From 9e6443a15fe3dabcbf2d0b377f40678292e62bab Mon Sep 17 00:00:00 2001
From: unknown <david.hoksza@gmail.com>
Date: Wed, 23 Oct 2019 15:13:52 +0200
Subject: [PATCH] ability to process non-multi sbmls; sanitization of names
---
gui_config.ini | 2 +-
talent/common.py | 3 +++
talent/sbml.py | 41 ++++++++++++++++++++--------------------
talent/utils/transfer.py | 5 +++--
4 files changed, 28 insertions(+), 23 deletions(-)
diff --git a/gui_config.ini b/gui_config.ini
index 4fde66e..a78bc57 100644
--- a/gui_config.ini
+++ b/gui_config.ini
@@ -3,6 +3,6 @@ openTgtFileDir=C:/projects/git/talent/tmp/pd_test1.sbml
openTmpFileDir=C:/projects/git/talent/tmp/pd_test2.sbml
openOutputPathButton=C:/projects/git/talent/out
openOutputPath=C:/projects/git/talent/out
-opnBcFile=C:/projects/git/talent/out/pd_test1-cc_0--from--pd_test2-cc0-tmp_order_0-tgt-ddup_False_tmp-ddup_False.pkl
+opnBcFile=C:/projects/git/talent/out/pd_test1-cmp_Autophagy-cc_1--from--MTORAMPKsignaling-cc0-tmp_order_0-tgt-ddup_False_tmp-ddup_False.pkl
cbTgtType=1
cbTmpType=1
diff --git a/talent/common.py b/talent/common.py
index d682af8..2cb6acf 100644
--- a/talent/common.py
+++ b/talent/common.py
@@ -132,4 +132,7 @@ def str2bool(v):
else:
raise argparse.ArgumentTypeError('Boolean value expected.')
+def sanitize_string(s: str):
+ return "".join(x for x in s if x.isalnum() or x in "_-")
+
diff --git a/talent/sbml.py b/talent/sbml.py
index a31a534..f02ef27 100644
--- a/talent/sbml.py
+++ b/talent/sbml.py
@@ -410,25 +410,26 @@ class SbmlHelper:
def __assign_features_to_species(self, features:Dict[str, MultiSpeciesType]) -> Dict:
sid_features = {}
- for species in self.model.getListOfSpecies():
- s_id = species.getId()
- sid_features[s_id] = []
- multi = species.getPlugin('multi')
- st = multi.getSpeciesType()
- for sf in multi.getListOfSpeciesFeatures():
- occ = sf.getOccur()
- sft = sf.getSpeciesFeatureType()
- fsft = features[st].value[sft]
- vals = []
- for val in sf.getListOfSpeciesFeatureValues():
- valval = val.getValue()
- assert (st in features)
- assert (sft in features[st].value)
- assert (valval in fsft.value)
- vals.append(fsft.value[valval])
- # for i in range(occ):
- # sid_features[s_id].append(features[st][sftZZ][valval])
- sid_features[s_id].append(be.SpeciesFeature(cnt=occ, feature_type=sft, feature_name=fsft.name, values=vals))
+ if self.multiPlugin:
+ for species in self.model.getListOfSpecies():
+ s_id = species.getId()
+ sid_features[s_id] = []
+ multi = species.getPlugin('multi')
+ st = multi.getSpeciesType()
+ for sf in multi.getListOfSpeciesFeatures():
+ occ = sf.getOccur()
+ sft = sf.getSpeciesFeatureType()
+ fsft = features[st].value[sft]
+ vals = []
+ for val in sf.getListOfSpeciesFeatureValues():
+ valval = val.getValue()
+ assert (st in features)
+ assert (sft in features[st].value)
+ assert (valval in fsft.value)
+ vals.append(fsft.value[valval])
+ # for i in range(occ):
+ # sid_features[s_id].append(features[st][sftZZ][valval])
+ sid_features[s_id].append(be.SpeciesFeature(cnt=occ, feature_type=sft, feature_name=fsft.name, values=vals))
# TODO: possibly remove features which are shared across all species because those are irrelevant for discerning whether two glyps differ
@@ -628,7 +629,7 @@ class SbmlHelper:
compartmentName=compartments[s.getCompartment()] if s.getCompartment() else 'default',
sboTerm= s.getSBOTerm(),
layout=self.getSpeciesLayoutData(s_id),
- features=sid_features[s_id]
+ features=sid_features[s_id] if s_id in sid_features else []
# 'bbox': bbox,
# 'center': [bbox['x']+ bbox['width'] / 2, bbox['y']+ bbox['height'] / 2]
))
diff --git a/talent/utils/transfer.py b/talent/utils/transfer.py
index 21ad2b9..6995a37 100644
--- a/talent/utils/transfer.py
+++ b/talent/utils/transfer.py
@@ -293,8 +293,9 @@ def map_transfer_store(tgt, tmps, cache_path, output_path, ix_connected_componen
# BeautificationOp(BEAUTY_OPERATION_TYPE.HANDLE_REACTION_SPECIES_OVERLAPS)
# ])
# bc.run()
- fname = "{}/{}-tmp_order_{}-tgt-ddup_{}_tmp-ddup_{}.pkl".format(output_path, get_tgt_tmp_name(tgt, tmp), i,
- tgt.is_ddup(), tmp.is_ddup())
+ fname = "{}/{}-tmp_order_{}-tgt-ddup_{}_tmp-ddup_{}.pkl".format(output_path,
+ common.sanitize_string(get_tgt_tmp_name(tgt, tmp)),
+ i, tgt.is_ddup(), tmp.is_ddup())
output_fnames.append(fname)
# fname = "{}_cc-{}_k-{}.pkl".format(output_path, ix_connected_component, i)
logging.info("Storing transferred layout into {}".format(fname))
--
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