Merge branch 'release/2.1.5'

CHANGES.md

@@ -1,6 +1,11 @@
 
 ## Release Notes
 
+**v2.1.5 - June 22, 2020**
+
+* **refactor**: tunnel changes due to new jump box installation at QUB
+* **fixed:** some NED galaxies not reported if redshift does not exist but a semi-major axis is given
+
 **v2.1.4 - June 18, 2020**
 
 * **fixed**: an empty crossmatch set could cause a transient database update when not required

sherlock/__version__.py

@@ -1 +1 @@
-__version__ = '2.1.4'
+__version__ = '2.1.5'

sherlock/catalogue_conesearch.py

@@ -18,6 +18,7 @@
 from HMpTy.mysql import conesearch as hmptyConesearch
 import copy
 
+
 class catalogue_conesearch(object):
     """
     *The worker class for the conesearch module*
@@ -34,7 +35,7 @@ class catalogue_conesearch(object):
     - ``nearestOnly`` -- return only the nearest object. Default *False*
     - ``physicalSearch`` -- is this a physical search, so only return matches with distance information. Default *False*
     - ``upperMagnitudeLimit`` -- the upper magnitude limit if a magnitude cut is requird with the conesearch. Default *False*
-    
+
 
         - ``lowerMagnitudeLimit`` -- the lower magnitude limit if a magnitude cut is requird with the conesearch. Default *False*
         - ``magnitudeLimitFilter`` -- the filter to use for the magnitude limit if requird. Default *False*, ("_u"|"_g"|"_r"|"_i"|"_z"|"_y"|"U"|"B"|"V"|"R"|"I"|"Z"|"J"|"H"|"K"|"G")
@@ -104,7 +105,7 @@ class catalogue_conesearch(object):
         ra=["23:01:07.99", 45.36722, 13.875250],
         dec=["-01:58:04.5", 30.45671, -25.26721],
         radiusArcsec=60.,
-    
+
 
             colMaps=colMaps,
             tableName="tcs_view_agn_milliquas_v4_5",
@@ -210,12 +211,12 @@ def search(self):
 
         - ``matchIndies`` -- the indicies of the input transient sources (syncs with ``uniqueMatchDicts``)
         - ``uniqueMatchDicts`` -- the crossmatch results
-        
+
 
         **Usage**
 
         See class docstring for usage examples
-        
+
 
         .. todo ::
 

sherlock/database.py

@@ -20,6 +20,7 @@
 from docopt import docopt
 from fundamentals.mysql import readquery
 
+
 class database(object):
     """
     *the database object for sherlock, setting up ssh tunnels and various database connections*
@@ -32,12 +33,12 @@ class database(object):
 
     - ``log`` -- logger
     - ``settings`` -- the settings dictionary
-    
+
 
     **Return**
 
     - ``dbConns`` -- a dictionary of the database connections required by sherlock
-    
+
 
     **Usage**
 
@@ -54,7 +55,7 @@ class database(object):
     transientsDbConn = dbConns["transients"]
     cataloguesDbConn = dbConns["catalogues"]
     ```
-    
+
 
     .. todo ::
 
@@ -86,7 +87,7 @@ def connect(self):
 
         - ``transientsDbConn`` -- the database hosting the transient source data
         - ``cataloguesDbConn`` -- connection to the database hosting the contextual catalogues the transients are to be crossmatched against
-        
+
 
         See the class docstring for usage
 
@@ -117,10 +118,12 @@ def connect(self):
         dbConns = []
         for dbSettings in [transientSettings, catalogueSettings]:
             port = False
-            if dbSettings and dbSettings["tunnel"]:
+            if dbSettings and "tunnel" in dbSettings and dbSettings["tunnel"]:
                 port = self._setup_tunnel(
                     tunnelParameters=dbSettings["tunnel"]
                 )
+            elif dbSettings and "port" in dbSettings and dbSettings["port"]:
+                port = int(dbSettings["port"])
 
             if dbSettings:
                 # SETUP A DATABASE CONNECTION FOR THE STATIC CATALOGUES
@@ -179,12 +182,12 @@ def _setup_tunnel(
         **Key Arguments**
 
         - ``tunnelParameters`` -- the tunnel parameters found associated with the database settings
-        
+
 
         **Return**
 
         - ``sshPort`` -- the port the ssh tunnel is connected via
-        
+
 
         .. todo ::
 

sherlock/transient_catalogue_crossmatch.py

@@ -840,11 +840,12 @@ def physical_separation_crossmatch_against_catalogue(
                 thisMatch = False
                 physical_separation_kpc = row["physical_separation_kpc"]
                 newsearch_name = search_name
-
                 # FIRST CHECK FOR MAJOR AXIS MEASUREMENT
                 # BYPASS NED FAULTY AXES MEASUREMENTS:
                 # https://gist.github.com/search?utf8=%E2%9C%93&q=user%3Athespacedoctor+ned
+
                 if row["major_axis_arcsec"] and ("ned" not in search_name or (row["unkMag"] and row["unkMag"] < 20.)):
+
                     if row["separationArcsec"] < row["major_axis_arcsec"] * self.settings["galaxy radius stetch factor"]:
                         thisMatch = True
                         newsearch_name = newsearch_name + \
@@ -879,8 +880,18 @@ def physical_separation_crossmatch_against_catalogue(
         if matchSubset:
 
             from operator import itemgetter
-            matchSubset = sorted(matchSubset, key=itemgetter(
-                'physical_separation_kpc'), reverse=False)
+
+            physicalDicts = []
+            physicalDicts[:] = [m for m in matchSubset if m[
+                'physical_separation_kpc']]
+
+            semiMajor = []
+            semiMajor[:] = [m for m in matchSubset if not m[
+                'physical_separation_kpc']]
+
+            matchSubset = sorted(physicalDicts, key=itemgetter(
+                'physical_separation_kpc'), reverse=False) + sorted(semiMajor, key=itemgetter(
+                    'separationArcsec'), reverse=False)
 
             if nearestOnly == True:
                 theseMatches = matchSubset[0]

sherlock/transient_classifier.py

@@ -1025,7 +1025,7 @@ def _rank_classifications(
             if mergedMatch["direct_distance_scale"]:
                 mergedMatch["physical_separation_kpc"] = mergedMatch[
                     "direct_distance_scale"] * mergedMatch["separationArcsec"]
-                print(mergedMatch["physical_separation_kpc"])
+
             elif mergedMatch["scale"]:
                 mergedMatch["physical_separation_kpc"] = mergedMatch[
                     "scale"] * mergedMatch["separationArcsec"]
@@ -1359,8 +1359,6 @@ def classification_annotations(
             elif classType in [2, 3]:
                 annotation.append("is possibly associated with")
 
-            print(xm["catalogue_object_id"])
-
         self.log.debug('completed the ``classification_annotations`` method')
         return None