Incorporate @guillermo-carrasco changes i.r.t waking up couchdb and b…

…asic test, still cannot connect to the database programatically

facs/utils/helpers.py

@@ -4,6 +4,7 @@
 import shutil
 import json
 import warnings
+import requests
 from contextlib import contextmanager
 
 import couchdb
@@ -44,10 +45,33 @@ def generate_dummy_fastq(fname, num_reads, case=''):
                 f.write('arvestad' * stride + os.linesep)
 
 
-def send_couchdb(server, db, user, passwd, doc):
+def _wake(server, retries=5):
+    """Try to wake up server by retrying get requests.
+
+    This method is basically used to wake up the public database facs.iriscouch.com
+    used to store the tests results.
+    """
+    status_code = requests.codes.NO_RESPONSE
+    while status_code != requests.codes.OK and retries:
+        try:
+            r = requests.get(db)
+            status_code = r.status_code
+            retries = 0
+        except requests.ConnectionError:
+            if retries == 1:
+                raise requests.ConnectionError("There was a problem connecting to {} and the " \
+                                               "results could not be uploaded".format(db))
+            else:
+                retries -= 1
+                pass
+
+
+def send_couchdb(server, db, user, passwd, doc, wake_up=False):
     ''' Send JSON document to couchdb
     '''
     try:
+        if wake_up:
+            _wake(server)
         couch = couchdb.Server(server)
         couch.resource.credentials = (user, passwd)
         db = couch[db]

setup.py

@@ -46,6 +46,7 @@
             "nose",
             "nose-timer",
             "jinja2",
+            "requests",
             "couchdb"
       ],
       entry_points="""

tests/test_basic.py

@@ -66,6 +66,18 @@ def test_1_build_ref(self):
                 json_doc = facs.build(org, bf)
                 self.results.append(json_doc)
 
+    def test_2_query(self):
+        """ Query against datasets (generated by simNGS)
+        """
+
+        for sample in glob.glob(os.path.join(self.synthetic_fastq, "*.fastq")):
+            for ref in os.listdir(self.reference):
+                qry = os.path.join(self.synthetic_fastq, sample)
+                bf = os.path.join(self.bloom_dir, os.path.splitext(ref)[0]+".bloom")
+                print(qry, bf)
+                json_doc = facs.query(qry, bf)
+                self.results.append(json_doc)
+
     def test_3_query_custom(self):
         """ Query against the uncompressed FastQ files files manually deposited
             in data/custom folder.