Reworking perform mapping page/submission/etc

base/application.py

@@ -97,7 +97,7 @@ def gs_static(url, prefix='static'):
 from base.views.data import data_bp
 app.register_blueprint(data_bp, url_prefix='/data')
 
-# Mapping Pages - 
+# Mapping Pages -
 from base.views.mapping import mapping_bp
 app.register_blueprint(mapping_bp, url_prefix='/mapping')
 

base/forms.py

@@ -81,18 +81,44 @@ def total(self):
             total_price += price
         return total_price
 
+import json
+import pandas as pd
+from base.views.api.api_strain import query_strains
+def process_phenotype_data(input_data):
+    try:
+        data = json.loads(input_data)
+    except ValueError as e:
+        raise ValidationError(e.msg)
+    # Read in data
+    headers = data.pop(0)
+    df = pd.DataFrame(data, columns=headers) \
+           .dropna(thresh=1) \
+           .dropna(thresh=1, axis=1)
+    rows, columns = df.shape
+    if rows < 30:
+        raise ValidationError("A minimum of 30 strains are required.")
+
+    # Resolve isotypes
+    #print(df)
+    #print(query_strains(df[['STRAIN']], list_only=True, as_scaler=True))
+    df = df.assign(isotype=[query_strains(x, resolve_isotype=True) for x in df.STRAIN])
+    print(df)
+
+
+
 
 class mapping_submission_form(Form):
     """
         Form for mapping submission
     """
     report_name = StringField('Report Name', [Required(), Length(min=1, max=50)])
     is_public = RadioField('Release', choices=[("True", 'public'), ("False", 'private')])
-    description = TextAreaField('Description', [Length(min=1, max=1000)])
+    description = TextAreaField('Description', [Length(min=0, max=1000)])
     phenotype_data = HiddenField()
 
     def validate_phenotype_data(form, field):
-        pass
+        phenotype_data = form.phenotype_data.data
+        data = process_phenotype_data(phenotype_data)
 
 
 

base/templates/mapping.html

@@ -89,12 +89,12 @@ <h4>DISCLAIMER</h4>
 <div class='row'>
 <br />
 <div class='col-md-10'>
-<div class='well well-compact'><strong>If you are not redirected to a reports page after clicking the submit button, please notify us of the issue via the feedback form.</strong>
-</div>
+    <br />
+<strong>If you are not redirected to a reports page after clicking the submit button, please notify us of the issue via the feedback form.</strong>
 </div>
 <div class='col-md-2'>
 
-            <button type="submit" style="margin-top: 15px;" class="btn btn-primary btn-lg submit" disabled>Submit</button>
+            <button type="submit" style="margin-top: 15px;" class="btn btn-primary btn-lg btn-block submit" disabled>Submit</button>
 
 
 </div>

base/utils/decorators.py

@@ -1,6 +1,6 @@
+import werkzeug
 from functools import wraps
 from flask import request, jsonify
-from logzero import logger
 
 
 def jsonify_request(func):

base/utils/gcloud.py

@@ -16,7 +16,7 @@ def store_item(kind, name, **kwargs):
     ds = google_datastore()
     m = datastore.Entity(key=ds.key(kind, name))
     for key, value in kwargs.items():
-        if type(value) == dict:
+        if isinstance(value, dict):
             m[key] = 'JSON:' + json.dumps(value)
         else:
             m[key] = value

base/views/api/api_strain.py

@@ -2,37 +2,59 @@
 from base.models2 import strain_m
 from base.application import app
 from base.utils.decorators import jsonify_request
+from sqlalchemy import or_
 
 
 @app.route('/api/strain/')
 @app.route('/api/strain/<string:strain_name>')
 @app.route('/api/strain/isotype/<string:isotype_name>')
 @jsonify_request
-def query_strains(strain_name=None, isotype_name=None, release=None, list_only=False):
+def query_strains(strain_name=None, isotype_name=None, release=None, all_strain_names=False, resolve_isotype=False):
     """
         Return the full strain database set
 
         strain_name - Returns data for only one strain
         isotype_name - Returns data for all strains of an isotype
         release - Filters results released prior to release data
-        list_only - Return list of strains only (internal use).
+        all_strain_names - Return list of all possible strain names (internal use).
+        resolve_isotype - Use to search for strains and return their isotype
     """
     base_query = strain_m.query
     if release:
         base_query = base_query.filter(strain_m.release <= release)
-
     if strain_name:
-        results = base_query.filter(strain_m.strain == strain_name).first()
+        results = base_query.filter(or_(strain_m.previous_names.like(f"%{strain_name}|%"),
+                                        strain_m.previous_names.like(f"%,{strain_name}|"),
+                                        strain_m.previous_names.like(f"%{strain_name}"),
+                                        strain_m.previous_names == strain_name,
+                                        strain_m.strain == strain_name)).first()
     elif isotype_name:
         results = base_query.filter(strain_m.isotype == isotype_name).all()
     else:
         results = base_query.all()
 
-    if list_only:
-        results = [x.strain for x in results]
+    if all_strain_names:
+        previous_strain_names = sum([x.previous_names.split("|") for x in results if x.previous_names], [])
+        results = [x.strain for x in results] + previous_strain_names
+    if resolve_isotype:
+        if results:
+            print(results, "RESULTS")
+            return results.isotype
     return results
 
 
+def resolve_strain(query):
+    """
+        Resolve train name
+    """
+
+    base_query.query.filter(or_(strain_m.previous_names.like(f"%{strain_name},%"),
+                              strain_m.previous_names.like(f"%,{strain_name},"),
+                              strain_m.previous_names.like(f"%{strain_name}",
+                              strain_m.previous_names == strain_name,
+                              strain_m.strain == strain_name))).first()
+
+
 @app.route('/api/isotype')
 @jsonify_request
 def get_isotypes(known_origin=False, list_only=False):

base/views/mapping.py

@@ -4,8 +4,6 @@
 import os
 import time
 
-from base.application import app, cache
-
 from base.utils.email import send_email, MAPPING_SUBMISSION_EMAIL
 
 from base.application import autoconvert
@@ -52,7 +50,7 @@ def mapping():
     form = mapping_submission_form(request.form)
 
     VARS = {'title': 'Perform Mapping',
-            'strain_list': query_strains(list_only=True),
+            'strain_list': query_strains(all_strain_names=True),
             'form': form}
 
     if form.validate_on_submit():

base/views/primary.py

@@ -6,8 +6,7 @@
 
 
 """
-import os
-from flask import render_template, url_for, request, redirect, Blueprint, session
+from flask import render_template, url_for, request, redirect, Blueprint
 from base.utils.text_utils import render_markdown
 from base.utils.data_utils import sorted_files
 from datetime import datetime
@@ -18,14 +17,17 @@
 primary_bp = Blueprint('primary',
                        __name__)
 
-# Homepage
+
 @primary_bp.route('/')
 def primary():
+    """
+        The home page
+    """
     page_title = "Caenorhabditis elegans Natural Diversity Resource"
     files = sorted_files("base/static/content/news/")
     VARS = {'page_title': page_title,
             'files': files}
-    #latest_mappings = list(report.filter(report.release == 0, trait.status == "complete").join(trait).order_by(
+    # latest_mappings = list(report.filter(report.release == 0, trait.status == "complete").join(trait).order_by(
     #    trait.submission_complete.desc()).limit(5).select(report, trait).distinct().dicts().execute())
     return render_template('primary/home.html', **VARS)
 
@@ -39,9 +41,10 @@ def reroute_software():
 @primary_bp.route("/news/")
 @primary_bp.route("/news/<filename>/")
 def news_item(filename=""):
+    """
+        News
+    """
     files = sorted_files("base/static/content/news/")
-    # sorts the thing in the right order on the webpage 
-    # after clicking on the server
     if not filename:
         filename = files[0].strip(".md")
     title = filename[11:].strip(".md").replace("-", " ")
@@ -51,14 +54,16 @@ def news_item(filename=""):
 @primary_bp.route("/help/")
 @primary_bp.route("/help/<filename>/")
 def help_item(filename=""):
+    """
+        Help
+    """
     files = ["FAQ", "Variant-Browser", "Variant-Prediction", "Methods", "Software", "Change-Log"]
     if not filename:
         filename = "FAQ"
     title = filename.replace("-", " ")
     return render_template('help_item.html', **locals())
 
 
-
 @primary_bp.route('/feed.atom')
 def feed():
     """
@@ -90,4 +95,3 @@ def outreach():
 def contact():
     title = "Contact Us"
     return render_template('contact.html', **locals())
-

tests/test_api.py

@@ -5,5 +5,5 @@
 from base.views.api import *
 
 
-def test_one():
+def test_function():
     assert 1 == 1