Merge conflict.

.travis.yml

@@ -2,9 +2,14 @@ language: python
 
 python:
     - 2.7
-    - 3.3
     - 3.4
     - 3.5
+    - 3.6
+
+before_script:
+  - "export DISPLAY=:99.0" # xvfb is used to ensure matplotlib plots don't fail
+  - "sh -e /etc/init.d/xvfb start"
+  - sleep 3 # give xvfb some time to start
 
 env:
     global:
@@ -16,7 +21,7 @@ env:
         # For this package-template, we include examples of Cython modules,
         # so Cython is required for testing. If your package does not include
         # Cython code, you can set CONDA_DEPENDENCIES=''
-        - CONDA_DEPENDENCIES='matplotlib'
+        - CONDA_DEPENDENCIES='matplotlib pandas'
     matrix:
         # Make sure that egg_info works without dependencies
         # - SETUP_CMD='egg_info'
@@ -25,13 +30,12 @@ env:
 
 matrix:
     allow_failures:
-        - python: 3.3
         - python: 3.4
-        - python: 3.5
 
 install:
     - git clone git://github.com/astropy/ci-helpers.git
     - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
+    - pip install requests
 
 script:
     - $SETUP_CMD

astrodbkit/__init__.py

@@ -1,2 +1,2 @@
 from pkg_resources import get_distribution
-__version__ = '0.3.0.post7'
+__version__ = '0.6.4'

astrodbkit/tests/test_astrodb.py

@@ -3,52 +3,172 @@
 import os
 from astropy.utils.data import download_file
 from .. import astrodb
+from sqlite3 import IntegrityError
+
+filename = os.path.join(tempfile.mkdtemp(), 'empty_db.db')
 
 
 def setup_module(module):
-    db_path = download_file("http://github.com/BDNYC/BDNYCdb/raw/master/BDNYCv1.0.db")
+    try:
+        db_path = download_file("http://github.com/BDNYC/BDNYCdb/raw/master/bdnyc_database.db")
+    except:
+        db_path = download_file("http://github.com/BDNYC/BDNYCdb/raw/master/BDNYCv1.0.db")
     module.bdnyc_db = astrodb.Database(db_path)
-    filename = os.path.join(tempfile.mkdtemp(), 'empty_db.db')
-    module.empty_db = astrodb.create_database(filename)
+    astrodb.create_database(filename)
+    module.empty_db = astrodb.Database(filename)
+
 
-def test_loaddb():
+def test_load_bdnyc():
     print(bdnyc_db)
+    assert not isinstance(bdnyc_db, type(None))
+
+
+def test_load_empty():
     print(empty_db)
+    assert not isinstance(empty_db, type(None))
+
 
 def test_search(): 
-    bdnyc_db.search('1234','sources')
+    bdnyc_db.search('young', 'sources')
+    bdnyc_db.search((222.106, 10.533), 'sources')
+    bdnyc_db.search((338.673, 40.694), 'sources', radius=5)
+    bdnyc_db.search((338.673, 40.694), 'sources', radius=5, sql_search=True)
+
 
 def test_inventory():
-    bdnyc_db.inventory(825)
+    bdnyc_db.inventory(1)
+    bdnyc_db.inventory(11)
+
 
 def test_sqlquery():
     bdnyc_db.query("SELECT s.id, s.ra, s.dec, s.shortname, p.source_id, p.band, p.magnitude "
         "FROM sources as s JOIN photometry as p ON s.id=p.source_id "
         "WHERE s.dec<=-10 AND p.band=='W1'")
 
+
 def test_schema():
     bdnyc_db.schema('sources')
-
-@pytest.mark.xfail
-def test_add_data():
-    assert False
-
-@pytest.mark.xfail
-def test_clean_up():
-    assert False
+    empty_db.schema('sources')
+
+
+def test_table():
+    columns = ['id', 'ra', 'dec', 'shortname', 'source_id']
+    types = ['INTEGER', 'REAL', 'REAL', 'TEXT', 'INTEGER']
+    constraints = ['NOT NULL UNIQUE', '', '', '', '']
+    empty_db.table('new_sources', columns, types, constraints, new_table=True)
+    t = empty_db.query("PRAGMA table_info(new_sources)", fmt='table')
+    print(t)
+    assert sorted(columns) == sorted(t['name'])
+
+
+def test_add_data_empty():
+    t1 = empty_db.query('SELECT * FROM sources', fmt='array')
+
+    if isinstance(t1, type(None)):
+        len_t1 = 0
+    else:
+        len_t1 = len(t1)
+
+    data = list()
+    data.append(['ra', 'dec', 'shortname', 'comments'])
+    data.append([12, -12, 'fakesource', ''])
+    empty_db.add_data(data, 'sources', verbose=True)
+
+    t2 = empty_db.query('SELECT * FROM sources', fmt='array')
+    assert len(t2) == len_t1 + 1
+
+
+def test_new_ids():
+    available = bdnyc_db._lowest_rowids('sources', 10)
+    t = bdnyc_db.query('SELECT id FROM sources')
+    assert available not in t
+
+
+def test_add_foreign_key():
+    empty_db.add_foreign_key('new_sources', ['sources'], ['source_id'], ['id'])
+
+
+def test_foreign_key_support():
+    data = list()
+    data.append(['ra', 'dec', 'shortname', 'source_id'])
+    data.append([12, -12, 'fakesource', 9999])
+    with pytest.raises(IntegrityError):
+        empty_db.add_data(data, 'new_sources')  # Foreign key error expected
+
+
+def test_lookup():
+    bdnyc_db.lookup([1, '2MASS'], 'sources')
+
+
+def test_clean_up(monkeypatch):
+    data = list()
+    data.append(['ra', 'dec', 'shortname', 'source_id'])
+    data.append([12, -12, 'fakesource', 1])
+    data.append([12, -12, 'fakesource2', 1])
+
+    # Fake user input
+    inputs = ['help', 'r', 'y']
+    input_generator = (i for i in inputs)
+    monkeypatch.setattr('astrodbkit.astrodb.get_input', lambda prompt: next(input_generator))
+
+    empty_db.add_data(data, 'new_sources', verbose=True)  # This internally calls clean_up
+
+    t = empty_db.query('SELECT * FROM new_sources', fmt='table')
+    assert len(t) == 1  # Only one record should have been kept
+
 
 @pytest.mark.xfail
 def test_merge():
+    empty_db.modify('DROP TABLE new_sources')
+    bdnyc_db.merge(filename, 'sources')
     assert False
 
-@pytest.mark.xfail
+
 def test_output_spectrum():
-    assert False
+    t = bdnyc_db.query('SELECT spectrum FROM spectra LIMIT 1', fmt='array', fetch='one')
+    try:
+        w, f = t[0].data
+    except ValueError:
+        w, f, e = t[0].data
+    assert any(w)  # extracted wavelength
+    assert any(f)  # extracted flux
+
 
-@pytest.mark.xfail
 def test_plot_spectrum():
-    assert False
+    t = bdnyc_db.query('SELECT id FROM spectra LIMIT 1', fmt='array', fetch='one')
+    bdnyc_db.plot_spectrum(t[0])
 
-@pytest.mark.xfail
-def test_table():
-    assert False
+
+def test_cuny():
+    file = 'http://academicworks.cuny.edu/context/hc_pubs/article/1093/type/native/viewcontent'  # txt file
+    data = astrodb.convert_spectrum(file)
+    assert not isinstance(data, type(''))
+
+    file = 'http://academicworks.cuny.edu/context/hc_pubs/article/1118/type/native/viewcontent'  # FITS file
+    data = astrodb.convert_spectrum(file)
+    assert not isinstance(data, type(''))
+
+
+def test_references():
+    t = bdnyc_db.query('SELECT id FROM publications', fmt='table')
+    id = t['id'][0]
+    bdnyc_db.references(id, column_name='publication_id')
+
+
+def test_get_bibtex():
+    bdnyc_db.get_bibtex(52)
+    bdnyc_db.get_bibtex('Cruz03')
+
+
+def test_save():
+    empty_db.save(directory='tempempty')
+    bdnyc_db.save(directory='tempdata')
+
+
+def test_close(monkeypatch):
+    # Fake user input
+    inputs = ['n', 'n']
+    input_generator = (i for i in inputs)
+    monkeypatch.setattr('astrodbkit.astrodb.get_input', lambda prompt: next(input_generator))
+
+    bdnyc_db.close()

astrodbkit/votools.py

@@ -8,42 +8,6 @@
 from astropy.io.votable import from_table
 
 
-def table_add(tab, data, col):
-    """
-    Function to parse dictionary list **data** and add the data to table **tab** for column **col**
-
-    Parameters
-    ----------
-    tab: Table class
-      Table to store values
-    data: list
-      Dictionary list from the SQL query
-    col: str
-      Column name (ie, dictionary key) for the column to add
-
-    Returns
-    -------
-    None
-
-    """
-
-    x = []
-    for i in range(len(data)):
-
-        # If the particular key is not present, use a place-holder value (used for photometry tables)
-        if col not in data[i]:
-            temp = ''
-        else:
-            temp = data[i][col]
-
-        # Fix up None elements
-        if temp is None: temp = ''
-
-        x.append(temp)
-
-    print('Adding column {}'.format(col))
-    tab.add_column(Column(x, name=col))
-
 def dict_tovot(tabdata, tabname='votable.xml', phot=False, binary=True):
     """
     Converts dictionary table **tabdata** to a VOTable with name **tabname**
@@ -60,10 +24,6 @@ def dict_tovot(tabdata, tabname='votable.xml', phot=False, binary=True):
       Parameter specifying if the VOTable should be saved as a binary.
       This is necessary for tables with lots of text columns.
 
-    Returns
-    -------
-    None
-
     """
 
     # Check if input is a dictionary
@@ -123,7 +83,9 @@ def photaddline(tab, sourceid):
 
     Returns
     -------
-      Dictionary with all the data for the specified source
+    tmpdict: dict
+        Dictionary with all the data for the specified source
+
     """
 
     colnames = tab[0].keys()
@@ -182,4 +144,37 @@ def photparse(tab):
         tmpdict = photaddline(tab, sourceid)
         newtab.append(tmpdict)
 
-    return newtab
+    return newtab
+
+
+def table_add(tab, data, col):
+    """
+    Function to parse dictionary list **data** and add the data to table **tab** for column **col**
+
+    Parameters
+    ----------
+    tab: Table class
+      Table to store values
+    data: list
+      Dictionary list from the SQL query
+    col: str
+      Column name (ie, dictionary key) for the column to add
+
+    """
+
+    x = []
+    for i in range(len(data)):
+
+        # If the particular key is not present, use a place-holder value (used for photometry tables)
+        if col not in data[i]:
+            temp = ''
+        else:
+            temp = data[i][col]
+
+        # Fix up None elements
+        if temp is None: temp = ''
+
+        x.append(temp)
+
+    print('Adding column {}'.format(col))
+    tab.add_column(Column(x, name=col))

docs/conf.py

@@ -57,9 +57,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.3'
+version = '0.5'
 # The full version, including alpha/beta/rc tags.
-release = '0.3.0'
+release = '0.5.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.