))
22692257
if is_sequence(param):
22702258
for p in param:
22712259
if not p.type_:

‎cwl_utils/cwl_v1_1_expression_refactor.py‎

Lines changed: 21 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -17,17 +17,7 @@
1717
import cwl_utils.parser.cwl_v1_1_utils as utils
1818
from cwl_utils.errors import JavascriptException, WorkflowException
1919
from cwl_utils.expression import do_eval, interpolate
20-
from cwl_utils.parser.cwl_v1_1_utils import (
21-
AnyTypeSchema,
22-
BasicCommandInputTypeSchemas,
23-
BasicCommandOutputTypeSchemas,
24-
BasicInputTypeSchemas,
25-
BasicOutputTypeSchemas,
26-
CommandInputTypeSchemas,
27-
CommandOutputTypeSchemas,
28-
InputTypeSchemas,
29-
OutputTypeSchemas,
30-
)
20+
from cwl_utils.parser.utils import param_for_source_id
3121
from cwl_utils.types import (
3222
CWLDirectoryType,
3323
CWLFileType,
@@ -68,7 +58,7 @@ def escape_expression_field(contents: str) -> str:
6858

6959

7060
def _clean_type_ids(
71-
cwltype: InputTypeSchemas | CommandOutputTypeSchemas,
61+
cwltype: utils.InputTypeSchemas | utils.CommandOutputTypeSchemas,
7262
) -> None:
7363
if isinstance(cwltype, cwl.ArraySchema):
7464
if is_sequence(cwltype.items):
@@ -94,8 +84,8 @@ def _clean_type_ids(
9484

9585

9686
def clean_type_ids(
97-
cwltype: AnyTypeSchema,
98-
) -> AnyTypeSchema:
87+
cwltype: utils.AnyTypeSchema,
88+
) -> utils.AnyTypeSchema:
9989
"""Simplify type identifiers."""
10090
result = copy.deepcopy(cwltype)
10191
if is_sequence(result):
@@ -180,8 +170,8 @@ def get_expression(
180170

181171

182172
def _plain_input_schema_to_clt_input_schema(
183-
input_type: BasicInputTypeSchemas,
184-
) -> BasicCommandInputTypeSchemas:
173+
input_type: utils.BasicInputTypeSchemas,
174+
) -> utils.BasicCommandInputTypeSchemas:
185175
match input_type:
186176
case cwl.InputArraySchema():
187177
return cwl.CommandInputArraySchema.fromDoc(
@@ -207,8 +197,8 @@ def _plain_input_schema_to_clt_input_schema(
207197

208198

209199
def plain_input_schema_to_clt_input_schema(
210-
input_type: InputTypeSchemas,
211-
) -> CommandInputTypeSchemas:
200+
input_type: utils.InputTypeSchemas,
201+
) -> utils.CommandInputTypeSchemas:
212202
if is_sequence(input_type):
213203
return [
214204
_plain_input_schema_to_clt_input_schema(input_type_item)
@@ -218,8 +208,8 @@ def plain_input_schema_to_clt_input_schema(
218208

219209

220210
def _plain_input_schema_to_plain_output_schema(
221-
input_type: BasicInputTypeSchemas,
222-
) -> BasicOutputTypeSchemas:
211+
input_type: utils.BasicInputTypeSchemas,
212+
) -> utils.BasicOutputTypeSchemas:
223213
match input_type:
224214
case cwl.InputArraySchema():
225215
return cwl.OutputArraySchema.fromDoc(
@@ -245,8 +235,8 @@ def _plain_input_schema_to_plain_output_schema(
245235

246236

247237
def plain_input_schema_to_plain_output_schema(
248-
input_type: InputTypeSchemas,
249-
) -> OutputTypeSchemas:
238+
input_type: utils.InputTypeSchemas,
239+
) -> utils.OutputTypeSchemas:
250240
if is_sequence(input_type):
251241
return [
252242
_plain_input_schema_to_plain_output_schema(input_type_item)
@@ -256,8 +246,8 @@ def plain_input_schema_to_plain_output_schema(
256246

257247

258248
def _plain_output_type_to_clt_output_type(
259-
output_type: BasicOutputTypeSchemas,
260-
) -> BasicCommandOutputTypeSchemas:
249+
output_type: utils.BasicOutputTypeSchemas,
250+
) -> utils.BasicCommandOutputTypeSchemas:
261251
match output_type:
262252
case cwl.OutputArraySchema():
263253
return cwl.CommandOutputArraySchema.fromDoc(
@@ -283,8 +273,8 @@ def _plain_output_type_to_clt_output_type(
283273

284274

285275
def plain_output_type_to_clt_output_type(
286-
output_type: OutputTypeSchemas,
287-
) -> CommandOutputTypeSchemas:
276+
output_type: utils.OutputTypeSchemas,
277+
) -> utils.CommandOutputTypeSchemas:
288278
if is_sequence(output_type):
289279
return [
290280
_plain_output_type_to_clt_output_type(output_type_item)
@@ -527,9 +517,9 @@ def generate_etool_from_expr(
527517
if self_type is None:
528518
self_type = target
529519
assert self_type is not None
530-
new_type: InputTypeSchemas
520+
new_type: utils.InputTypeSchemas
531521
if is_sequence(self_type):
532-
new_type_list: MutableSequence[BasicInputTypeSchemas] = []
522+
new_type_list: MutableSequence[utils.BasicInputTypeSchemas] = []
533523
for entry in self_type:
534524
clean_type = clean_type_ids(entry.type_)
535525
if is_sequence(clean_type):
@@ -1647,7 +1637,7 @@ def traverse_CommandLineTool(
16471637
modified = True
16481638
inp_id = "_{}_glob".format(outp.id.split("#")[-1])
16491639
etool_id = f"_expression_{step_id}{inp_id}"
1650-
glob_target_type: CommandInputTypeSchemas = [
1640+
glob_target_type: utils.CommandInputTypeSchemas = [
16511641
"string",
16521642
cwl.CommandInputArraySchema("string", "array"),
16531643
]
@@ -2193,7 +2183,7 @@ def traverse_step(
21932183
) = None
21942184
if inp.source:
21952185
input_source_id = []
2196-
source_types: list[BasicInputTypeSchemas] = []
2186+
source_types: list[utils.BasicInputTypeSchemas] = []
21972187
for source in inp.source:
21982188
source_id = source.split("#")[-1]
21992189
input_source_id.append(source_id)
@@ -2278,9 +2268,7 @@ def workflow_step_to_WorkflowInputParameters(
22782268
for inp in step_ins:
22792269
inp_id = inp.id.split("#")[-1].split("/")[-1]
22802270
if inp.source and inp_id != except_in_id:
2281-
param = copy.deepcopy(
2282-
utils.param_for_source_id(parent, sourcenames=inp.source)
2283-
)
2271+
param = copy.deepcopy(param_for_source_id(parent, sourcenames=inp.source))
22842272
if is_sequence(param):
22852273
for p in param:
22862274
if not p.type_:

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