MRG: more upgrades! (#16)

* add basic uptime script

* fix bugs, add/adjust language

* add some upload tests

* upd gitignore

* upd testing mode

* bump version

Author: ctb

.gitignore

@@ -6,3 +6,5 @@
 *.rocksdb
 chill_filter.egg-info/
 dist/
+build/
+chill-data/

chill_filter_web/__init__.py

@@ -19,7 +19,8 @@
 
 default_settings = dict(
     UPLOAD_FOLDER = os.path.join(os.path.dirname(__file__), '../chill-data'),
-    EXAMPLES_DIR = os.path.join(os.path.dirname(__file__), "examples/")
+    EXAMPLES_DIR = os.path.join(os.path.dirname(__file__), "examples/"),
+    MAX_CONTENT_LENGTH = 10*1000*1000,
 )
 
 
@@ -66,6 +67,8 @@ def create_app():
 ### actual Web site stuff
 ###
 
+
+# handles default index, plus upload of precalculated sketch.
 @app.route("/", methods=["GET", "POST"])
 def index():
     if request.method == "POST":
@@ -95,28 +98,33 @@ def index():
     return render_template("index.html")
 
 
+# handles client-side sketch w/JSON sig
 @app.route("/sketch", methods=["GET", "POST"])
 def sketch():
     if request.method == "POST":
         # check if the post request has the file part
         if "signature" not in request.form:
-            flash("No file part")
+            flash("No file part") # @CTB
             return redirect(request.url)
 
         # take uploaded file and save
         sig_json = request.form["signature"]
         success = False
         filename = f"t{int(time.time())}.sig.gz"
-        outpath = os.path.join(UPLOAD_FOLDER, filename)
+        outpath = os.path.join(app.config['UPLOAD_FOLDER'], filename)
         with gzip.open(outpath, "wt") as fp:
             fp.write(f"[{sig_json}]")
 
         ss = load_sig(outpath)
         if ss:
             # success? build URL & redirect
             md5 = ss.md5sum()[:8]
+            if app.config['TESTING']:
+                return "TESTING MODE: upload successful"
             return redirect(f"/{md5}/{filename}/search")
 
+    print('fallthru')
+
     # default: redirect to /
     return redirect(url_for("index"))
 

chill_filter_web/templates/guide.md

@@ -8,6 +8,8 @@
       {% filter markdownify %}
 # The chill-filter user guide
 
+[Home page](/) | [Frequently Asked questions](/faq)
+
 chill-filter is a rapid sample-screening Web application that comprehensively
 determines the composition of a shotgun sequence data set. It should take
 about 10 seconds to process an uploaded sample.
@@ -20,7 +22,7 @@ You could use it to:
 
 chill-filter will sensitively detect the presence of large genomes
 (500kb and up) at sequencing depths as low as 0.1x. It searches your entire
-sample: it does not select a subset of the data set.
+sample: it does not select a subset of your data.
 
 The main value of chill-filter is that it is fast, sensitive, and
 _comprehensive_. Within the limits of the available reference database,
@@ -38,7 +40,7 @@ data sets (ChIP-seq or ATAC-seq) or RNA data.
 **<font style="color:red">chill-filter is a research service and should not be relied upon for
 clinical diagnostics or confirmatory analyses.</font>**
 
-## What does chill-filter aim to do?
+## What are chill-filter's goals?
 
 chill-filter aims to be a sensitive, specific, and comprehensive
 approach to figuring out what is in your sample. It will always

chill_filter_web/templates/index.html

@@ -8,11 +8,12 @@
         <img src="/static/alembic-small.jpg" align="right">
         <h2 style="margin: 10px">chill-filter: What's in my sample?</h2>
         <p style="margin: 10px">
-          Quite fast sample screening.
+          Quite fast sample screening - see <a href="/guide">user guide</a> and <A href="#examples">examples</a>.
+    <hr style="border-width: 3px; border-color: black">
         </p>
 
       <h4>
-       Choose a large genome or shotgun sequencing FASTA/FASTQ file, and click submit to compress it and send it for screening!
+       Choose a large genome or shotgun sequencing FASTA/FASTQ file, and click submit to compress and screen it!
       </h4>
 
       <div style="margin: 50px">
@@ -45,7 +46,8 @@ <h4>
     <hr style="border-width: 3px; border-color: black">
 
     <main class="container">
-      <h4>Examples:</h4>
+      <a id="examples"></a>
+        <h4>Examples:</h4>
       <ul>
         <li><a href="/example?filename=SRR606249.k51.s100_000.sig.zip">SRR606249: A mock microbial community</a>
         <li><a href="/example?filename=SRR5650070.k51.s100_000.sig.zip">SRR5650070: A human gut metagenome from the iHMP</a>

pyproject.toml

@@ -2,7 +2,7 @@
 name = "chill-filter"
 description = "rapid sample screening for shotgun DNA sequencing data sets"
 readme = "README.md"
-version = "0.3.0"
+version = "0.3.1"
 authors = [
   { name="C. Titus Brown" },
 ]

scripts/check-site.py

@@ -0,0 +1,37 @@
+#! /usr/bin/env python
+import sys
+import argparse
+import requests
+
+
+def main():
+    p = argparse.ArgumentParser()
+    p.add_argument('--host', default='https://chill-filter.sourmash.bio')
+    args = p.parse_args()
+
+    url = args.host + '/'
+    print('getting:', url)
+    r = requests.get(url)
+    assert r.status_code == 200
+    assert '<title>chill-filter sample screening - home page</title>' in r.text
+
+    url = args.host + '/example?filename=SRR606249.k51.s100_000.sig.zip'
+    print('getting:', url)
+    r = requests.get(url)
+    assert r.status_code == 200, r.status_code
+    assert '95.0% (5.1 Gbp)' in r.text
+
+    url = args.host + '/ee6adb3e/SRR606249.k51.s100_000.sig.zip/delete'
+    print('getting:', url)
+    r = requests.get(url)
+    assert r.status_code == 200, r.status_code
+
+    url = args.host + '/example?filename=SRR606249.k51.s100_000.sig.zip'
+    print('getting:', url)
+    r = requests.get(url)
+    assert r.status_code == 200
+    assert '95.0% (5.1 Gbp)' in r.text
+
+
+if __name__ == '__main__':
+    sys.exit(main())

tests/test_basic.py

@@ -118,5 +118,3 @@ def test_sample_download_csv(client):
     data = response.get_data()
     print(data)
     assert data.startswith(b'intersect_bp,f_orig_query,f_match,')
-
-

tests/test_upload.py

@@ -0,0 +1,60 @@
+import os
+import shutil
+import json
+
+import pytest
+
+import sourmash
+from chill_filter_web import utils
+
+
+def test_sample_upload_precalc(app):
+    # test upload of precalculated sketch via POST to /
+    #
+    # NOTE: this does not actually run the search, since there is a precalc
+    # .csv in the test upload directory.
+    with app.app_context():
+        client = app.test_client()
+
+        sigfile = os.path.join(app.config['EXAMPLES_DIR'],
+                               'Bu5.abund.k51.s100_000.sig.zip')
+
+        form_d = dict(sketch=(open(sigfile, 'rb'),
+                              'Bu5.abund.k51.s100_000.sig.zip',
+                              'application/zip'))
+        
+        response = client.post('/', data=form_d,
+                               follow_redirects=True)
+
+
+        print(response.data)
+        assert b'18.5% unknown' in response.data
+
+
+def test_sample_upload_sketch(app):
+    # test upload of client-side sketch via POST to /sketch
+    #
+    # uses testing mode to avoid running the actual search.
+    with app.app_context():
+        client = app.test_client()
+
+        sigfile = os.path.join(app.config['EXAMPLES_DIR'],
+                               'no-matches.sig.zip')
+        ss = utils.load_sig(sigfile)
+        assert ss
+
+        sig_json = sourmash.save_signatures_to_json([ss])
+
+        # this returns an array, and the upload needs a single encoded
+        # signature. So pull off the first element and re-encode.
+        sig2 = json.loads(sig_json)
+        sig2 = sig2[0]
+        sig2_json = json.dumps(sig2)
+
+        # submit!
+        form_d = dict(signature=sig2_json)
+        response = client.post('/sketch', data=form_d,
+                               follow_redirects=True)
+
+        print(response.data)
+        assert b'TESTING MODE: upload successful'