diff options
Diffstat (limited to 'gn3/llms/process.py')
| -rw-r--r-- | gn3/llms/process.py | 48 |
1 files changed, 41 insertions, 7 deletions
diff --git a/gn3/llms/process.py b/gn3/llms/process.py index ab2a80e..ade4104 100644 --- a/gn3/llms/process.py +++ b/gn3/llms/process.py @@ -35,7 +35,7 @@ class DocIDs(): raise FileNotFoundError(f"{file_path}-- FIle does not exist\n") def format_doc_ids(self, docs): - """method to format doc_ids for list items""" + """method to format doc_ids for list items doc_id and doc_name""" for _key, val in docs.items(): if isinstance(val, list): for doc_obj in val: @@ -43,7 +43,14 @@ class DocIDs(): self.doc_ids.update({doc_obj["id"]: doc_name}) def get_info(self, doc_id): - """ interface to make read from doc_ids""" + """ interface to make read from doc_ids + and extract info data else returns + doc_id + Args: + doc_id: str: a search key for doc_ids + Returns: + an object with doc_info if doc_id in doc_ids + """ if doc_id in self.doc_ids.keys(): return self.doc_ids[doc_id] else: @@ -51,7 +58,8 @@ class DocIDs(): def format_bibliography_info(bib_info): - """Function for formatting bibliography info""" + """Utility function for formatting bibliography info + """ if isinstance(bib_info, str): return bib_info.removesuffix('.txt') elif isinstance(bib_info, dict): @@ -66,7 +74,15 @@ def filter_response_text(val): def parse_context(context, get_info_func, format_bib_func): - """function to parse doc_ids content""" + """Function to parse doc_ids content + Args: + context: raw references from fahamu api + get_info_func: function to get doc_ids info + format_bib_func: function to foramt bibliography info + Returns: + an list with each item having (doc_id,bib_info, + combined reference text) + """ results = [] for doc_ids, summary in context.items(): combo_txt = "" @@ -81,7 +97,12 @@ def parse_context(context, get_info_func, format_bib_func): def load_file(filename, dir_path): - """function to open and load json file""" + """Utility function to read json file + Args: + filename: file name to read + dir_path: base directory for the file + Returns: json data read to a dict + """ file_path = os.path.join(dir_path, f"{filename}") if not os.path.isfile(file_path): raise FileNotFoundError(f"{filename} was not found or is a directory") @@ -90,8 +111,19 @@ def load_file(filename, dir_path): def fetch_pubmed(references, file_name, data_dir=""): - """method to fetch and populate references with pubmed""" + """ + Fetches PubMed data from a JSON file and populates the\ + references dictionary. + + Args: + references (dict): Dictionary with document IDs as keys\ + and reference data as values. + filename (str): Name of the JSON file containing PubMed data. + data_dir (str): Base directory where the data files are located. + Returns: + dict: Updated references dictionary populated with the PubMed data. + """ try: pubmed = load_file(file_name, os.path.join(data_dir, "gn-meta/lit")) for reference in references: @@ -123,4 +155,6 @@ def get_gnqa(query, auth_token, data_dir=""): answer = resp_text['data']['answer'] context = resp_text['data']['context'] return task_id, answer, fetch_pubmed(parse_context( - context, DocIDs().get_info, format_bibliography_info), "pubmed.json", data_dir) + context, DocIDs().get_info, + format_bibliography_info), + "pubmed.json", data_dir) |