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bernt-matthias committed Mar 24, 2022
1 parent 1b4815a commit 04d0e99
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Showing 2 changed files with 6 additions and 0 deletions.
5 changes: 5 additions & 0 deletions lib/galaxy/tools/parameters/__init__.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""
Classes encapsulating Galaxy tool parameters.
"""
import logging

from json import dumps

Expand All @@ -24,6 +25,8 @@
UploadDataset,
)

log = logging.getLogger(__name__)

REPLACE_ON_TRUTHY = object()

# Some tools use the code tag and access the code base, expecting certain tool parameters to be available here.
Expand Down Expand Up @@ -507,6 +510,7 @@ def populate_state(
def _populate_state_legacy(
request_context, inputs, incoming, state, errors, prefix="", context=None, check=True, simple_errors=True
):
log.error(f"_populate_state_legacy inputs {inputs}")
context = ExpressionContext(state, context)
for input in inputs.values():
state[input.name] = input.get_initial_value(request_context, context)
Expand Down Expand Up @@ -622,6 +626,7 @@ def _get_incoming_value(incoming, key, default):
Fetch value from incoming dict directly or check special nginx upload
created variants of this key.
"""
log.error(f"_get_incoming_value incoming {incoming} key {key} default {default}")
if f"__{key}__is_composite" in incoming:
composite_keys = incoming[f"__{key}__keys"].split()
value = dict()
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1 change: 1 addition & 0 deletions lib/galaxy/tools/parameters/basic.py
Original file line number Diff line number Diff line change
Expand Up @@ -938,6 +938,7 @@ def get_legal_names(self, trans, other_values):
return {n: v for n, v, _ in self.get_options(trans, other_values)}

def from_json(self, value, trans, other_values=None, require_legal_value=True):
log.error(f"from_json value {value} trans {trans} other_values {other_values} require_legal_value {require_legal_value}")
other_values = other_values or {}
try:
legal_values = self.get_legal_values(trans, other_values, value)
Expand Down

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