From 195e10203217eb9772afc1d6f428a9805b1b9d09 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 19 Mar 2025 11:03:00 +0100
Subject: [PATCH] Update the extarct emits -> it wans't working correctly (it
works on 404 and 314)
---
src/emitted.py | 2 +-
src/operation.py | 40 ++++++++++++++++++++++++++++++++++++----
2 files changed, 37 insertions(+), 5 deletions(-)
diff --git a/src/emitted.py b/src/emitted.py
index b29a0fa..b5c93ed 100644
--- a/src/emitted.py
+++ b/src/emitted.py
@@ -75,7 +75,7 @@ class Emitted(Channel):
else:
if(thing_which_emits.get_type()=='Subworkflow'):
if(len(thing_which_emits.emit)!=1):
- raise BioFlowInsightError(f"One channel was expected in the emit '{self.get_code()}'. Even though multiple emits are defined for the workflow '{self.emitted_by.get_name()}'", num=6, origin=self)
+ raise BioFlowInsightError(f"One channel was expected in the emit '{self.get_code()}'. Even though multiple emits are defined for the workflow '{self.emitted_by.get_first_element_called().get_name()}'", num=6, origin=self)
self.emits = thing_which_emits.emit[0]
else:
raise Exception("This shoudn't happen!")
diff --git a/src/operation.py b/src/operation.py
index ef5b570..7d2b11c 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -297,6 +297,30 @@ class Operation(Executor):
if(bool(re.fullmatch(r"\( *\w+ *(\, *\w+)+ *\) *= *Call_\d+", operation.strip()))):
raise BioFlowInsightError(f"A tuple is associated with an call{self.get_string_line(self.get_code(get_OG= True))}. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.", num=9, origin=self)
+ searching_for_emits = True
+ while(searching_for_emits):
+ searching_for_emits = False
+ stop_pattern_search = False
+ for pattern in [constant.EMIT_NAME, constant.EMIT_TAB, constant.EMIT_ALONE]:
+ for match in re.finditer(pattern, operation+" "):
+ try:
+ full_code, name_called, name_emitted = match.group(0), match.group(1), match.group(3)
+ except:
+ full_code, name_called, name_emitted = match.group(0)[:-1], match.group(1), ""
+ if(name_emitted==""):
+ self.add_origin_emits(full_code, name_called, "")
+ if(name_emitted in constant.LIST_OPERATORS):
+ full_code = '.'.join(full_code.split(".")[:-1])
+ self.add_origin_emits(full_code, name_called, "")
+ else:
+ self.add_origin_emits(full_code, name_called, name_emitted)
+ operation = operation.replace(full_code, "")
+ searching_for_emits = True
+ stop_pattern_search = True
+ break
+ if(stop_pattern_search):
+ break
+
case_operation_starts_with_emit = False
#---------------------------
@@ -384,11 +408,19 @@ class Operation(Executor):
#TODO -> check this
#I've changed this to avoid problems like this : "ch_svdb_dbs.out_occs.toList()"
for match in re.finditer(constant.EMIT_OPERATION, operation+" "):
+ #full_code, name_called = match.group(1), match.group(2)
+ #self.add_origin_emits(full_code, name_called, "")
+ ##Remove the emit from the operation code -> so we don't extract it agian
+ #operation = operation.replace(full_code, "")
+
+ #Old
full_code, name_called = match.group(1), match.group(2)
- self.add_origin_emits(full_code, name_called, "")
- #Remove the emit from the operation code -> so we don't extract it agian
- operation = operation.replace(full_code, "")
-
+ #Check that it's a the begining of the operation
+ operation_until_out = operation[:operation.find("out")]
+ if(operation_until_out==full_code[:full_code.find("out")]):
+ self.add_origin_emits(full_code, name_called, "")
+ case_operation_starts_with_emit = True
+ operation = operation.replace(full_code, "")
--
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