pre-release, article ranking and download set up

Author: VergaJU

.gitignore

@@ -153,4 +153,5 @@ cython_debug/
 
 # Cheshire Cat Plugin settings
 data/
-
+literature/
+hissmed/

hissmed_literature_assistant.py

@@ -16,9 +16,16 @@ def hisscat_download_literature(user_message, cat):
     log.info(f"Action input: {action_input}") # Log the action input
     settings = cat.mad_hatter.get_plugin().load_settings()
     log.info(f"User email: {settings['email']}")  # Log the user email
-    PapersDownloader.set_email(email=settings['email'])
+    email = settings['email']
+    top_n_articles = settings['top_n_articles']
+    top_references = settings['top_references']
+    citation_weight = settings['citation_weight']
+    year_weight = settings['year_weight']
+    journal_weight = settings['journal_weight']
+    PapersDownloader.set_email(email=email)
     log.info(f"Saving articles in {os.path.join(os.getcwd(),'literature')}")  # Log the output folder
-    PapersDownloader.run(user_message) # Download the articles
+    PapersDownloader.create_directory()
+    PapersDownloader.batch_download_pdfs(query=query, top_n_articles=top_n_articles, citation_w=citation_weight, year_w=year_weight, journal_w=journal_weight)
     log.info(f"Downloaded articles") # Log the download status
     return user_message
 

plugin.json

@@ -1,6 +1,6 @@
 {
     "name": "HissMed Literature Assistant",
-    "version": "0.0.1",
+    "version": "0.1.0",
     "description": "HissMed literature assistant, fetch your queries on PubMed central and gives you answers and references.",
     "author_name": "Jacopo Umberto Verga",
     "plugin_url": "https://github.com/VergaJU/HissMed",

requirements.txt

@@ -1 +1,4 @@
-biopython>=1.85
+biopython>=1.85
+pandas
+numpy
+xml

settings.py

@@ -4,6 +4,10 @@
 class MySettings(BaseModel):
     email: str = "your.email@mail.com"
     top_references: int = 5
+    top_n_articles: int=10
+    citation_weight: float=0.7
+    year_weight: float=0.5
+    journal_weight: float=0.9
 
     @field_validator("email")
     @classmethod
@@ -12,6 +16,43 @@ def email_validator(cls, email):
             raise ValueError("Invalid email address")
         elif "your.email@mail.com" == email:
             raise ValueError("Please set your email address")
+    
+    @field_validator("top_references")
+    @classmethod
+    def top_references_validator(cls, top_references):
+        assert isinstance(top_references, int), f"Top references is {type(top_references)}, it must be an integer"
+        if top_references < 0:
+            raise ValueError("Invalid top references")
+        
+    
+    @field_validator("top_n_articles")
+    @classmethod
+    def top_n_articles_validator(cls, top_n_articles):
+        assert isinstance(top_n_articles, int), f"Top n articles is {type(top_n_articles)}, it must be an integer"
+        if top_n_articles < 0:
+            raise ValueError("Invalid top n articles")
+    
+    @field_validator("citation_weight")
+    @classmethod
+    def citation_weight_validator(cls, citation_weight):
+        assert isinstance(citation_weight, float), f"Citation weight is {type(citation_weight)}, it must be a float"
+        if citation_weight < 0 or citation_weight > 1:
+            raise ValueError("Invalid citation weight")
+
+    @field_validator("year_weight")
+    @classmethod
+    def year_weight_validator(cls, year_weight):
+        assert isinstance(year_weight, float), f"Year weight is {type(year_weight)}, it must be a float"
+        if year_weight < 0 or year_weight > 1:
+            raise ValueError("Invalid year weight")
+    
+    @field_validator("journal_weight")
+    @classmethod
+    def journal_weight_validator(cls, journal_weight):
+        assert isinstance(journal_weight, float), f"Journal weight is {type(journal_weight)}, it must be a float"
+        if journal_weight < 0 or journal_weight > 1:
+            raise ValueError("Invalid journal weight")
+
 
 @plugin
 def settings_model():