hotfix:make airtable conn work (#1554)

ersilia/hub/content/base_information.py

@@ -26,7 +26,6 @@
     InputBaseInformationError,
     InputShapeBaseInformationError,
     LicenseBaseInformationError,
-    ModeBaseInformationError,
     OutputBaseInformationError,
     OutputConsistencyBaseInformationError,
     OutputDimensionBaseInformationError,
@@ -83,8 +82,6 @@ def __init__(self, config_json=None):
             Placeholder for the model’s title.
         _description : None
             Placeholder for a description of the model.
-        _mode : None
-            Placeholder for the training mode, one of 'retrained', 'pretrained', 'in-house', or 'online'.
         _task : None
             Placeholder for the primary task associated with the model, such as 'classification', or 'regression'.
         _subtask : None
@@ -151,7 +148,6 @@ def __init__(self, config_json=None):
         self._status = None
         self._title = None
         self._description = None
-        self._mode = None
         self._task = None
         self._subtask = None
         self._input = None
@@ -360,37 +356,6 @@ def description(self, new_description):
             raise DescriptionBaseInformationError
         self._description = new_description
 
-    @property
-    def mode(self):
-        """
-        Get the model mode.
-
-        Returns
-        -------
-        str
-            The model mode.
-        """
-        return self._mode
-
-    @mode.setter
-    def mode(self, new_mode):
-        """
-        Set the model mode.
-
-        Parameters
-        ----------
-        new_mode : str
-            The new model mode.
-
-        Raises
-        ------
-        ModeBaseInformationError
-            If the mode is not valid.
-        """
-        if new_mode not in self._read_default_fields("Mode"):
-            raise ModeBaseInformationError
-        self._mode = new_mode
-
     @property
     def source(self):
         """
@@ -983,7 +948,10 @@ def publication_year(self, new_publication_year):
         """
         if type(new_publication_year) is not int:
             raise PublicationYearBaseInformationError
-        if new_publication_year < 1900 or new_publication_year > datetime.today("Y"):
+        if (
+            new_publication_year < 1900
+            or new_publication_year > datetime.date.today().year
+        ):
             raise PublicationBaseInformationError
         self._publication_year = new_publication_year
 
@@ -1265,7 +1233,9 @@ def environment_size(self, new_environment_size):
         EnvironmentSizeMbBaseInformationError
             If the environment size value is not valid.
         """
-        if not isinstance(new_environment_size, (int, float)):
+        if not new_environment_size:
+            new_environment_size = 0
+        elif not isinstance(new_environment_size, (int, float)):
             raise EnvironmentSizeMbBaseInformationError
         self._environment_size_mb = new_environment_size
 
@@ -1294,7 +1264,9 @@ def image_size_mb(self, new_image_size_mb):
         ImageSizeMbBaseInformationError
             If `new_image_size_mb` is not an integer.
         """
-        if not isinstance(new_image_size_mb, (int, float)):
+        if not new_image_size_mb:
+            new_image_size_mb = 0
+        elif not isinstance(new_image_size_mb, (int, float)):
             raise ImageSizeMbBaseInformationError
         self._image_size_mb = new_image_size_mb
 
@@ -1323,7 +1295,9 @@ def computational_performance_one(self, new_value):
         ComputationalPerformanceOneBaseInformationError
             If `new_value` is not an int or float.
         """
-        if not isinstance(new_value, (int, float)):
+        if not new_value:
+            new_value = 0
+        elif not isinstance(new_value, (int, float)):
             raise ComputationalPerformanceOneBaseInformationError
         self._computational_performance_one = new_value
 
@@ -1352,7 +1326,9 @@ def computational_performance_ten(self, new_value):
         ComputationalPerformanceTenBaseInformationError
             If `new_value` is not an int or float.
         """
-        if not isinstance(new_value, (int, float)):
+        if not new_value:
+            new_value = 0
+        elif not isinstance(new_value, (int, float)):
             raise ComputationalPerformanceTenBaseInformationError
         self._computational_performance_ten = new_value
 
@@ -1381,7 +1357,9 @@ def computational_performance_hund(self, new_value):
         ComputationalPerformanceHundredBaseInformationError
             If `new_value` is not an int or float.
         """
-        if not isinstance(new_value, (int, float)):
+        if not new_value:
+            new_value = 0
+        elif not isinstance(new_value, (int, float)):
             raise ComputationalPerformanceHundredBaseInformationError
         self._computational_performance_hund = new_value
 
@@ -1400,7 +1378,6 @@ def as_dict(self):
             "Status": self.status,
             "Title": self.title,
             "Description": self.description,
-            "Mode": self.mode,
             "Source": self.source,
             "Source Type": self.source_type,
             "Input": self.input,
@@ -1451,7 +1428,6 @@ def from_dict(self, data):
         self._assign("status", "Status", data)
         self._assign("title", "Title", data)
         self._assign("description", "Description", data)
-        self._assign("mode", "Mode", data)
         self._assign("source", "Source", data)
         self._assign("source_type", "Source Type", data)
         self._assign("input", "Input", data)

ersilia/hub/content/card.py

@@ -43,6 +43,7 @@ class RepoMetadataFile(ErsiliaBase):
     def __init__(self, model_id=None, config_json=None):
         self.model_id = model_id
         ErsiliaBase.__init__(self, config_json=config_json, credentials_json=None)
+        self.is_json = False
 
     def _github_json_url(self, org=None, branch=None):
         if org is None:
@@ -73,6 +74,7 @@ def _get_file_content_from_github(self, org, branch):
             else:
                 return yaml.safe_load(r.content)
         else:
+            self.is_json = True
             return json.loads(r.content)
 
     def get_json_or_yaml_file(self, org: str = None, branch: str = None) -> dict:
@@ -154,7 +156,7 @@ def write_information(
             path = json_or_yaml_path
             with open(path, "w") as f:
                 json.dump(data, f, indent=4)
-        elif json_or_yaml_path.endswith(".yaml"):
+        elif json_or_yaml_path.endswith(".yml"):
             path = json_or_yaml_path
             with open(path, "w") as f:
                 yaml.dump(data, f)

ersilia/hub/content/metadata/biomedical_area.txt

@@ -1,3 +1,4 @@
 ADMET
 Malaria
-Tuberculosis
+Tuberculosis
+Any

ersilia/hub/content/metadata/target_organism.txt

@@ -1,3 +1,5 @@
 Human
 Plasmodium spp.
-Mycobacterium tuberculosis
+Mycobacterium tuberculosis
+Plasmodium falciparum
+Not Applicable