walker-database/templates/admin.html

{% extends "base.html" %}
{% block content %}
    <link rel="stylesheet"
          href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/11.7.0/styles/default.min.css">
    <script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/11.7.0/highlight.min.js"></script>
    <script>hljs.highlightAll();</script>
    <h1>Admin Dashboard</h1>
    <article>
        <p>Logged in as {{user}}</p>
        <a href="{{url_for('chemical_create')}}">
            <button>
                Add a Chemical
            </button>
        </a>
        <a href="{{url_for('batch_add_request')}}">
            <button>
                Batch Add Chemicals
            </button>
        </a>
        <a href="{{url_for('batch_query_request')}}">
            <button>
                Batch Search Chemicals
            </button>
        </a>
        <h2>Admin Authentication</h2>
        <p>
            Since there is now an admin, only admins can create new admin accounts. You can do so through the <code>/admin/create</code>
            route.
        </p>
        <h2>API Routes</h2>
        <ul>
            <li><code>/chemical/all</code> - returns all chemicals in the database as JSON</li>
            <li><code>/chemical/search</code> - returns JSON for search queries. This endpoint takes GET parameters as follows:
                <ul>
                    <li>mz_min: Minimum M/Z Ratio</li>
                    <li>mz_max: Maximum M/Z Ratio</li>
                    <li>rt_min: Minimum Retention Time</li>
                    <li>rt_max: Maximum Retention Time</li>
                </ul>
            </li>
            <li><code>/chemical/&lt;chemical id&gt;/{view,update,delete}</code> - CRUD endpoints for chemicals.</li>
        </ul>
        <h2>Programmatically adding Chemicals</h2>
        <p>
            You need admin credentials to access the <code>/chemical/create</code> endpoint, so using an HTTP library
            like python's requests library is highly recommended for keeping track of session cookies.
        </p>
        <pre><code class="language-python">
import requests
session = requests.session()
baseurl = "chemicaldb.teidkim.me"
session.post(baseurl + "/admin/login", {"username": (username), "password": (password)})
fields = {
    "chemical_db_id": &lt;db id from another database&gt;,
    "library": (library, is a string),
    "person_name": (name of person who uploaded, string)
    # name, formula, and mass are required fields!
    "metabolite_name": (name of the chemical, is a string),
    "formula": (molecular formula, is a string),
    "mass": (monoisotopic mass, is a float),
    "pubchem_cid": &lt;string&gt;,
    "pubmed_refcount": &lt;integer&gt;
    "standard_class": &lt;string&gt;
    "inchikey": &lt;string&gt;,
    "inchikey14": &lt;string&gt;,
    # final_mz and final_rt are required fields!
    "final_mz": (m/z ratio after experiment, is a float),
    "final_rt": (retention time after experiment, is a float),
    "final_adduct": &lt;string&gt;,
    "final_adduct": &lt;string&gt;,
    "detected_adducts": &lt;string&gt;,
    "adduct_calc_mz": &lt;string&gt;,
    "msms_detected": &lt;string if yes, do not include this field otherwise&gt;
    "msms_purity": &lt;float&gt;
    "date": "YYYY-MM-DD"
}
session.post(baseurl + "/chemical/create", fields)
        </code></pre>
    <h2>Programmatically Searching For Matching Compounds</h2>
    <pre><code class="language-python">
import requests
baseurl = "chemicaldb.teidkim.me"
# initialize parameters

def generate_parameters(mz, mz_range_ppm, rt, rt_range):
    return dict(
      mz_min=(mz - mz_range_ppm/10**6),
      mz_max=(mz + mz_range_ppm/10**6),
      rt_min=(rt - rt_range),
      rt_max=(rt + rt_range)
    )

mz = &lt; theoretical mz ratio &gt;
mz_range_ppm = &lt;threshold the mz value should be in ppm units&gt;
rt = &lt; theoretical retention time &gt;
rt_range = &lt; seconds in which the rt needs to be in &gt;

# make a request to the endpoint.
response = requests.get(baseurl + "/chemical/search", params=generate_parameters(mz, mz_range_ppm, rt, rt_range))
# make sure to include some error handling code.
results = response.json()

# results is a json containing a list of chemicals with the same schema as above.
# There are up to 10 search results per query, so you should write some code to
# determine which result is best.
    </code></pre>

    </article>
{% endblock %}