Update copy on results pages, rearrange buttons, responsive titles and error message, refactor assessment logic

README.md

@@ -35,3 +35,5 @@ MacOS:
 ###NB
 If you change the routes please update the route-order "page_flow" tuple in 'utils/back_function.py' so the back button works correctly 
 + the routes.txt file which shows the route function and paired route
+
+To make changes to question pages there is one partial for all the F/S questions and then the single-question items are less templated so need to be modified directly (dsq/viral.html and short_form/reduction.html)

utils/screener_utils.py

@@ -0,0 +1,72 @@
+from flask import render_template, session
+import plotly.graph_objects as go
+import json
+import plotly.utils
+
+# screener questions
+# 'fatigue13c', 'remember36c', 'minimum17c', 'unrefreshed19c',
+
+def screener_diagnose():
+    # we *25 to scale 4pt scale to 100 pt scale
+    fatiguescore = fit_domain_score('fatiguescore')
+    pemscore = fit_domain_score('pemscore')
+    sleepscore = fit_domain_score('sleepscore')
+    cogscore = fit_domain_score('cogscore')
+
+    responses = [fatiguescore, pemscore, sleepscore, cogscore]
+    iomfatiguecheck = "No"
+    iompemcheck = "No"
+    iomsleepcheck = "No"
+    iomcogcheck = "No"
+    dx_met = False
+
+    if session['fatiguescoref'] >= 2 and session['fatiguescores'] >= 2:
+        iomfatiguecheck = "Yes"
+    if session['minexf'] >= 2 and session['minexs'] >= 2:
+        iompemcheck = "Yes"
+    if session['sleepf'] >= 2 and session['sleeps'] >= 2:
+        iomsleepcheck = "Yes"
+    if session['rememberf'] >= 2 and session['remembers'] >= 2:
+        iomcogcheck = "Yes"
+
+    screen_message = 'Your responses to the screener questions are scored below. <br> Scores range from 0 to 100, with higher scores indicate more frequent and severe problems.'
+    if iomfatiguecheck == "Yes" or iompemcheck == "Yes" or iomsleepcheck == "Yes" or iomcogcheck == "Yes":
+        dx_met = True
+
+    composite_scores = responses
+    categories = ['Fatigue', 'Post-exertional malaise', 'Sleep problems',
+                  'Cognitive problems']
+
+    colors = ['#56A8A0' for score in composite_scores]
+
+    # composite f/s score graph
+    fig = go.Figure(
+        data=[
+            go.Bar(y=composite_scores, x=categories, name="Your scores", marker=dict(color=colors))],
+        layout=go.Layout(
+            title=go.layout.Title(text='Your Summary Score', x=0.5),
+            showlegend=True, 
+            legend=dict(
+                orientation="h",
+                yanchor="bottom",
+                y=1.02,
+                xanchor="right",
+                x=1
+            ),
+            autosize=True
+        )
+    )
+    fig.update_layout(
+        yaxis_title='Combined Frequency and Severity Scores',
+        xaxis_title='Symptom Domains'
+    )
+    fig.update_yaxes(range=[0, 100], dtick=25, titlefont=dict(size=15))
+    fig.update_xaxes(tickfont=dict(size=13), titlefont=dict(size=15))
+    graphJSON = json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
+    return render_template("results/graph.html",
+                           graphJSON = graphJSON, 
+                           screen_message = screen_message,
+                           dx_met = dx_met)
+
+def fit_domain_score(session_var_string):
+    return 1 if session[session_var_string] == 0 else session[session_var_string] * 25

utils/short_form_utils.py

@@ -0,0 +1,187 @@
+from flask import render_template, session
+import numpy as np
+import plotly.graph_objects as go
+import json
+import plotly.utils
+
+# short form questions:
+# 'fatigue13c', 'soreness15c', 'minimum17c', 'unrefreshed19c',
+# 'musclepain25c', 'bloating29c', 'remember36c', 'difficulty37c',
+# 'bowel46c', 'unsteady48c', 'limbs56c', 'hot58c', 'flu65c','smells66c'
+
+def short_form_diagnose():
+    import domainScores as ds
+
+    fatiguescore = (int(session["fatiguescoref"]) + int(session["fatiguescores"])) / 2
+    pemscore = (int(session["minexf"]) + int(session["minexs"]) + int(session['soref']) + int(session['sores'])) / 4
+    sleepscore = (int(session["sleepf"]) + int(session["sleeps"])) / 2
+    cogscore = (int(session["rememberf"]) + int(session["remembers"]) + int(session['attentionf']) +
+                int(session['attentions'])) / 4
+    painscore = (int(session['musclef']) + int(session['muscles'])) / 2
+    gastroscore = (int(session['bloatf']) + int(session['bloats']) + int(session['bowelf']) +
+                   int(session['bowels'])) / 4
+    orthoscore = (int(session['unsteadyf']) + int(session['unsteadys'])) / 2
+    circscore = (int(session['limbsf']) + int(session['limbss']) + int(session['hotf']) + int(session['hots'])) / 4
+    immunescore = (int(session['fluf']) + int(session['flus'])) / 2
+    neuroenscore = (int(session['smellf']) + int(session['smells'])) / 2
+
+    user_scores = [fatiguescore, pemscore, sleepscore, cogscore, painscore, gastroscore, orthoscore, circscore,
+                   immunescore, neuroenscore]
+
+    df = ds.sdf
+    mecfs = df[(df['dx'] == 1)]
+    cfsdomains = np.mean(mecfs.iloc[:, 110:120], axis=0)
+
+    # This assesses the IOM Criteria
+    responses = [fatiguescore, pemscore, sleepscore, cogscore]
+    iomfatiguecheck = "No"
+    iomreductioncheck = "No"
+    iompemcheck = "No"
+    iomsleepcheck = "No"
+    iomcogcheck = "No"
+    iomorthocheck = "No"
+
+    if int(session['fatiguescoref']) >= 2 and int(session['fatiguescores']) >= 2:
+        iomfatiguecheck = "Yes"
+    if int(session['reduction']) == 1:
+        iomreductioncheck = "Yes"
+    if (int(session['minexf']) >= 2 and int(session['minexs'] >= 2) or (
+            int(session['soref']) >= 2 and int(session['sores']) >= 2)):
+        iompemcheck = "Yes"
+    if int(session['sleepf']) >= 2 and int(session['sleeps']) >= 2:
+        iomsleepcheck = "Yes"
+    if (int(session['rememberf']) >= 2 and int(session['remembers']) >= 2 ) or (
+            int(session['attentionf']) >= 2 and int(session['attentions']) >= 2):
+        iomcogcheck = "Yes"
+    if int(session['unsteadyf']) >= 2 and int(session['unsteadys']) >= 2:
+        iomorthocheck = "Yes"
+
+    if iomfatiguecheck == "Yes" and iomreductioncheck == "Yes" and iompemcheck == "Yes" and iomsleepcheck == "Yes" and (iomcogcheck == "Yes" or iomorthocheck == "Yes"):
+        iom_msg = "Your responses suggest you meet the IOM Criteria for ME/CFS. To improve the accuracy" \
+                  " of your assessment with more questions continue to the next section."
+        iomdxcheck = "Met"
+
+    else:
+        iom_msg = "Your responses do not meet the IOM Criteria for ME/CFS."
+        iomdxcheck = "Not met"
+
+    # This assesses the Canadian Consensus Criteria, one of the three major case definitions we use
+
+    ccc_dx = False
+
+    if int(session['fatiguescoref']) >= 2 and int(session['fatiguescores']) >= 2:
+        ccc_fatigue = 1
+        ccc_fatiguecheck = "Yes"
+    else:
+        ccc_fatigue = 0
+        ccc_fatiguecheck = "No"
+    if int(session['reduction']) == 1:
+        ccc_reduction = 1
+        ccc_reductioncheck = "Yes"
+    else:
+        ccc_reduction = 0
+        ccc_reductioncheck = "No"
+    if int(session['musclef']) >= 2 and int(session['muscles']) >= 2:
+        ccc_pain = 1
+        ccc_paincheck = "Yes"
+    else:
+        ccc_pain = 0
+        ccc_paincheck = "No"
+    if int(session['sleepf']) >= 2 and int(session['sleeps']) >= 2:
+        ccc_sleep = 1
+        ccc_sleepcheck = "Yes"
+    else:
+        ccc_sleep = 0
+        ccc_sleepcheck = "No"
+    if (int(session['minexf']) >= 2 and int(session['minexs']) >= 2) or (
+            int(session['soref']) >= 2 and int(session['sores']) >= 2):
+        ccc_pem = 1
+        ccc_pemcheck = "Yes"
+    else:
+        ccc_pem = 0
+        ccc_pemcheck = "No"
+    if (int(session['rememberf']) >= 2 and int(session['remembers']) >= 2) or (
+            int(session['attentionf']) >= 2 and int(session['attentions']) >= 2):
+        ccc_cog = 1
+        ccc_cogcheck = "Yes"
+    else:
+        ccc_cog = 0
+        ccc_cogcheck = "No"
+
+    if (int(session['unsteadyf']) >= 2 and int(session['unsteadys']) >= 2) or (
+            int(session['bowelf']) >= 2 and int(session['bowels']) >= 2) or (
+            int(session['bloatf']) >= 2 and int(session['bloats']) >= 2):
+        ccc_auto = 1
+        ccc_autocheck = "Yes"
+    else:
+        ccc_auto = 0
+        ccc_autocheck = "No"
+    if (int(session['limbsf']) >= 2 and int(session['limbss']) >= 2) or (
+            int(session['hotf']) >= 2 and int(session['hots']) >= 2):
+        ccc_neuro = 1
+        ccc_neurocheck = "Yes"
+    else:
+        ccc_neuro = 0
+        ccc_neurocheck = "No"
+    if (int(session['fluf']) >= 2 and int(session['flus']) >= 2) or (
+            int(session['smellf']) >= 2 and int(session['smells']) >= 2):
+        ccc_immune = 1
+        ccc_immunecheck = "Yes"
+    else:
+        ccc_immune = 0
+        ccc_immunecheck = "No"
+    ccc_poly = np.sum([ccc_auto, ccc_neuro, ccc_immune])
+    # most of the symptoms are required, but there is one polythetic criteria, shown here by ccc_poly
+    if np.sum([ccc_fatigue, ccc_reduction, ccc_pem, ccc_sleep, ccc_pain, ccc_cog]) >= 6 and ccc_poly >= 2:
+        ccc_dx = "Met"
+        ccc_msg = "Your responses suggest that you meet the Canadian Consensus Criteria for ME/CFS. " \
+                  "To improve the accuracy of your assessment with more questions continue to the next section."
+    else:
+        ccc_dx = "Not met"
+        ccc_msg = "Your responses do not meet the Canadian Consensus Criteria for ME/CFS."
+
+    # categories = [*feature_list, feature_list[0]]
+    categories = ['Fatigue', 'PEM', 'Sleep', 'Cognitive Impairment', 'Pain', 'Gastro Problems',
+                  'Orthostatic Intolerance', 'Circulatory Problems', 'Immune System', 'Neuroendocrine Problems']
+
+    # converts scores to 100pt scale
+    user_scores = np.multiply(user_scores, 25).tolist()
+    cfsdomains = np.multiply(cfsdomains, 25).tolist()
+
+    # diagnostic message ccc OR iom
+    dx_met = False
+    if ccc_dx == "Met" or iomdxcheck == "Met":
+        short_form_message = "Based on your responses there is a chance you might have MECFS. <br> Please continue to the next section for a more accurate assessment."
+        dx_met = True
+    else:
+        short_form_message = "Based on your responses it does not appear you have MECFS."
+
+    # Creates a figure using the plotly library, which can be dynamically embedded in the HTML page
+    fig = go.Figure(
+        data=[
+            go.Bar(y=user_scores, x=categories, name="Your scores"),
+            go.Bar(y=cfsdomains, x=categories, name="Average ME/CFS scores")],
+        layout=go.Layout(
+            title=go.layout.Title(text='Your scores compared with our dataset of <br>'
+                                       'over 2,400 participants with ME/CFS', x=0.5),
+            showlegend=True, legend=dict(
+                orientation="h",
+                yanchor="bottom",
+                y=1.02,
+                xanchor="right",
+                x=1)))
+    fig.update_layout(yaxis_title='Averaged Frequency and Severity Scores',
+                      xaxis_title='Symptom Domains')
+    fig.update_yaxes(range=[0, 100], dtick=25)
+    # This converts to figure fig to a JSON object so it can be dynamically rendered with javascript on the page
+    graphJSON = json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
+
+    return render_template("results/graph2.html", graphJSON=graphJSON, ccc_msg=ccc_msg, ccc_fatiguecheck=ccc_fatiguecheck,
+                           ccc_pemcheck=ccc_pemcheck, ccc_paincheck=ccc_paincheck, ccc_sleepcheck=ccc_sleepcheck,
+                           ccc_cogcheck=ccc_cogcheck, ccc_autocheck=ccc_autocheck, ccc_immunecheck=ccc_immunecheck,
+                           ccc_neurocheck=ccc_neurocheck, ccc_dx=ccc_dx, ccc_reductioncheck=ccc_reductioncheck, ccc_poly=ccc_poly,
+                           iomfatiguecheck=iomfatiguecheck, iomreductioncheck=iomreductioncheck,
+                           iompemcheck=iompemcheck, iomdxcheck=iomdxcheck, iom_msg=iom_msg,
+                           iomsleepcheck=iomsleepcheck, iomcogcheck=iomcogcheck, iomorthocheck=iomorthocheck,
+                           short_form_message=short_form_message,dx_met=dx_met
+                           )