rdrf #2453 fixed names in BC all patients

rdrf/dashboards/components/common.py

@@ -37,11 +37,12 @@ def __init__(
         static_followups={},
     ):
         self.config_model = config_model
-        self.registry = config_model.registry
         if self.config_model is not None:
             self.config = config_model.config
+            self.registry = config_model.registry
         else:
             self.config = None
+            self.registry = None
         self.data = data
         self.title = title
         self.patient = patient  # none if all patients

rdrf/dashboards/components/cpr.py

@@ -1,6 +1,8 @@
 from .common import BaseGraphic
 from dash import dcc, html
 from ..data import lookup_cde_value
+from ..data import has_static_followups
+from ..data import get_static_followups_handler
 from ..utils import get_colour_map
 from ..utils import add_seq_name
 import plotly.express as px
@@ -36,6 +38,15 @@ class ChangesInPatientResponses(BaseGraphic):
     """
 
     def get_graphic(self):
+        if self.registry is not None:
+            if has_static_followups(self.registry):
+                logger.debug("cpr has static")
+                self.sfuh = get_static_followups_handler(self.registry)
+                self.data = self.sfuh.fix_ordering_of_static_followups(self.data)
+                from dashboards.utils import dump
+
+                dump(f"cpr-{self.title}.csv", self.data)
+
         field_dicts = self.config["fields"]
         items = []
         for field_dict in field_dicts:
@@ -74,6 +85,7 @@ def _create_stacked_bar_px(self, df, field, label, colour_map):
 
         df = add_seq_name(df)
         df = df.round(1)
+
         df["text"] = df.apply(
             lambda row: "<b>"
             + str(row["counts"])
@@ -116,6 +128,9 @@ def fix_xaxis(self, fig, data):
         # this replaces the SEQ numbers on the x-axis
         # with names
 
+        logger.debug("fixing x axis for cpr")
+        logger.debug(data)
+
         seq_totals = data.groupby(["SEQ"])["counts"].sum()
 
         def get_ticktext(row):
@@ -124,7 +139,20 @@ def get_ticktext(row):
             seq_name = row["SEQ_NAME"]
             return seq_name + " (" + str(seq_total) + ")"
 
-        data["ticktext"] = data.apply(get_ticktext, axis=1)
+        def get_ticktext2(row):
+            logger.debug(row)
+            seq = row["SEQ"]
+            seq_total = seq_totals[seq]
+            old_seq_name = row["SEQ_NAME"]
+            seq_name = self.sfuh.get_static_form_name_from_seq_name(old_seq_name)
+            return seq_name + " (" + str(seq_total) + ")"
+
+        if hasattr(self, "sfuh"):
+            func = get_ticktext2
+        else:
+            func = get_ticktext
+
+        data["ticktext"] = data.apply(func, axis=1)
 
         fig.update_layout(
             xaxis=dict(

rdrf/dashboards/data.py

@@ -3,6 +3,7 @@
 from rdrf.models.definition.models import ClinicalData
 from rdrf.models.definition.models import RDRFContext
 from rdrf.models.definition.models import CommonDataElement
+from rdrf.models.definition.models import RegistryForm
 
 from registry.patients.models import Patient
 
@@ -113,13 +114,10 @@ def _parse_config(self, config_dict: dict):
 
         if self.followup_forms:
             self.multiform = True
-            logger.debug("is multiform")
         else:
             self.multiform = False
-            logger.debug("is NOT multiform")
 
     def _order_by_collection_date(self, df: pd.DataFrame):
-        logger.debug("ordering dataframe by collection date")
         # it's more likely collection date on baseline form
         # will be null hence the na_position of first
         self.df.sort_values(by=[cdf], inplace=True, na_position="first")
@@ -142,19 +140,14 @@ def update_seq(row):
                 return row["SEQ"]
 
         if not self.multiform:
-            logger.debug("applying update seq")
             self.df["SEQ"] = self.df.apply(update_seq, axis=1)
         else:
-            logger.debug("multiform!")
             self.df = self._custom_ordering(self.df)
 
         # must do this if we re-sequence:
         self.df = self._assign_seq_names(self.df)
-
         # self._sanity_check(self.df)
 
-        logger.debug("finished ordering")
-
     def _sanity_check(self, df):
         for index, row in df.iterrows():
             if row["TYPE"] == "baseline":
@@ -166,8 +159,6 @@ def _reseq(self, df):
         pass
 
     def _custom_ordering(self, df):
-        logger.debug("applying custom ordering")
-
         def seq_from_form(form):
             if form == self.baseline_form:
                 return 0
@@ -203,8 +194,6 @@ def _reload_dataframe(self):
         self.df = self._assign_seq_names(self.df)
 
     def _assign_seq_names(self, df):
-        logger.debug("assigning sequence names")
-
         def get_aus_date(row):
             try:
                 d = row["COLLECTIONDATE"].date()
@@ -531,7 +520,6 @@ def combine_data(
 
     combined_data = indiv_data.merge(avg_data, how="left", on="SEQ")
     combined_data = combined_data.merge(count_data, how="left", on="SEQ")
-    logger.debug(f"combined data including counts = {combined_data}")
     return combined_data
 
 
@@ -565,16 +553,18 @@ def __init__(self, registry, baseline_form, static_followups):
             x["name"] for x in self.static_followups if x["seq"] != "+"
         ]
 
+        self.multiform = [x["name"] for x in self.static_followups if x["seq"] == "+"][
+            0
+        ]
+
     def fix_ordering_of_static_followups(self, df: pd.DataFrame) -> pd.DataFrame:
         changed = False
         for index, row in df.iterrows():
             if row["FORM"] == self.baseline_form:
                 old_seq = row["SEQ"]
                 df.at[index, "SEQ"] = 0
-                logger.debug(f"""static baseline fix: {row["FORM"]} {old_seq} -> 0""")
                 changed = True
             elif row["FORM"] in self.static_form_names:
-                logger.debug(f"""fixing row for static followup {row["FORM"]}""")
                 self.fixup_static_followup(df, index, row)
                 changed = True
 
@@ -600,23 +590,36 @@ def fixup_static_followup(self, df: pd.DataFrame, index, row):
                 static_seq = static_form_dict["seq"]
                 old_seq = row["SEQ"]
                 df.at[index, "SEQ"] = static_seq
-                logger.debug(
-                    f"""static fu fix: {row["FORM"]} {old_seq} -> {static_seq}"""
-                )
 
     def get_static_form_name(self, seq, form):
         from rdrf.models.definition.models import RegistryForm
 
         if form == self.baseline_form:
             form_model = RegistryForm.objects.get(name=form)
-            return form_model.display_name
+            name = form_model.display_name
+            return name
         else:
             for form_dict in self.static_followups:
                 if form_dict["name"] == form:
                     form_model = RegistryForm.objects.get(name=form)
-                    return form_model.display_name
+                    name = form_model.display_name
+                    return name
+
         return form
 
+    def get_static_form_name_from_seq_name(self, seq_name):
+        if seq_name == "Baseline":
+            return RegistryForm.objects.get(name=self.baseline_form).display_name
+        else:
+            from dashboards.utils import seq_names as names_dict
+
+            for seq, name in names_dict.items():
+                if name == seq_name:
+                    for d in self.static_followups:
+                        if d["seq"] == seq:
+                            return RegistryForm.objects.get(name=d["name"]).display_name
+            return RegistryForm.objects.get(name=self.multiform).display_name
+
 
 def get_static_followups_handler(registry):
     try: