Add all project files including workflows and scripts

src/BioModelsCache/biomodels_cache.py

@@ -0,0 +1,73 @@
+import json
+from biomodels_restful_api_client import services as bmservices
+import re
+
+def remove_html_tags(text):
+    """
+    Removes html tags from a string
+
+    Parameters:
+    1. text: A string of text with HTML tags that must be removed.
+
+    Returns:
+    str: The input string with all HTML tags removed.
+    """
+    clean = re.compile('<.*?>')
+    return re.sub(clean, '', text)
+
+def update_cache(model, modelResults):
+    """
+    Update the cache with the model data if it's a curated BioModel and not already present.
+
+    Parameters:
+        1. model: A dictionary representing the model data to be cached.
+        2. modelResults : A dictionary representing the cached models.
+
+    Returns:
+        bool: Returns True if the cache was updated with the model, False if it is not a BioModel or if the Biomodel
+        is already in the cache.
+    """
+    modelNumber = model['publicationId']
+    if "BIOMD" not in modelNumber:
+        return False 
+
+    if modelNumber in modelResults and modelResults[modelNumber] == model:
+        return False 
+
+    if "description" in model:
+        model["description"] = remove_html_tags(model["description"])
+
+    modelResults[modelNumber] = model
+    return True
+
+def cache_biomodels():
+    """
+    Fetch and cache information for a set number of BioModels.
+    """
+    totalModels = 2000
+    i = 0
+
+    modelIdentifiers = bmservices.get_model_identifiers()
+    models = modelIdentifiers["models"]
+    modelResults = {}
+
+    for nModel in models:
+        if i < totalModels:
+            result = bmservices.get_model_info(nModel)
+            if 'publicationId' in result:
+              updated_cache = update_cache(result, modelResults)
+              if updated_cache:
+                  i += 1
+    save_to_json(modelResults)
+
+
+def save_to_json(modelInfo):
+    """ 
+    Saves the cached biomodel to the Json file.
+
+    Parameters:
+        1. modelInfo: A dictionary containing the model data to be saved to the file.
+    """
+    with open('cached_biomodels.json', 'w') as json_file:
+        json.dump(modelInfo, json_file)
+