Update some wonky SED-ML.

(for biomodels 978 and 1008.) Couldn't fix 978 through scripts; had to do the manual-fixes thing. The problem was there was a 'parameter scan' that didn't change any parameters, and had exactly one 'loop'.
sys-bio · Nov 18, 2024 · 8f56e73 · 8f56e73
1 parent 556d81a
commit 8f56e73
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Showing 4 changed files with 93 additions and 174 deletions.
diff --git a/fix_manual_corrections.yml b/fix_manual_corrections.yml
@@ -1245,6 +1245,11 @@ BIOMD0000000983:
     type: replace_text
     old: '<uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="126" numberOfSteps="126">'
     new: '<uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="125" numberOfSteps="125">'
+BIOMD0000001008:
+  - filename: 'BIOMD0000000539.sedml'
+    type: replace_text
+    old: '<uniformRange id="range02" start="1e-14" end="1e-06" numberOfSteps="10000000" type="linear"/>'
+    new: '<uniformRange id="range02" start="1e-14" end="1e-06" numberOfSteps="1000" type="log"/>'
 BIOMD0000001013:
   - filename: 'Fig 3a (CAR-T cells).png'
     type: 'rename_file'

diff --git a/fix_sbml_validity.py b/fix_sbml_validity.py
@@ -49,7 +49,7 @@ def fixHasProperty(file):
     doc = libsbml.readSBMLFromFile(file)
     sstr = libsbml.writeSBMLToString(doc)
     sstr = sstr.replace("bqmodel:hasProperty", "bqbiol:hasProperty")
-    out = open(file, "w", encoding="utf8")
+    out = open(file, "w", encoding="utf-8")
     out.write(sstr)
     out.close()