remove unused code; clean up __init__

.travis.yml

@@ -7,7 +7,7 @@ cache:
 before_install:
 - openssl aes-256-cbc -K $encrypted_d05b1deeaa37_key -iv $encrypted_d05b1deeaa37_iv
   -in client-secret.json.enc -out client-secret.json -d
-- export VERSION=version-1-1-0
+- export VERSION=version-1-1-1
 - pip install --upgrade pip
 - mkdir -p lib
 install:

cendr/__init__.py

@@ -1,18 +1,16 @@
+import json
+import os
+import time
+import re
+import requests
+import yaml
 from flask import Flask, g
 from peewee import *
 from flask_restful import Api
 from flask_debugtoolbar import DebugToolbarExtension
 from datetime import date
 from flask_cache import Cache
-from jinja2 import contextfilter
-import json
-import yaml
-import os
 from gcloud import datastore
-import MySQLdb
-import _mysql
-import requests
-import time
 
 
 # Caching
@@ -24,6 +22,8 @@
 releases = ["20170531",
             "20160408"]
 
+app.config['CURRENT_RELEASE'] = releases[0]
+
 
 def get_vcf(release = releases[0]):
     return "http://storage.googleapis.com/elegansvariation.org/releases/{release}/WI.{release}.vcf.gz".format(release=release)
@@ -35,19 +35,6 @@ def get_ds():
             g.ds = datastore.Client(project="andersen-lab")
         return g.ds
 
-def get_google_sheet():
-    with app.app_context():
-        if not hasattr(g, 'gc'):
-            import gspread
-            from oauth2client.service_account import ServiceAccountCredentials
-            ds = get_ds()
-            sa = ds.get(ds.key("credential", "service_account"))
-            sa = json.loads(sa["json"])
-            scope = ['https://spreadsheets.google.com/feeds']
-            credentials = ServiceAccountCredentials.from_json_keyfile_dict(sa, scope)
-            gc = gspread.authorize(credentials)
-            g.gc = gc
-        return g.gc
 
 ds = get_ds()
 
@@ -104,15 +91,16 @@ def autoconvert(s):
             pass
     return s
 
-class CustomEncoder(json.JSONEncoder):
 
+class CustomEncoder(json.JSONEncoder):
     def default(self, o):
         if type(o) == decimal.Decimal:
             return float(o)
         if isinstance(o, datetime.date):
             return str(o)
         return super(CustomEncoder, self).default(o)
 
+
 if os.getenv('HOME') == "/root":
     # Running on server
     # cache = Cache(app, config={'CACHE_TYPE': 'gaememcached'})
@@ -122,7 +110,9 @@ def default(self, o):
     app.config["debug"] = False
     from flask_sslify import SSLify
     # Ignore leading slash of urls; skips must use start of path
-    sslify = SSLify(app, skips=['strains/global-strain-map', '.well-known', 'cronmapping'])
+    sslify = SSLify(app, skips=['strains/global-strain-map',
+                                '.well-known',
+                                'cronmapping'])
 else:
     # Running locally
     cache = Cache(app, config={'CACHE_TYPE': 'simple'})
@@ -132,20 +122,37 @@ def default(self, o):
     toolbar = DebugToolbarExtension(app)
 
 
-version = [x for x in yaml.load(open(".travis.yml", 'r').read())['before_install'] if 'VERSION' in x][0].split("=")[1]
-app.config['version'] = version.split(".")[0].replace("-",".").replace("version.","")
-app.config["TEMPLATE_AUTO_RELOAD"] = True
+version = re.search("VERSION=version-(.*)\n", open(".travis.yml", 'r').read()) \
+            .group(1) \
+            .replace('-', '.')
+
+app.config['VERSION'] = version
+app.config['TEMPLATE_AUTO_RELOAD'] = True
 api = Api(app)
 app.config['SECRET_KEY'] = os.getenv("SECRET_KEY")
 app.config['DEBUG_TB_INTERCEPT_REDIRECTS'] = False
 
+
+def get_google_order_sheet():
+    with app.app_context():
+        if not hasattr(g, 'gc'):
+            import gspread
+            from oauth2client.service_account import ServiceAccountCredentials
+            ds = get_ds()
+            sa = ds.get(ds.key("credential", "service_account"))
+            sa = json.loads(sa["json"])
+            scope = ['https://spreadsheets.google.com/feeds']
+            credentials = ServiceAccountCredentials.from_json_keyfile_dict(sa, scope)
+            gc = gspread.authorize(credentials)
+            g.gc = gc
+        return gc.open_by_key("1BCnmdJNRjQR3Bx8fMjD_IlTzmh3o7yj8ZQXTkk6tTXM").worksheet("orders")
+
+
 def add_to_order_ws(row):
     """
         Stores order info in a google sheet.
     """
-    gc = get_google_sheet()
-    orders = gc.open_by_key("1BCnmdJNRjQR3Bx8fMjD_IlTzmh3o7yj8ZQXTkk6tTXM")
-    ws = orders.worksheet("orders")
+    ws = get_google_order_sheet()
     index = sum([1 for x in ws.col_values(1) if x]) + 1
 
     header_row = filter(len, ws.row_values(1))
@@ -159,10 +166,9 @@ def add_to_order_ws(row):
     row = map(str, row)
     ws.insert_row(values, index)
 
+
 def lookup_order(invoice_hash):
-    gc = get_google_sheet()
-    orders = gc.open_by_key("1BCnmdJNRjQR3Bx8fMjD_IlTzmh3o7yj8ZQXTkk6tTXM")
-    ws = orders.worksheet("orders")
+    ws = get_google_order_sheet()
     find_row = ws.findall(invoice_hash)
     if len(find_row) > 0:
         row = ws.row_values(find_row[0].row)

cendr/models.py

@@ -200,19 +200,6 @@ class Meta:
             )
 
 
-class tajimaD(Model):
-    CHROM = CharField(index=True)
-    BIN_START = IntegerField(index=True)
-    BIN_END = IntegerField(index=True)
-    N_Sites = IntegerField(index=True)
-    N_SNPs = IntegerField(index=True)
-    TajimaD = FloatField(index=True)
-
-    class Meta:
-        database = db
-        db_table = "WI_{current_build}_tajimad".format(current_build = current_build)
-
-
 class wb_gene(Model):
     CHROM = CharField(index = True, max_length = 5)
     start = IntegerField(index = True)
@@ -246,13 +233,3 @@ class wb_orthologs(Model):
     method = CharField(index=True) # Method used to assign ortholog
     class Meta:
         database = db
-
-def autoconvert(s):
-    if s is None or s == "" or s == "NA":
-        return None
-    for fn in (float, int):
-        try:
-            return fn(s)
-        except ValueError:
-            pass
-    return s

cendr/static/content/help/Change-Log.md

@@ -2,6 +2,17 @@
 
 --- 
 
+### v1.1.1 ()
+
+* Fixed Drawing of the Tajimas D plot on report pages.
+
+### v1.1.0 (2017-06-16)
+
+* A revamped genome browser, which offers the ability to download data in a tab-delimited format (TSV).
+* The release of a larger set of strains (our 2017-05-31 set). The site now has 249 isotypes available, and a fourth set of strains.
+* The Data page has been renamed as the 'releases' page to reflect the fact that our set of genomic data continues to evolve.
+* Many other bug-fixes and minor enhancements.
+
 ### v1.0.9 (2017-01-24)
 
 * Released transposon data.

cendr/templates/_includes/footer.html

@@ -7,7 +7,7 @@
         <div class="col-md-12">
             <div class="panel panel-default">
                 <div class="panel-body text-center">
-                  <small>{{ config.version }}</small>
+                  <small>{{ config.VERSION }}</small>
                 </div>
             </div>
         </div>

cendr/views/api/report_api.py

@@ -27,60 +27,4 @@ def report_by_date(date):
         ) \
         .dicts()
         .execute())
-    return jsonify(data)
-
-
-#class report_progress(Resource):
-#
-#    def post(self, trait_slug, report_slug=None, report_hash=None):
-#        queue = get_queue()
-#        current_status = list(trait.select(trait.status)
-#                              .join(report)
-#                              .filter(trait.trait_slug == trait_slug, ((report.report_slug == report_slug) and (report.release == 0)) | (report.report_hash == report_hash))
-#                              .dicts()
-#                              .execute())[0]["status"]
-#        if trait_slug:
-#            try:
-#                trait_data = [x for x in report_data if x[
-#                    'trait_slug'] == trait_slug[0]]
-#            except:
-#                return Response(response="", status=404, catch_all_404s=True)
-#            title = trait_data["report_name"]
-#            subtitle = trait_data["trait_name"]
-#
-#            if trait_data["release"] == 0:
-#                report_url_slug = trait_data["report_slug"]
-#            else:
-#                report_url_slug = trait_data["report_hash"]
-#        else:
-#
-#            try:
-#                first_trait = list(report_data)[0]
-#            except:
-#                return Response(response="", status=404, catch_all_404s=True)
-#
-#        report_slug = trait_data["report_slug"]
-#        base_url = "https://storage.googleapis.com/cendr/" + report_slug + "/" + trait_slug
-#
-#        report_files = list(storage.Client().get_bucket("cendr").list_blobs(
-#            prefix=report_slug + "/" + trait_slug + "/tables"))
-#        report_files = [os.path.split(x.name)[1] for x in report_files]
-#
-#        report_url = base_url + "/report.html"
-#        report_html = requests.get(report_url).text.replace(
-#            'src="', 'src="' + base_url + "/")
-#
-#        if not report_html.startswith("<?xml"):
-#            report_html = report_html[report_html.find("<body>"):report_html.find("</body")].replace(
-#                "</body", " ").replace("<body>", "").replace('<h1 class="title">cegwas results</h1>', "")
-#        else:
-#            report_html = ""
-#        return Response(response=report_html, status=200, mimetype="application/json")
-#
-#status_urls = ['/api/<string:report_slug>/<string:trait_slug>',
-#                '/api/<string:report_slug>/<string:trait_slug>']
-#
-#
-#api.add_resource(report_progress, status_urls)
-#
-#
+    return jsonify(data)