current version of formulary linker

FormulariesMatching/FormulariesMatching/db_interface.py

@@ -43,6 +43,7 @@ def check_connection(app):
 
 def get_trial_summary(db_conn,nct_id):
     sql_summary ="""
+/*get brief and detailed descriptions*/
 select 
     s.nct_id,
     brief_title ,
@@ -64,22 +65,39 @@ where c.nct_id = %s
 ;
 """
     sql_keywords="""
+/*get keywords*/
 select nct_id ,downcase_name 
 from ctgov.keywords k 
 where k.nct_id = %s
 ;
 """
+
+    sql_indications='''
+select downcase_mesh_term 
+from ctgov.browse_interventions bi 
+where bi.nct_id = %s and mesh_type = 'mesh-list' 
+'''
+    
+
     with db_conn.cursor() as curse:
         curse.execute(sql_summary,[nct_id])
         summary = curse.fetchall()
 
         curse.execute(sql_keywords,[nct_id])
-        keywords = curse.fetchall()
+        keywords = [ x[1] for x in curse.fetchall()]
 
         curse.execute(sql_conditions,[nct_id])
-        conditions = curse.fetchall()
+        conditions = [ x[2] for x in curse.fetchall()]
 
-    return {"summary":summary, "keywords":keywords, "conditions":conditions}
+        curse.execute(sql_indications,[nct_id])
+        indications = [ x[0] for x in curse.fetchall()]
+
+    return {
+            "summary":summary, 
+            "keywords":keywords, 
+            "conditions":conditions,
+            "indications":indications
+            }
 
 
 def get_trials_unmatched_to_formularies(db_conn):
@@ -106,20 +124,40 @@ where nct_id not in (
         select nct_id from "Formularies".uspdc_most_recent_matched_status umrms
         where status is not null
     )
-; '''
-    uspmmg_sql = ''' Null; '''
+    and nct_id in (select distinct nct_id from public.formatted_data_mat fd  )
+;
+'''
+    uspmmg_sql = '''\
+/*
+Get the trials that have not been proceesed.
+First: get most recent matched status
+Second: only include those who have non-null status
+Third: check list of trials against this and remove any of them.
+This leaves unmatched trials.
+*/
+select distinct(nct_id) 
+from "DiseaseBurden".trial_to_icd10 tti 
+where nct_id not in (
+        select nct_id from "Formularies".uspmmg_most_recent_matched_status umrms
+        where status is not null
+    )
+    and nct_id in (select distinct nct_id from public.formatted_data_mat fd  )
+;
+'''
     vaform_sql = ''' Null; '''
 
     #query each formulary, adding data to dict
     formulary_list = dict()
 
-    with db_conn.cursor as curse:
+    with db_conn.cursor() as curse:
 
         # uspdc
         curse.execute(uspdc_sql)
         formulary_list["uspdc"] = curse.fetchall()
 
         # uspmm
+        curse.execute(uspmmg_sql)
+        formulary_list["uspmmg"] = curse.fetchall()
         # vaform
 
     return formulary_list

FormulariesMatching/FormulariesMatching/matching.py

@@ -12,9 +12,11 @@ import FormulariesMatching.uspdc_db as uspdc
 import FormulariesMatching.uspmmg_db as uspmmg
 import FormulariesMatching.vaform_db as vaform
 
+import re
+
 FORMULARIES = {
         "USP DC":uspdc,
-#        "USP MMG":uspmmg,
+       "USP MMG":uspmmg,
 #        "VA Formulary":vaform,
         }
 
@@ -28,10 +30,14 @@ def get_remaining_trials():
     db_conn = get_db()
 
     #get list of trials
-    connection_valid = get_trials_unmatched_to_formularies(db_conn)
+    unmatched_trials = get_trials_unmatched_to_formularies(db_conn)
+    unmatched_trials_list = list(set([  x[0] for y in unmatched_trials for x in unmatched_trials[y]] ))    
 
     #return html
-    return connection_valid
+#    return {"formularies":unmatched_trials,"nctids":nctid_list}
+    return render_template('formulary_index.html', 
+                           unmatched_trials=unmatched_trials_list,
+                           )
 
 
 @bp.route("/<nct_id>", methods=['GET',"POST"])
@@ -62,8 +68,36 @@ def match_trial_to_formulary_groups(nct_id):
                                )
 
     elif request.method == "POST":
-        pass
-        #build array of data to insert
+        
+        #For each Formulary
+        translation={"('":None,"')":None}
+        
+        for key in request.form.keys():
+            match key.split("|"):
+                case ["select_box", formulary]:
+                    #parse data
+                    result = request.form["select_box|{}".format(formulary)]
+                    if result == 'difficult':
+                        FORMULARIES[formulary].insert_match(db_conn,nct_id,None,None,'difficult')
+                    else:
+                        category,uspclass = [re.sub("['\(\)]","",x).strip() for x in result.split("', '")]
+
+                        FORMULARIES[formulary].insert_match(db_conn,nct_id,category,uspclass,'accepted')
+
+                    
+                case ["check_box", data]:
+                    formulary_trial,category,uspclass =  [re.sub("['\(\)]","",x).strip() for x in data.split("', '")]
+                    formulary,_ = formulary_trial.split(",")
+                    #Insert data
+
+                    FORMULARIES[formulary].insert_match(db_conn,nct_id,category,uspclass,'accepted')
+
+                case _:
+                    return 400
+
+        return redirect(url_for("formularies.get_remaining_trials"))
+                    
+
 
     else:
         raise Exception("HTTP method <{}> not implemented".format(request.method))

FormulariesMatching/FormulariesMatching/templates/formulary_index.html

@@ -8,16 +8,14 @@
 
 <h2>Unlinked Trials</h2>
 
-<table>
-<th>Trials</th>
-{% for trial in unlinked_trials %}
-<tr><td>
-    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
-        {{ trial [0] }}
+<ul>
+	{% for trial in unmatched_trials %}
+	<li>	    <a href="{{ url_for('formularies.match_trial_to_formulary_groups', nct_id=trial ) }}">
+		{{ trial }}
 	    </a> 
-</td></tr> 
-{% endfor %}
-</table>
+	 </li>
+	{% endfor %}
+</ul>
 
 <h2>Linked Trials</h2>
 

FormulariesMatching/FormulariesMatching/templates/trial_formularies.html

@@ -10,18 +10,75 @@
 
 {% block content %}
 
-Based on the drugs associated with a trial,
-the following are the formulary group suggestions.
+<div class=trial_summary>
+<h3> Trial Summary </h3>
+<table>
+	<tr>
+	<th>Short Title</th>
+	<td>{{ summary['summary'][0][1] }}</td>
+	</tr>
+	<tr>
+	<th>Complete Title</th>
+	<td>{{ summary['summary'][0][2] }}</td>
+	</tr>
+	<tr>
+	<th>Summary</th>
+	<td>{{ summary['summary'][0][3] }}</td>
+	</tr>
+	<tr>
+	<th>Summary 2</th>
+	<td>{{ summary['summary'][0][4] }}</td>
+	</tr>
+	<tr>
+	<th>Indicated Drugs</th>
+	<td>
+		<ul>
+		{% for drug in  summary['indications'] %}
+		<li>
+			<a 
+				href="https://www.drugs.com/search.php?searchterm={{drug}}"
+				target="_blank"
+				>
+				{{drug}}
+			</a>
+		</li>
+		{% endfor %}
+		</ul>
+	</td>
+	</tr>
+	<tr>
+	<th>Conditions</th>
+	<td>
+		<ul>
+		{% for condition in  summary['conditions'] %}
+		<li>
+		    <a 
+		        href="https://www.mayoclinic.org/search/search-results?q={{condition}}"
+			target="_blank"
+			>
+			{{condition}}
+		    </a>
+		</li>
+		{% endfor %}
+		</ul>
+	</td>
+	</tr>
+	<tr>
+	<th>keywords</th>
+	<td>{{ summary['keywords'] }}</td>
+	</tr>
+</table>
+</div>
 
-<form>
+<form method="post">
+<h2>Matching Classes</h2>
 {% for formulary in potential_matches %}
 <div class=formulary_matches>
-<h2>
+<h3>
 {{ formulary }}
-</h2>
+</h3>
 
 <p>
-{% for formulary in potential_matches %}
 
 <table>
 	<tr>
@@ -36,7 +93,7 @@ the following are the formulary group suggestions.
 		<td> <input 
 			type="checkbox"
 			id="{{ formulary,row }}" 
-			name={{ formulary,row }} 
+			name="check_box|{{ formulary,row }}"
 			value="selected"> 
 		</td>
 		<!-- add checkbox here -->
@@ -47,22 +104,21 @@ the following are the formulary group suggestions.
 </p>
 <p>
 If you've determined it belongs to another class
-<select name="{{ formulary }}-select_box" id="{{ formularay }}-select_box">
+<select name="select_box|{{ formulary }}" id="{{ formularay }}-select_box">
 	<option disabled selected value> -- select an option -- </option>
 	<option value="difficult">
 		Difficult to choose
 	</option>
 
 	{% for option in class_lists[formulary] %}
-	<option value={{ (option[0],option[1]) }}>
-		Category:{{ option[0] }} Class:{{ option[1] }} 
+	<option value="{{ (option[0],option[1]) }}">
+		Cat:{{ option[0] }} Class:{{ option[1] }} 
 		<!-- FIX this is really hard to read -->
 		<!-- FIX try to add opgroups? -->
 	</option>
 	{% endfor %}
 
 </select>
-{% endfor %}
 
 {% endfor %}
 

FormulariesMatching/FormulariesMatching/uspdc_db.py

@@ -32,7 +32,7 @@ def get_groups_per_nctid(db_conn, nct_id):
     '''
     pass
     sql = '''\
-select * from "Formularies".trial_to_uspdc_category_class ttucc 
+select * from "Formularies".uspdc_trial_to_category_class ttucc 
 where nct_id = %(nctid)s
 ;
 '''
@@ -43,5 +43,19 @@ where nct_id = %(nctid)s
         return curse.fetchall()
 
 
-def store_trial_to_formulary_group_matches():
-    pass
+def insert_match(db_conn, nct_id, category,uspclass,status):
+    sql = '''\
+INSERT INTO "Formularies".uspdc_matching 
+VALUES
+(
+    %(nct_id)s
+    ,%(category)s
+    ,%(uspclass)s
+    ,%(status)s
+    ,NOW()
+)
+;
+'''
+    with db_conn.cursor() as curse:
+        curse.execute(sql, {"nct_id":nct_id, "category":category, "uspclass":uspclass, "status":status} )
+    db_conn.commit()

FormulariesMatching/FormulariesMatching/uspmmg_db.py

@@ -13,23 +13,50 @@ def get_all_formulary_groups(db_conn):
     '''
     sql = '''\
 select distinct "USP Category", "USP Class"
-from "Formularies".usp_dc ud 
+from "Formularies".usp_mmg ud 
 order by "USP Category", "USP Class" 
 ;
 '''
-    
     #query
     with db_conn.cursor() as curse:
         curse.execute(sql)
         return curse.fetchall()
     
-def get_formulary_groups_per_NCTID(db_conn, nct_id):
+
+    
+
+def get_groups_per_nctid(db_conn, nct_id):
     '''
     Get the list of formulary groups associated with
     the drugs found in a trial identified by NCTID
     '''
     pass
+    sql = '''\
+select * from "Formularies".uspmmg_trial_to_category_class ttucc 
+where nct_id = %(nctid)s
+;
+'''
 
+    #query
+    with db_conn.cursor() as curse:
+        curse.execute(sql, {"nctid":nct_id})
+        return curse.fetchall()
 
-def store_trial_to_formulary_group_matches():
-    pass
+
+
+def insert_match(db_conn, nct_id, category,uspclass,status):
+    sql = '''\
+INSERT INTO "Formularies".uspmmg_matching 
+VALUES
+(
+    %(nct_id)s
+    ,%(category)s
+    ,%(uspclass)s
+    ,%(status)s
+    ,NOW()
+)
+;
+'''
+    with db_conn.cursor() as curse:
+        curse.execute(sql, {"nct_id":nct_id, "category":category, "uspclass":uspclass, "status":status} )
+    db_conn.commit()

FormulariesMatching/start.sh

@@ -1 +1,2 @@
-waitress-serve --port=5000 --call 'Icd10ConditionsMatching:create_app'
+waitress-serve --port=5000 --call 'FormulariesMatching:create_app'
+#flask --app FormulariesMatching run --debug