From b5c3c43522e0abf55fbef31d5ab4d130d71a7fbb Mon Sep 17 00:00:00 2001
From: Matthew Pitkin <matthew.pitkin@ligo.org>
Date: Mon, 27 Nov 2017 13:59:49 +0000
Subject: [PATCH] Fix use of ads module to only get references for returned
 pulsars rather than trying to get them all

---
 docs/source/conf.py   |  3 +++
 docs/source/query.rst |  1 -
 psrqpy/__init__.py    |  2 +-
 psrqpy/search.py      | 23 ++++++++++++++++++++---
 psrqpy/utils.py       | 18 +++++++++++++-----
 5 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index eeb47f3d..3e28e045 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -41,6 +41,9 @@
     'sphinx.ext.napoleon'
 ]
 
+autodoc_default_flags = ['members', 'show-inheritance']
+autodoc_member_order = 'bysource'
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
diff --git a/docs/source/query.rst b/docs/source/query.rst
index 01163bbc..28eb8bb7 100644
--- a/docs/source/query.rst
+++ b/docs/source/query.rst
@@ -4,4 +4,3 @@ Querying
 
 .. automodule:: psrqpy.search
    :members:
-
diff --git a/psrqpy/__init__.py b/psrqpy/__init__.py
index 56c88646..92b81572 100644
--- a/psrqpy/__init__.py
+++ b/psrqpy/__init__.py
@@ -2,7 +2,7 @@
 
 """ A Python tool for interacting with the ATNF pulsar catalogue """
 
-__version__ = "0.3.5"
+__version__ = "0.3.6"
 
 from .search import QueryATNF
 from .pulsar import Pulsar, Pulsars
diff --git a/psrqpy/search.py b/psrqpy/search.py
index fbd1bda1..a4393f73 100644
--- a/psrqpy/search.py
+++ b/psrqpy/search.py
@@ -132,7 +132,7 @@ def __init__(self, params=None, condition=None, psrtype=None, assoc=None, bincom
 
         # get references is required
         if self._include_refs:
-            self._refs = get_references(useads=self._adsref)
+            self._refs = get_references()
 
         # perform query
         self._query_content = self.generate_query()
@@ -390,8 +390,25 @@ def parse_query(self, requestcontent=''):
                                     refstring2 = re.sub(r'\s+', ' ', refstring.format(**thisref)) # remove any superfluous whitespace
                                     self._query_output[p+'_REF'][idx] = ','.join([a for a in refstring2.split(',') if a.strip()]) # remove any superfluous empty ',' seperated values
 
-                                    if self._adsref and 'ADS URL' in thisref:
-                                        self._query_output[p+'_REFURL'][idx] = thisref['ADS URL'] # remove any superfluous whitespace
+                                    if self._adsref:
+                                        if 'ADS URL' not in thisref: # get ADS reference
+                                            try:
+                                                import ads
+                                            except ImportError:
+                                                warnings.warn('Could not import ADS module, so no ADS information will be included', UserWarning)
+                                                article = []
+
+                                            try:
+                                                article = ads.SearchQuery(year=thisref['year'], first_author=thisref['authors'][0], title=thisref['title'])
+                                            except IOError:
+                                                warnings.warn('Could not get reference information, so no ADS information will be included', UserWarning)
+                                                article = []
+
+                                            article = list(article)
+                                            if len(article) > 0:
+                                                self._refs[reftag]['ADS URL'] = ADS_URL.format(list(article)[0].bibcode)
+
+                                        self._query_output[p+'_REFURL'][idx] = thisref['ADS URL']
                                 else:
                                     warnings.warn('Reference tag "{}" not found so omitting reference'.format(reftag), UserWarning)
                             vidx += 1
diff --git a/psrqpy/utils.py b/psrqpy/utils.py
index b949eca7..158358d0 100644
--- a/psrqpy/utils.py
+++ b/psrqpy/utils.py
@@ -61,7 +61,7 @@ def get_references(useads=False):
     queryrefs = requests.get(ATNF_BASE_URL + 'psrcat_ref.html')
 
     if queryrefs.status_code != 200:
-        warnings.warn("Could query the ATNF references. No references returned".format(ATNF_VERSION), UserWarning)
+        warnings.warn("Could query the ATNF references. No references returned", UserWarning)
     else:
         try:
             refsoup = BeautifulSoup(queryrefs.content, 'html.parser')
@@ -231,12 +231,20 @@ def get_references(useads=False):
                     warnings.warn('Could not import ADS module, so no ADS information will be included', UserWarning)
                     continue
 
+                refs[reftag]['ADS'] = None
+                refs[reftag]['ADS URL'] = ''
+
                 try:
-                    article = list(ads.SearchQuery(year=refs[reftag]['year'], first_author=refs[reftag]['authors'][0], title=refs[reftag]['title']))[0]
-                    refs[reftag]['ADS'] = article
-                    refs[reftag]['ADS URL'] = ADS_URL.format(article.bibcode)
+                    article = ads.SearchQuery(year=refs[reftag]['year'], first_author=refs[reftag]['authors'][0], title=refs[reftag]['title'])
                 except IOError:
-                    warnings.warn('Could not import ADS module, so no ADS information will be included', UserWarning)
+                    warnings.warn('Could not get reference information, so no ADS information will be included', UserWarning)
+                    continue
+
+                article = list(article)
+
+                if len(article) > 0:
+                    refs[reftag]['ADS'] = list(article)[0]
+                    refs[reftag]['ADS URL'] = ADS_URL.format(list(article)[0].bibcode)
 
     return refs