date for biocurator

src/pyphetools/__init__.py

@@ -4,7 +4,7 @@
 from . import visualization
 from . import validation
 
-__version__ = "0.9.81"
+__version__ = "0.9.82"
 
 __all__ = [
     "creation",

src/pyphetools/creation/import_template.py

@@ -252,7 +252,7 @@ def create_hpoa_from_phenopackets(self,
         if target is not None:
             ppkt_list = TemplateImporter.filter_diseases(target, ppkt_list)
         TemplateImporter.check_disease_entries(ppkt_list)
-        builder = HpoaTableBuilder(phenopacket_list=ppkt_list)
+        builder = HpoaTableBuilder(phenopacket_list=ppkt_list, created_by=self._created_by)
         if moi == "Autosomal dominant":
             builder.autosomal_dominant(pmid)
         elif moi == "Autosomal recessive":

src/pyphetools/visualization/hpoa_table_creator.py

@@ -1,6 +1,8 @@
 import os
 import json
 from typing import List, Dict
+from datetime import datetime as d
+
 
 from google.protobuf.json_format import Parse
 
@@ -119,6 +121,9 @@ def __init__(self, phenopacket_list, onset_term_d,  moi_d, created_by:str=None)
         :type: Dict[str, OnsetTerm]
         :param moi_d: Dictionary with key PMID and value Mode of inheritance
         """
+        date = d.now()
+        todays_date = date.strftime("%Y-%m-%d")
+        self._todays_date = f"[{todays_date}]"
         self._phenopackets = phenopacket_list
         self._created_by = created_by
         self._all_hpo_d = self._get_all_hpos()
@@ -128,6 +133,7 @@ def __init__(self, phenopacket_list, onset_term_d,  moi_d, created_by:str=None)
         self._onset_rows = self._add_age_of_onset_terms(onset_term_d)
         self._moi_rows = self._add_moi_rows(moi_d)
 
+
 
     def _get_all_hpos(self) -> Dict[str,HpTerm]:
         """Get a dictionary of HpTerms, with key being HPO id and the value the corresponding HpTerm
@@ -211,6 +217,10 @@ def _count_hpos(self):
                 if pf.excluded is not None and not pf.excluded:
                     hpo_counter.increment_observed(hpterm.id)
         return hpo_counter_d
+
+    def _format_biocurator(self, bcurator):
+        return f"{bcurator}{self._todays_date}"
+
 
     def _add_age_of_onset_terms(self, onset_term_d) -> List[HpoaTableRow]:
         """
@@ -219,7 +229,7 @@ def _add_age_of_onset_terms(self, onset_term_d) -> List[HpoaTableRow]:
         """
         onset_rows  = list() # reset
         for pmid, oterm_list in onset_term_d.items():
-            biocurator = self._biocurator_d.get(pmid)
+            biocurator = self._format_biocurator(self._biocurator_d.get(pmid))
             for oterm in oterm_list:
                 hpo_onset_term = HpTerm(hpo_id=oterm.id, label=oterm.label)
                 row = HpoaTableRow(disease=self._disease, hpo_term=hpo_onset_term, publication=pmid, biocurator=biocurator, freq_num=oterm.numerator, freq_denom=oterm.denominator)
@@ -239,7 +249,9 @@ def _add_moi_rows(self, moi_d) -> List[HpoaTableRow]:
             # If we add an MOI outside of the template, then it will not have a PMID
             # the template builder requires a created_by field which is designed for this.
             if biocurator is None:
-                biocurator = self._created_by
+                biocurator = biocurator = self._format_biocurator(self._created_by)
+            else:
+                biocurator = self._format_biocurator(biocurator)
             for hpterm in hpterm_list:
                 row = HpoaTableRow(disease=self._disease, hpo_term=hpterm, publication=pmid, biocurator=biocurator)
                 moi_rows.append(row)
@@ -253,6 +265,7 @@ def get_dataframe(self):
                         "description", "publication","evidence", "biocuration"]
         for pmid, counter in self._hpo_counter_d.items():
             biocurator = self._biocurator_d.get(pmid)
+            biocurator = self._format_biocurator(biocurator)
             measured_d = counter.get_measured_d()
             observed_d = counter.get_observed_d()
             # by construction, there can be no term in observed_d that is not in measured_d
@@ -282,7 +295,7 @@ def write_data_frame(self):
 
 class HpoaTableBuilder:
 
-    def __init__(self, indir=None, phenopacket_list=None, created_by:str=None) -> None:
+    def __init__(self, created_by:str, indir=None, phenopacket_list=None) -> None:
         if indir is not None:
             if not os.path.isdir(indir):
                 raise ValueError(f"indir argument {indir} must be directory!")