queries with max date

2-5-23.txt

@@ -2,11 +2,11 @@
 
 - Show how to make a network request in R to the server
 - Version Control (what date a compound was added)
-  - createdAt, but configurable.
+  - createdAt, but configurable. DONE
   - Compare the database to the list of compunds and you only want compounds
-    from that date or before?
+    from that date or before? DONE
 
-- Emphasizing Local? - Accessible through a url.
+- Emphasizing Local? - Accessible through a url. DONE, all fields accessible.
 
 - Shiny app
   - Permissions System (revoke, access API keys)

app.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 
+from datetime import date
 from flask import Flask, render_template, session, request, abort, redirect, url_for, jsonify
 from flask_sqlalchemy import SQLAlchemy
 from sqlalchemy import inspect, and_
@@ -69,7 +70,7 @@ class Chemical(db.Model):
     name = db.Column(db.String, nullable=False)
     formula = db.Column(db.String, nullable=False)
     mass = db.Column(db.Float, nullable=False)
-    
+
     pubchem_cid = db.Column(db.Integer)
     pubmed_refcount = db.Column(db.Integer)
     standard_class = db.Column(db.String)
@@ -86,6 +87,7 @@ class Chemical(db.Model):
     msms_detected = db.Column(db.Boolean)
     msms_purity = db.Column(db.Float)
 
+    # serialized into datetime.date
     createdAt = db.Column(db.Date)
 
 
@@ -123,13 +125,15 @@ def admin_create():
     if request.method == "GET":
         return render_template("register.html")
     else:
-        username, pw = request.form.get('username'), request.form.get('password')
+        username, pw = request.form.get(
+            'username'), request.form.get('password')
         if username is None or pw is None:
             return render_template("register.html", fail="Invalid Input.")
         elif db.session.execute(db.select(Admin).filter_by(username=username)).fetchone():
             return render_template("register.html", fail="Username already exists.")
         else:
-            db.session.add(Admin(username=username, password=Admin.generate_password(pw)))
+            db.session.add(
+                Admin(username=username, password=Admin.generate_password(pw)))
             db.session.commit()
             return render_template("register.html", success=True)
 
@@ -137,7 +141,8 @@ def admin_create():
 @app.route('/admin/login', methods=['GET', 'POST'])
 def admin_login():
     if request.method == "POST":
-        username, pw = request.form.get('username', ''), request.form.get('password', '')
+        username, pw = request.form.get(
+            'username', ''), request.form.get('password', '')
         if Admin.authenticate(username, pw):
             return render_template("login.html", success=True)
         else:
@@ -184,7 +189,7 @@ def chemical_create():
 def chemical_update(id: int):
     if not session.get('admin'):
         abort(403)
-    current_chemical:Chemical = Chemical.query.filter_by(id=id).one_or_404()
+    current_chemical: Chemical = Chemical.query.filter_by(id=id).one_or_404()
     dct = object_as_dict(current_chemical)
     if request.method == "POST":
         form = ChemicalForm(**request.form)
@@ -206,7 +211,7 @@ def chemical_update(id: int):
 def chemical_delete(id: int):
     if not session.get('admin'):
         abort(403)
-    current_chemical:Chemical = Chemical.query.filter_by(id=id).one_or_404()
+    current_chemical: Chemical = Chemical.query.filter_by(id=id).one_or_404()
     db.session.delete(current_chemical)
     db.session.commit()
     return render_template("delete_chemical.html", id=id)
@@ -214,7 +219,7 @@ def chemical_delete(id: int):
 
 @app.route("/chemical/<int:id>/view")
 def chemical_view(id: int):
-    current_chemical:Chemical = Chemical.query.filter_by(id=id).one_or_404()
+    current_chemical: Chemical = Chemical.query.filter_by(id=id).one_or_404()
     dct = object_as_dict(current_chemical)
     return render_template("view_chemical.html", id=id, chemical=dct)
 
@@ -223,40 +228,42 @@ def chemical_view(id: int):
 def chemical_all():
     if not session.get('admin'):
         abort(403)
-    result = Chemical.query.all()
+    result: list[Chemical] = Chemical.query.all()
     data = []
     for x in result:
-        data.append({"url": url_for("chemical_view", id=x.id), "name": x.name, "mz": x.final_mz, "rt": x.final_rt})
+        data.append({c.name: getattr(x, c.name) for c in x.__table__.columns})
     return jsonify(data)
 
-@app.route("/chemical/search")
+
+@app.route("/chemical/search", methods=["POST"])
 def search_api():
-    mz_min, mz_max = request.args.get('mz_min'), request.args.get('mz_max')
-    rt_min, rt_max = request.args.get('rt_min'), request.args.get('rt_max')
-    if (mz_min is None and mz_max is None) or (rt_min is None and rt_max is None):
-        return jsonify({"error": "invalid data"}), 400
+    query = request.json
+    if query is None:
+        return jsonify([])
+    for field in query:
+        query[field] = float(query[field])
+    mz_min, mz_max = query.get('mz_min'), query.get('mz_max')
+    rt_min, rt_max = query.get('rt_min'), query.get('rt_max')
+    year_max, month_max, day_max = int(query.get(
+        'year_max')), int(query.get('month_max')), int(query.get('day_max'))
+
     try:
-        if mz_min is not None and mz_max is None:
-            mz_max = float(mz_min) + 3
-        elif mz_max is not None and mz_min is None:
-            mz_min = float(mz_max) - 3
-        if rt_min is not None and rt_max is None:
-            rt_max = float(rt_min) + 3
-        elif rt_max is not None and rt_min is None:
-            rt_min = float(rt_max) - 3
-        mz_min, mz_max = float(mz_min), float(mz_max)
-        rt_min, rt_max = float(rt_min), float(rt_max)
-    except ValueError:
-        return jsonify({"error": "invalid data"}), 400
-
-    mz_filter = and_(mz_max > Chemical.final_mz, Chemical.final_mz > mz_min)
-    rt_filter = and_(rt_max > Chemical.final_rt, Chemical.final_rt > rt_min)
+        mz_filter = and_(mz_max > Chemical.final_mz,
+                         Chemical.final_mz > mz_min)
+        rt_filter = and_(rt_max > Chemical.final_rt,
+                         Chemical.final_rt > rt_min)
+        date_filter = date(year_max, month_max, day_max) >= Chemical.createdAt
+    except ValueError as e:
+        return jsonify({"error": str(e)}), 400
+
     result = Chemical.query.filter(
-               and_(mz_filter, rt_filter)
-            ).limit(10).all()
+        and_(mz_filter, rt_filter, date_filter)
+    ).limit(20).all()
+
     data = []
     for x in result:
-        data.append({"url": url_for("chemical_view", id=x.id), "name": x.name, "mz": x.final_mz, "rt": x.final_rt})
+        data.append({"url": url_for("chemical_view", id=x.id),
+                    "name": x.name, "mz": x.final_mz, "rt": x.final_rt})
     return jsonify(data)
 
 

templates/search.html

@@ -26,28 +26,55 @@
                     mz_max: 0,
                     rt_min: 0,
                     rt_max: 0,
+                    // query parameters for the maximum date possible.
+                    year_max: 2021,
+                    month_max: 1,
+                    day_max: 31,
+                    // results
                     results: [],
                     error: null,
                 }
             },
             methods: {
                 // methods
-                async fetch_data() {
-                    if (!(valid(this.mz_min) && valid(this.mz_max) && valid(this.rt_max) && valid(this.rt_min))) {
-                        return
+                prepare_query() {
+                  // validation
+                  let query = {}
+                  const fields = ["mz_min", "mz_max", "rt_min", "rt_max",
+                  "year_max", "month_max", "day_max"]
+                  for (let i = 0; i < fields.length; i++) {
+                    const field = fields[i];
+                    if (!valid(this[field])) {
+                      console.log(query, field, this[field])
+                      return null;
+                    } else {
+                      query[field] = this[field]
                     }
-                    const url = `/chemical/search?mz_min=${this.mz_min}&mz_max=${this.mz_max}&rt_min=${this.rt_min}&rt_max=${this.rt_max}`
-                    fetch(url).then(res => {
+                  }
+                  return query
+                },
+                async fetch_data() {
+                    const query = this.prepare_query()
+                    if (query === null) return;
+                    const api = `/chemical/search`;
+                    fetch(api, {
+                      method: 'POST',
+                      headers: {
+                        'Content-Type': 'application/json',
+                      },
+                      body: JSON.stringify(query)
+                    }).then(async res => {
                         if (res.status !== 200) {
                             console.log(`Error Status, ${res.status}`)
+                            const json = await res.json()
+                            throw Error(json.error);
                         }
                         return res.json()
                     }).then(json => {
                         this.results = json;
                         this.error = null;
                     }).catch(e => {
-                        console.error(e);
-                        this.error = true;
+                        this.error = e.message;
                     })
                 }
             },
@@ -67,7 +94,7 @@
                     <label for="mz_min">Minimum M/Z Ratio</label>
                 </td>
                 <td>
-                    <input id="mz_min" type="number" name="mz_min" v-model="mz_min" @input="fetch_data()" value="0">
+                    <input id="mz_min" type="number" name="mz_min" v-model="mz_min" value="0">
                 </td>
             </tr>
             <tr>
@@ -75,7 +102,7 @@
                     <label for="mz_min">Maximum M/Z Ratio</label>
                 </td>
                 <td>
-                    <input id="mz_max" type="number" name="mz_max" v-model="mz_max" @input="fetch_data()" value="0">
+                    <input id="mz_max" type="number" name="mz_max" v-model="mz_max" value="0">
                 </td>
             </tr>
             <tr>
@@ -83,7 +110,7 @@
                     <label for="mz_min">Minimum Retention Time</label>
                 </td>
                 <td>
-                    <input id="rt_min" type="number" name="rt_min" v-model="rt_min" @input="fetch_data()" value="0">
+                    <input id="rt_min" type="number" name="rt_min" v-model="rt_min" value="0">
                 </td>
             </tr>
             <tr>
@@ -91,21 +118,32 @@
                     <label for="mz_min">Maximum Retention Time</label>
                 </td>
                 <td>
-                    <input id="rt_max" type="number" name="rt_max" v-model="rt_max" @input="fetch_data()" value="0">
+                    <input id="rt_max" type="number" name="rt_max" v-model="rt_max" value="0">
+                </td>
+            </tr>
+            <tr>
+                <td>
+                    <label for="mz_min">Maximum Date</label>
+                </td>
+                <td>
+                    <input id="year_max" type="number" name="year_max"
+                    v-model="year_max" placeholder="year">
+                    <input id="month_max" type="number" name="month_max"
+                    v-model="month_max" placeholder="month">
+                    <input id="day_max" type="number" name="day_max"
+                    v-model="day_max" placeholder="day">
                 </td>
             </tr>
         </table>
 
-        <!--
         <br>
         <button @click="fetch_data()">Search</button>
-        -->
     </main>
     <hr>
     {% raw %}
     <div id="search">
-        <div v-if="error" style="color: red;">
-            Uh Oh! There is an Error!
+        <div v-if="error !== null" style="color: red;">
+          Uh Oh! There is an Error! {{error}}
         </div>
         <div v-for="result in results">
             <a :href="result.url">
@@ -127,4 +165,4 @@
     {% endraw %}
     </div>
 
-{% endblock %}
+{% endblock %}