From 233d35f23d36c8201db286edb6e4ed46f56d2ed2 Mon Sep 17 00:00:00 2001
From: David Brawand <dbrawand@nhs.net>
Date: Tue, 20 Sep 2016 16:55:34 +0100
Subject: [PATCH] bugfix in genePred reader

---
 run.py                       |  4 +++-
 zippy/templates/index.html   |  6 +++---
 zippy/unittest/data/test.csv |  3 +++
 zippy/views.py               | 33 ++++++++++++---------------------
 zippy/zippy.py               |  6 +++---
 zippy/zippylib/files.py      |  2 ++
 6 files changed, 26 insertions(+), 28 deletions(-)
 create mode 100644 zippy/unittest/data/test.csv

diff --git a/run.py b/run.py
index d0a0f49..494de10 100755
--- a/run.py
+++ b/run.py
@@ -1,4 +1,6 @@
-#!zippyvenv/bin/python
+#!venv/bin/python
+
+'''runs flask development server'''
 
 from zippy import app
 
diff --git a/zippy/templates/index.html b/zippy/templates/index.html
index ea47131..590987e 100755
--- a/zippy/templates/index.html
+++ b/zippy/templates/index.html
@@ -18,7 +18,7 @@ <h3>Batch PCR</h3>
             <h3>Primer Query</h3>
             <form action="/adhoc_design/" method="post" enctype="multipart/form-data">
                 <span class="pop">BED, VCF, GenePred &nbsp</span><input type="file" name="filePath"><br><br>
-                or&nbsp<span class="pop">Chromosome:Start-End:[+-] &nbsp</span><input type="text" name="locus"><br><br>
+                or&nbsp<span class="pop">Chromosome:Start-End:[+-] &nbsp</span><input type="text" name="locus"> and <input type="text" name="gap"><br><br>
                 <input type="checkbox" name="design" value="True" checked>design &nbsp
                 <input type="checkbox" name="deep" value="True">deep search &nbsp
                 <input type="checkbox" name="store" value="True">store<br><br>
@@ -30,7 +30,7 @@ <h3>Primer Query</h3>
         </div>
         <div id="left";>
             <h3>Primer Pair Query</h3>
-            <p>Search by primer pair name or date (yyyy-mm-dd)</p>
+            <p>Name or date (yyyy-mm-dd)</p>
             <form action="/specify_searchname/" method="post" enctype="multipart/form-data">
                 <span class="pop">Search for &nbsp</span><input type="text" name="searchName"><br><br>
                 <input type="submit" id="revSubmit" value="Search">
@@ -40,7 +40,7 @@ <h3>Primer Pair Query</h3>
         </div>
         <div id="right">
             <h3>Storage Location</h3>
-            <p>Upload a batch of primer storage locations as CSV file</p>
+            <p>Update from CSV file (PrimerName,Box,Well)</p>
             <form action="/upload_batch_locations/" method="post" enctype="multipart/form-data">
                 <span class="pop">CSV file &nbsp</span><input type="file" name="locationsheet"><br><br>
                 <input type="submit" id="revSubmit" value="Upload">
diff --git a/zippy/unittest/data/test.csv b/zippy/unittest/data/test.csv
new file mode 100644
index 0000000..fd8dbd2
--- /dev/null
+++ b/zippy/unittest/data/test.csv
@@ -0,0 +1,3 @@
+PrimerName,Box,Well
+MTRR_3_fwd,10,Z9
+MTRR_3_rev,10,A1
diff --git a/zippy/views.py b/zippy/views.py
index 3aefbf8..36e9948 100755
--- a/zippy/views.py
+++ b/zippy/views.py
@@ -21,24 +21,7 @@
 app.config['DOWNLOAD_FOLDER'] = 'results'
 APP_ROOT = os.path.dirname(os.path.abspath(__file__))
 app.config['CONFIG_FILE'] = os.path.join(APP_ROOT, 'zippy.json')
-app.secret_key = 'someKey'
-
-# app.config['CELERY_BROKER_URL'] = 'redis://localhost:6379/0'
-# app.config['CELERY_RESULT_BACKEND'] = 'redis://localhost:6379/0'
-#
-# celery = Celery(app.name, broker=app.config['CELERY_BROKER_URL'])
-# celery.conf.update(app.config)
-#
-# @celery.task(bind=True)
-# def query_zippy(uploadFile):
-#     filename = secure_filename(uploadFile.filename)
-#     print >> sys.stderr, filename
-#     uploadFile.save(os.path.join(app.config['UPLOAD_FOLDER'], filename))
-#     print >> sys.stderr, "file saved to ./uploads/%s" % filename
-#     os.chdir('./app/')
-#     print >> sys.stderr, subprocess.call(['./zippy.py', 'get', '--outfile', outfile, '../uploads/%s'% filename], shell=False)
-#     return "running zippy..."
-
+app.secret_key = 'Zippy is the best handpuppet out there'
 
 def allowed_file(filename):
     return '.' in filename and \
@@ -112,7 +95,12 @@ def adhocdesign():
     locus = request.form.get('locus')
     design = request.form.get('design')
     deep = request.form.get('deep')
+    gap = request.form.get('gap')
     store = request.form.get('store')
+
+    print >> sys.stderr, 'locus', locus
+    print >> sys.stderr, 'gap', gap
+
     # if locus:
     if re.match('\w{1,2}:\d+-\d+',locus) or (uploadFile and allowed_file(uploadFile.filename)):
         # get target
@@ -129,7 +117,10 @@ def adhocdesign():
             config = json.load(conf, object_hook=ascii_encode_dict)
             db = PrimerDB(config['database'])
         # run Zippy
-        primerTable, resultList, missedIntervals = zippyPrimerQuery(config, target, design, None, db, store, deep)
+        primerTable, resultList, missedIntervals = zippyPrimerQuery(config, target, design, None, db, store, deep, gap)
+
+        print >> sys.stderr, primerTable
+
         # get missed and render template
         missedIntervalNames = []
         for interval in missedIntervals:
@@ -272,8 +263,8 @@ def blacklist_pair(pairname):
 def upload_samplesheet():
     if request.method == 'POST':
         locationsheet = request.files['locationsheet']
-        if not locationsheet:
-            flash('No csvfile submitted. Please try again','warning')
+        if not locationsheet or not locationsheet.filename.endswith('.csv'):
+            flash('Not a CSV file. Please try again','warning')
         else:
             filename = secure_filename(locationsheet.filename)
             saveloc = os.path.join(app.config['UPLOAD_FOLDER'], filename)
diff --git a/zippy/zippy.py b/zippy/zippy.py
index c6f2f96..18f2e37 100755
--- a/zippy/zippy.py
+++ b/zippy/zippy.py
@@ -237,7 +237,7 @@ def getPrimers(intervals, db, design, config, deep=True, rename=None, compatible
     except:
         print >> sys.stderr, 'Could not read blacklist cache, check permissions'
         print >> sys.stderr, os.getcwd(), config['blacklistcache']
-    maxTier = len(config['design']['primer3']) if deep else 1  # only search first tier unless deep
+    maxTier = len(config['design']['primer3']) if deep or compatible else 1  # only search first tier unless deep or compatibility mode
     seqhash = lambda x,y: hashlib.sha1(','.join([x,y])).hexdigest()  # sequence pair hashing function
     # build gap primers and hash valid pairs
     if compatible:
@@ -608,14 +608,14 @@ def readprimerlocations(locationfile):
     header = []
     updateList = []
     with open(locationfile) as csvfile:
-        readfile = csv.reader(csvfile, delimiter='\t')
+        readfile = csv.reader(csvfile, delimiter=',')
         for line in readfile:
             if not header:
                 header = line
             else:
                 try:
                     row = dict(zip(header,line))
-                    updateList.append([row['Primer Name'], Location(row['Box'].strip('Bbox'), row['Well'])])
+                    updateList.append([row['PrimerName'], Location(row['Box'].strip('Bbox'), row['Well'])])
                 except:
                     raise Exception('InputFormatError')
     return updateList
diff --git a/zippy/zippylib/files.py b/zippy/zippylib/files.py
index 411b88a..e08a92d 100755
--- a/zippy/zippylib/files.py
+++ b/zippy/zippylib/files.py
@@ -42,6 +42,8 @@ def __init__(self,fh,getgenes=None,interval=None,overlap=None,flank=0,combine=Tr
                 gene = Interval(f[2],geneStart,geneEnd,f[12],reverse)
                 # parse exons
                 for e in zip(f[9].split(','),f[10].split(',')):
+                    if e[1] < geneStart or geneEnd < e[0]:
+                        continue  # noncoding
                     try:
                         exonStart = int(e[0]) if noncoding else max(geneStart,int(e[0]))
                         exonEnd = int(e[1]) if noncoding else min(geneEnd,int(e[1]))