Merge pull request #46 from DePaul-CCR/main

v0.81

docs/dsqitems_and_routes_map.txt

@@ -22,19 +22,19 @@ Remember36comp: '/remember' <-> screener_views.page4 | remember | "Problems reme
 #short_form (+11 qs)
 Soreness15comp: '/short_form/soreness' <-> short_form.expem1 | sore | "Next day soreness or fatigue after non-strenuous, everyday activities"
 Difficulty37comp: '/short_form/attention' <-> short_form.excog1 | attention | "Difficulty paying attention for a long period of time"
-Musclepain25comp: '/short_form/musclepain' <-> short_form.musclepain | "Pain or aching in your muscles"
-Bloating29comp: '/short_form/bloating' <-> short_form.bloating
-Bowel46comp: '/short_form/bowel' <-> short_form.bowel
-Unsteady48comp: '/short_form/unsteady' <-> short_form.unsteady
-Limbs56comp: '/short_form/cold_limbs' <-> short_form.cold_limbs
+Musclepain25comp: '/short_form/musclepain' <-> short_form.musclepain | muscle | "Pain or aching in your muscles"
+Bloating29comp: '/short_form/bloating' <-> short_form.bloating | bloat | "Bloating"
+Bowel46comp: '/short_form/bowel' <-> short_form.bowel | bowel | "Irritable bowel problems"
+Unsteady48comp: '/short_form/unsteady' <-> short_form.unsteady | unsteady | "Feeling unsteady on your feet, like you might fall"
+Limbs56comp: '/short_form/cold_limbs' <-> short_form.cold_limbs | limbs | "Cold limbs (e.g., arms, legs, hands)"
 Hot58comp: '/short_form/hot_cold' <-> short_form.hot_cold | hot | "Feeling hot or cold for no reason"
-Flu65comp: '/short_form/flu' <-> short_form.flu
+Flu65comp: '/short_form/flu' <-> short_form.flu | flu | "Flu-like symptoms"
 Smells66comp: '/short_form/smells' <-> short_form.smells | smell | "Some smells, foods, medications, or chemicals make you feel sick"
 Reduction97: '/short_form/reduction' <-> short_form.reduction
 '/short_form/short_form_dx' <-> short_form.graph2
 
-#dsq (+41 qs)
-Viral98: '/viral' <-> viral
+#dsq (+42 qs)
+Viral98: '/viral' <-> viral | viral |  Do you experience frequent viral infections with prolonged recovery periods?
 Heavy14comp: '/heavy' <-> expem3 | heavy | "Dead, heavy feeling after starting to exercise"
 Mental16comp: '/mentally' <-> expem4 | mental | "Mentally tired after the slightest effort"
 Drained18comp: '/drained' <-> expem2 | drained | "Physically drained or sick after mild activity"
@@ -43,12 +43,12 @@ Falling21comp: '/falling' <-> exsleep3 | fall | "Problems falling asleep"
 Staying22comp: '/staying' <-> exsleep1 | stay | "Problems staying asleep"
 Early23comp: '/early' <-> early | early | "Waking up early in the morning (e.g. 3am)"
 Allday24comp: '/allday' <-> exsleep4 | allday | "Sleep all day and stay awake all night"
-Jointpain26comp: '/jointpain' <-> jointpain
-Eyepain27comp: '/eyepain' <-> eyepain
-Chestpain28comp: '/chestpain' <-> chestpain
-Stomach30comp: '/stomach' <-> stomach
-Headaches31comp: '/headaches' <-> headaches
-Twitches32comp: '/twitches' <-> twitches
+Jointpain26comp: '/jointpain' <-> jointpain | jointpain | "Pain/stiffness/tenderness in more than one joint without swelling or redness"
+Eyepain27comp: '/eyepain' <-> eyepain | eyepain | "Eye pain"
+Chestpain28comp: '/chestpain' <-> chestpain | chestpain | "Chest pain"
+Stomach30comp: '/stomach' <-> stomach | stomach | "Abdomen/stomach pain"
+Headaches31comp: '/headaches' <-> headaches | headaches | "Headaches"
+Twitches32comp: '/twitches' <-> twitches | twitches | "Muscle twitches"
 Weakness33comp: '/weakness' <-> weakness | weak | "Muscle weakness"
 Noise34comp: '/noise' <-> noise | noise | "Sensitivity to noise"
 Lights35comp: '/lights' <-> lights | lights | "Sensitivity to bright lights"
@@ -59,22 +59,23 @@ Unable41comp: '/vision' <-> vision | vision | "Unable to focus vision and/or att
 Depth42comp: '/depth' <-> depth | depth | "Loss of depth perception"
 Slowness43comp: '/slowness' <-> slowness | slow | "Slowness of thought"
 Absent44comp: '/absent' <-> absent | absent | "Absent-mindedness or forgetfulness"
-Bladder45comp: '/bladder' <-> bladder
-Nausea47comp: '/nausea' <-> nausea
+Bladder45comp: '/bladder' <-> bladder | bladder | "Bladder problems"
+Nausea47comp: '/nausea' <-> nausea | nausea | "Nausea"
 Shortness49comp: '/shortness' <-> shortness | short | "Shortness of breath or trouble catching your breath"
-Dizzy50comp: '/dizzy' <-> dizzy
+Dizzy50comp: '/dizzy' <-> dizzy | dizzy | "Dizziness or fainting"
 Irregular51comp: '/heart' <-> heart | heart | "Irregular heart beats"
 Weight52comp: '/weight' <-> weight | weight | "Losing or gaining weight without trying"
 Appetite53comp: '/appetite' <-> appetite
-Sweating54comp: '/sweating' <-> sweating
-Night55comp: '/night' <-> night
-Chills57comp: '/chills' <-> chills
-HTemp59comp: '/hitemp' <-> hitemp
-LTemp60comp: '/lotemp' <-> lotemp
-Alcohol61comp: '/alcohol' <-> alcohol
-SoreThroat62comp: '/throat' <-> throat
-LympthNodes63comp: '/lymphnodes' <-> lymphnodes
-Fever64comp: '/fever' <-> fever
+Sweating54comp: '/sweating' <-> sweating | sweat | "Sweating hands"
+Night55comp: '/night' <-> night | night | "Night sweats"
+Chills57comp: '/chills' <-> chills | chills | "Feeling chills or shivers"
+HTemp59comp: '/hitemp' <-> hitemp | hitemp | "Feeling like you have a high temperature"
+LTemp60comp: '/lotemp' <-> lotemp | lotemp | "Feeling like you have a low temperature"
+Alcohol61comp: '/alcohol' <-> alcohol | alcohol | "Alcohol intolerance"
+SoreThroat62comp: '/throat' <-> throat | throat | "Sore throat"
+LympthNodes63comp: '/lymphnodes' <-> lymphnodes | lymphnodes | "Tender/sore lymph nodes"
+Fever64comp: '/fever' <-> fever | fever | "Fever"
+Intolerant99: '/intolerant' <-> intolerant | intolerant | "Are you intolerant of extremes of temperatures (when it is extremeley hot or cold)?
 '/dsq_dx' <-> graph3
 
 #other

main.py

@@ -705,7 +705,6 @@ def chills():
 @app.route('/hitemp', methods=['post', 'get'])
 def hitemp():
     global end
-
     form = FlaskForm()
     if request.method == "POST":
         hitempf = request.form.get("hitempf")
@@ -723,7 +722,6 @@ def hitemp():
 @app.route('/lotemp', methods=['post', 'get'])
 def lotemp():
     global end
-
     form = FlaskForm()
     if request.method == "POST":
         lotempf = request.form.get("lotempf")
@@ -741,7 +739,6 @@ def lotemp():
 @app.route('/alcohol', methods=['post', 'get'])
 def alcohol():
     global end
-
     form = FlaskForm()
     if request.method == "POST":
         alcoholf = request.form.get("alcoholf")
@@ -800,12 +797,23 @@ def fever():
         if feverf is not None and fevers is not None:
             session["feverf"] = feverf
             session["fevers"] = fevers
-            session['pagenum'] += 1
-            return redirect(url_for("graph3"))
+            return redirect(url_for("intolerant"))
         else:
             return render_template("dsq/fever64.html", message=message, pagenum=session['pagenum'])
     return render_template("dsq/fever64.html", message='', pagenum=session['pagenum'])
 
+@app.route('/intolerant', methods=['post', 'get'])
+def intolerant():
+    msg_intolerant = "Please select one of the options before continuing"
+    if request.method == 'POST':
+        intolerant = request.form.get('intolerant')
+        if intolerant is not None:
+            session['intolerant'] = intolerant
+            return redirect(url_for('graph3'))
+        else:
+            return render_template("dsq/intolerant99.html", message=msg_intolerant, pagenum=session['pagenum'])
+    return render_template('dsq/intolerant99.html', message='', pagenum=session['pagenum'])
+
 @app.route('/dsq_dx', methods=['get'])
 def graph3():
     return dsq_utils.dsq_diagnose()

utils/back_function.py

@@ -65,7 +65,8 @@ def previous_page(current_route):
 '/throat',
 '/lymphnodes',
 '/fever',
+'/intolerant',
 '/dsq_dx',
 '/about',
 '/aboutmecfs'
-)
+)

utils/dsq_utils.py

@@ -8,7 +8,7 @@
 # see dsqitems_and_routes_map.txt for info on each section of the screener
 
 def dsq_diagnose():
-    # IOM assessment
+    #---IOM Scoring----------------------------
     iomfatiguecheck = "No"
     iomreductioncheck = "No"
     iompemcheck = "No"
@@ -52,13 +52,13 @@ def dsq_diagnose():
         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."
+        iom_msg = "Your responses suggest that you meet the IOM criteria for ME/CFS."
         iomdxcheck = "Met"
     else:
-        iom_msg = "Your responses do not meet the IOM Criteria for ME/CFS."
+        iom_msg = "Your responses do not meet the IOM criteria for ME/CFS."
         iomdxcheck = "Not met"
 
-    # Canadian criteria assessment
+    #---CCC Scoring----------------------------
     ccc_dx = False
 
     if get_score('fatiguescoref') >= 2 and get_score('fatiguescores') >= 2:
@@ -178,23 +178,156 @@ def dsq_diagnose():
     else:
         ccc_dx = "Not met"
         ccc_msg = "Your responses do not meet the Canadian Consensus Criteria for ME/CFS."
+
+    #---ME-ICC Scoring----------------------------
+    meicc_sr = "No"
+    meicc_pene = "No"
+    meicc_cognitive = "No"
+    meicc_pain = "No"
+    meicc_sleep = "No"
+    meicc_sensory = "No"
+    meicc_flu = "No"
+    meicc_gastro = "No"
+    meicc_urinary = "No"
+    meicc_sensitivity = "No"
+    meicc_viral = "No"
+    meicc_cardio = "No"
+    meicc_respiratory = "No"
+    meicc_thermo = "No"
+    meicc_temp = "No"
+
+    # substantial reduction in functioning: dsq 97
+    if get_score('reduction') == 1:
+        meicc_sr = "Yes"
+
+    # PENE/PEM: 14-18
+    if (get_score("heavyf") >= 2 and get_score("heavys") >= 2) or (
+        get_score("soref") >= 2 and get_score("sores") >= 2) or (
+        get_score("mentalf") >= 2 and get_score("mentals") >= 2) or (
+        get_score("minexf") >= 2 and get_score("minexs") >= 2) or (
+        get_score("drainedf") >= 2 and get_score("draineds") >= 2):
+        meicc_pene = "Yes"
+
+    # neurcognitive: 36-44
+    if (get_score("rememberf") >= 2 and get_score("remembers") >= 2) or (
+        get_score("attentionf") >= 2 and get_score("attentions") >= 2) or (
+        get_score("wordf") >= 2 and get_score("words") >= 2) or (
+        get_score("understandf") >= 2 and get_score("understands") >= 2) or (
+        get_score("focusf") >= 2 and get_score("focuss") >= 2) or (
+        get_score("visionf") >= 2 and get_score("visions") >= 2) or (
+        get_score("depthf") >= 2 and get_score("depths") >= 2) or (
+        get_score("slowf") >= 2 and get_score("slows") >= 2) or (
+        get_score("absentf") >= 2 and get_score("absents") >= 2):
+        meicc_cognitive = "Yes"
+
+    # pain: 25-28; 31
+    if (get_score("musclef") >= 2 and get_score("muscles") >= 2) or (
+        get_score("jointpainf") >= 2 and get_score("jointpains") >= 2) or (
+        get_score("eyepainf") >= 2 and get_score("eyepains") >= 2) or (
+        get_score("chestpainf") >= 2 and get_score("chestpains") >= 2) or (
+        get_score("headachesf") >= 2 and get_score("headachess") >= 2):
+        meicc_pain = "Yes"
 
-    # diagnostic message true if ccc OR iom
-    if ccc_dx == "Met" or iomdxcheck == "Met":
+    # sleep: 19-24
+    if (get_score("sleepf") >= 2 and get_score("sleeps") >= 2) or (
+        get_score("napf") >= 2 and get_score("naps") >= 2) or (
+        get_score("fallf") >= 2 and get_score("falls") >= 2) or (
+        get_score("stayf") >= 2 and get_score("stays") >= 2) or (
+        get_score("earlyf") >= 2 and get_score("earlys") >= 2) or (
+        get_score("alldayf") >= 2 and get_score("alldays") >= 2):
+        meicc_sleep = "Yes"
+
+    # neurosensory, perceptual, motor: 32-35; 48
+    if (get_score("twitchesf") >= 2 and get_score("twitchess") >= 2) or (
+        get_score("weakf") >= 2 and get_score("weaks") >= 2) or (
+        get_score("noisef") >= 2 and get_score("noises") >= 2) or (
+        get_score("lightsf") >= 2 and get_score("lightss") >= 2) or (
+        get_score("unsteadyf") >= 2 and get_score("unsteadys") >= 2):
+        meicc_sensory = "Yes"
+
+    # flu-like: 62-65
+    if (get_score("throatf") >= 2 and get_score("throats") >= 2) or (
+        get_score("lymphnodesf") >= 2 and get_score("lymphnodess") >= 2) or (
+        get_score("feverf") >= 2 and get_score("fevers") >= 2) or (
+        get_score("fluf") >= 2 and get_score("flus") >= 2):
+        meicc_flu = "Yes"
+
+    # gastrointestinal: 29-30; 46-47
+    if (get_score("bloatf") >= 2 and get_score("bloats") >= 2) or (
+        get_score("stomachf") >= 2 and get_score("stomachs") >= 2) or (
+        get_score("bowelf") >= 2 and get_score("bowels") >= 2) or (
+        get_score("nauseaf") >= 2 and get_score("nauseas") >= 2):
+        meicc_gastro = "Yes"
+
+    # genitourinary: 45
+    if get_score("bladderf") >= 2 and get_score("bladders") >= 2:
+        meicc_urinary = "Yes"
+
+    # sensitivities: 61, 66
+    if (get_score("alcoholf") >= 2 and get_score("alcohols") >= 2) or (
+        get_score("smellf") >= 2 and get_score("smells") >= 2):
+        meicc_sensitivity = "Yes"
+
+    # viral: 98
+    if get_score("viral") == 1:
+        meicc_viral = "Yes"
+
+    # cardio: 50-51
+    if (get_score("dizzyf") >= 2 and get_score("dizzys") >= 2) or (
+        get_score("heartf") >= 2 and get_score("hearts") >= 2):
+        meicc_cardio = "Yes"
+
+    # respiratory: 49
+    if get_score("shortf") >= 2 and get_score("shorts") >= 2:
+        meicc_respiratory = "Yes"
+
+    # thermostatic: 54-60
+    if (get_score("sweatf") >= 2 and get_score("sweats") >= 2) or (
+        get_score("nightf") >= 2 and get_score("nights") >= 2) or (
+        get_score("limbsf") >= 2 and get_score("limbss") >= 2) or (
+        get_score("chillsf") >= 2 and get_score("chillss") >= 2) or (
+        get_score("hotf") >= 2 and get_score("hots") >= 2) or (
+        get_score("hitempf") >= 2 and get_score("hitemps") >= 2) or (
+        get_score("lotempf") >= 2 and get_score("lotemps") >= 2):
+        meicc_thermo = "Yes"
+
+    # temp intollerance: 99
+    if (get_score("intolerant")) == 1:
+        meicc_temp = "Yes"
+
+    meicc_neuro = np.sum([yes_to_one(meicc_cognitive), yes_to_one(meicc_pain), yes_to_one(meicc_sleep), yes_to_one(meicc_sensory)]) >= 3
+    meicc_igg = np.sum([yes_to_one(meicc_flu), yes_to_one(meicc_gastro), yes_to_one(meicc_urinary), yes_to_one(meicc_sensitivity), yes_to_one(meicc_viral)]) >= 3
+    meicc_energy = np.sum([yes_to_one(meicc_cardio), yes_to_one(meicc_respiratory), yes_to_one(meicc_thermo), yes_to_one(meicc_temp)]) >= 1
+
+    if np.sum([yes_to_one(meicc_sr), yes_to_one(meicc_pene), meicc_neuro, meicc_igg, meicc_energy]) == 5:
+        meicc_dx = "Met"
+        meicc_msg = "Your responses suggest that you meet the ME-ICC criteria for ME/CFS."
+    else:
+        meicc_dx = "Not Met"
+        meicc_msg = "Your responses do not meet the ME-ICC criteria for ME/CFS."
+
+    # diagnostic message True if ccc OR iom OR meicc
+    if ccc_dx == "Met" or iomdxcheck == "Met" or meicc_dx == "Met":
         dsq_message = "Based on your responses there is a chance you might have MECFS. <br> Please consult with your doctor for next steps."
     else:
         dsq_message = "Based on your responses it does not appear you have MECFS."
 
     graphJSON = dsq_graph()
 
-    return render_template("results/graph3.html", graphJSON=graphJSON,
+    return render_template("results/graph3.html", graphJSON=graphJSON, dsq_message=dsq_message, 
                            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, dsq_message=dsq_message)
+                           iomsleepcheck=iomsleepcheck, iomcogcheck=iomcogcheck, iomorthocheck=iomorthocheck,
+                           meicc_sr=meicc_sr, meicc_pene=meicc_pene, meicc_cognitive=meicc_cognitive, meicc_pain=meicc_pain, 
+                           meicc_sleep=meicc_sleep, meicc_sensory=meicc_sensory, meicc_flu=meicc_flu,
+                           meicc_gastro=meicc_gastro, meicc_urinary=meicc_urinary, meicc_sensitivity=meicc_sensitivity, 
+                           meicc_viral=meicc_viral, meicc_cardio=meicc_cardio, meicc_respiratory=meicc_respiratory,
+                           meicc_thermo=meicc_thermo, meicc_temp=meicc_temp, meicc_energy=meicc_energy,  meicc_msg=meicc_msg,
+                           meicc_igg=meicc_igg, meicc_neuro=meicc_neuro, meicc_dx=meicc_dx)
 
 def dsq_graph():
     fatigue_score = (get_score("fatiguescoref") + get_score("fatiguescores")) / 2
@@ -264,4 +397,9 @@ def dsq_graph():
     fig.update_layout(yaxis_title='Averaged Frequency and Severity Scores',
                       xaxis_title='Symptom Domains')
     fig.update_yaxes(range=[0, 100], dtick=25)
-    return json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
+    return json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
+
+def yes_to_one(domain_result):
+    if domain_result == "Yes":
+        return 1
+    return 0

utils/short_form_utils.py

@@ -37,11 +37,11 @@ def short_form_diagnose():
         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" \
+        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."
+        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