fix: fixed working directories of temporary files

biosimulators · Jan 3, 2022 · bb64fc5 · bb64fc5
1 parent e0efe47
commit bb64fc5
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/biosimulators_utils/_version.py b/biosimulators_utils/_version.py
@@ -1 +1 @@
-__version__ = '0.1.154'
+__version__ = '0.1.155'
diff --git a/biosimulators_utils/model_lang/smoldyn/validation.py b/biosimulators_utils/model_lang/smoldyn/validation.py
@@ -46,7 +46,7 @@ def validate_model(filename, name=None, config=None):
         if os.path.isfile(filename):
             config = read_smoldyn_simulation_configuration(filename)
             disable_smoldyn_graphics_in_simulation_configuration(config)
-            fid, config_filename = tempfile.mkstemp(suffix='.txt')
+            fid, config_filename = tempfile.mkstemp(suffix='.txt', dir=os.path.dirname(filename))
             os.close(fid)
             write_smoldyn_simulation_configuration(config, config_filename)
             with StandardOutputErrorCapturer(level=StandardOutputErrorCapturerLevel.c, relay=False) as captured:

diff --git a/biosimulators_utils/omex_meta/io.py b/biosimulators_utils/omex_meta/io.py
@@ -202,7 +202,7 @@ def read_rdf(cls, filename, config=None):
 
                 lines[0] = line
 
-                temp_fid, temp_filename = tempfile.mkstemp()
+                temp_fid, temp_filename = tempfile.mkstemp(dir=os.path.dirname(filename))
                 os.close(temp_fid)
                 with open(temp_filename, 'wb') as file:
                     for line in lines:

diff --git a/biosimulators_utils/sedml/exec.py b/biosimulators_utils/sedml/exec.py
@@ -545,7 +545,7 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
                 model = sub_task.task.model
                 if apply_xml_model_changes and is_model_language_encoded_in_xml(model.language):
                     original_model_source = model.source
-                    fid, model.source = tempfile.mkstemp(suffix='.xml')
+                    fid, model.source = tempfile.mkstemp(suffix='.xml', dir=os.path.dirname(original_model_source))
                     os.close(fid)
 
                     model_etrees[model.id].write(model.source,

diff --git a/biosimulators_utils/sedml/utils.py b/biosimulators_utils/sedml/utils.py
@@ -299,7 +299,7 @@ def resolve_model_and_apply_xml_changes(model, sed_doc, working_dir,
             # write model to file
             if save_to_file:
                 if temp_model_source is None:
-                    modified_model_file, temp_model_source = tempfile.mkstemp(suffix='.xml')
+                    modified_model_file, temp_model_source = tempfile.mkstemp(suffix='.xml', dir=os.path.dirname(model.source))
                     os.close(modified_model_file)
                     model.source = temp_model_source