Updating template parser

src/pyphetools/__init__.py

@@ -5,7 +5,7 @@
 from . import validation
 
 
-__version__ = "0.9.111"
+__version__ = "0.9.112"
 
 
 __all__ = [

src/pyphetools/creation/case_template_encoder.py

@@ -29,6 +29,8 @@
 CellType = Enum('Celltype', ['DATA', 'HPO', 'NTR', 'MISC', 'NULL'])
 
 class CellEncoder(metaclass=abc.ABCMeta):
+    """Superclass for classes that help to decode contents of individuals cells in the pyphetools Excel template.
+    """
     def __init__(self, name):
         self._name = name
 
@@ -181,24 +183,22 @@ def columntype(self) -> "CellType":
 
 EXPECTED_HEADERS = {"PMID", "title", "individual_id", "comment", "disease_id", "disease_label",
                     "HGNC_id", "gene_symbol", "transcript", "allele_1", "allele_2",
-                    "variant.comment", "age_of_onset", "age_at_last_encounter", "sex"}
+                    "variant.comment", "age_of_onset", "age_at_last_encounter", "deceased", "sex"}
 
 DATA_ITEMS = {"PMID", "title", "individual_id", "disease_id", "disease_label", "HGNC_id",
                 "gene_symbol", "transcript", "allele_1", "allele_2",  "age_of_onset",
                 "age_at_last_encounter", "deceased", "sex"}
 
 # note that the allele_2 field is option
 REQUIRED_H1_FIELDS = ["PMID", "title", "individual_id",	"comment", "disease_id", "disease_label",
-                    "HGNC_id", "gene_symbol", "transcript", "allele_1", "allele_2", "variant.comment", "age_of_onset", "age_at_last_encounter", "sex", "HPO"]
+                    "HGNC_id", "gene_symbol", "transcript", "allele_1", "allele_2", "variant.comment", 
+                    "age_of_onset", "age_at_last_encounter", "deceased", "sex", "HPO"]
 ALLELE_2_IDX = 8
 
 REQUIRED_H2_FIELDS = ["CURIE", "str",	"str", "optional", "CURIE", "str", "CURIE",	"str",
-                    "str","str","str","optional",  "age", "age", "M:F:O:U", "na"]
+                    "str","str","str","optional",  "age", "age", "yes/no/na", "M:F:O:U", "na"]
+
 
-OPTIONAL_H1_FIELDS = REQUIRED_H1_FIELDS
-OPTIONAL_H1_FIELDS.insert(14, "deceased")
-OPTIONAL_H2_FIELDS = REQUIRED_H2_FIELDS
-OPTIONAL_H2_FIELDS.insert(14, "yes/no/na")
 
 
 class CaseTemplateEncoder:
@@ -229,13 +229,8 @@ def __init__(self, df:pd.DataFrame, hpo_cr:HpoConceptRecognizer, created_by:str,
             raise ValueError("headers are different lengths. Check template file for correctness.")
         # check headers are well formed
         idx = 0
-        ## The deceased field is optional
-        if "deceased" in header_1:
-            required_h1 = OPTIONAL_H1_FIELDS
-            required_h2 = OPTIONAL_H2_FIELDS
-        else:
-            required_h1 = REQUIRED_H1_FIELDS
-            required_h2 = REQUIRED_H2_FIELDS
+        required_h1 = REQUIRED_H1_FIELDS
+        required_h2 = REQUIRED_H2_FIELDS
         for i in range(len(required_h1)):
             if idx == ALLELE_2_IDX and header_1[idx] != required_h1[idx]:
                 idx += 1 # skip optional index
@@ -286,8 +281,6 @@ def  _process_header(self,
             elif not in_hpo_range:
                 if h1 in EXPECTED_HEADERS:
                     index_to_decoder_d[i] = DataEncoder(h1=h1, h2=h2)
-                elif h1 == "deceased":
-                    index_to_decoder_d[i] = DataEncoder(h1=h1, h2=h2)
                 else:
                     raise ValueError(f"Malformed template header at column {i}: \"{h1}\"")
             elif in_hpo_range:
@@ -417,14 +410,14 @@ def _parse_individual(self,
         else:
             encounter_age = None
         vitStat = None
-        if "deceased" in data_items:
-            decsd = data_items.get("deceased")
-            if decsd == "yes" and encounter_age is not None:
-                vitStat = VitalStatus(status=VitalStatus.Status.DECEASED, time_of_death=encounter_age)
-            elif decsd == "no":
-                vitStat = VitalStatus(status=VitalStatus.Status.ALIVE)
-            else:
-                vitStat = VitalStatus(status=VitalStatus.Status.UNKNOWN_STATUS)
+        # deceased is a required field from version 0.9.112 on
+        decsd = data_items.get("deceased")
+        if decsd == "yes" and encounter_age is not None:
+            vitStat = VitalStatus(status=VitalStatus.Status.DECEASED, time_of_death=encounter_age)
+        elif decsd == "no":
+            vitStat = VitalStatus(status=VitalStatus.Status.ALIVE)
+        else:
+            vitStat = VitalStatus(status=VitalStatus.Status.UNKNOWN_STATUS)
         disease_id = data_items.get("disease_id")
         disease_label = data_items.get("disease_label")
         # common error -- e.g. PMID: 3000312 or OMIM: 600123 (whitespace after colon)