astro-otter 0.3.5__tar.gz → 0.4.1__tar.gz

{astro_otter-0.3.5/src/astro_otter.egg-info → astro_otter-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: astro-otter
-Version: 0.3.5
+Version: 0.4.1
 Author-email: Noah Franz <nfranz@arizona.edu>
 License: MIT License
         

{astro_otter-0.3.5 → astro_otter-0.4.1/src/astro_otter.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: astro-otter
-Version: 0.3.5
+Version: 0.4.1
 Author-email: Noah Franz <nfranz@arizona.edu>
 License: MIT License
         

{astro_otter-0.3.5 → astro_otter-0.4.1}/src/otter/_version.py

@@ -2,4 +2,4 @@
 Just define the package version in one place
 """
 
-__version__ = "0.3.5"
+__version__ = "0.4.1"

{astro_otter-0.3.5 → astro_otter-0.4.1}/src/otter/io/otter.py

@@ -63,15 +63,15 @@ class Otter(Database):
 
     def __init__(
         self,
-        url: str = "http://127.0.0.1:8529",
+        url: str = "https://otter.idies.jhu.edu/api",
         username: str = os.environ.get("ARANGO_USER_USERNAME", "user-guest"),
-        password: str = os.environ.get("ARANGO_USER_PASSWORD", ""),
+        password: str = os.environ.get("ARANGO_USER_PASSWORD", "test"),
         gen_summary: bool = False,
         datadir: str = None,
         debug: bool = False,
         **kwargs,
     ) -> None:
-        print("Attempting to login with the following credentials:")
+        print(f"Attempting to login to {url} with the following credentials:")
         print(f"username: {username}")
         print(f"password: {password}")
 
@@ -85,9 +85,6 @@ class Otter(Database):
 
         self.debug = debug
 
-        if gen_summary:
-            self.generate_summary_table(save=True)
-
         # make sure the data directory exists
         if not os.path.exists(self.DATADIR):
             try:
@@ -99,6 +96,9 @@ class Otter(Database):
                 )
                 pass
 
+        if gen_summary:
+            self.generate_summary_table(save=True)
+
         connection = Connection(username=username, password=password, arangoURL=url)
         super().__init__(connection, "otter", **kwargs)
 
@@ -943,7 +943,7 @@ class Otter(Database):
 
         # merge the meta and phot data
         if phot is not None:
-            data = pd.merge(phot, meta, on="name", how="inner")
+            data = pd.merge(phot, meta, on="name", how="outer")
         else:
             data = meta
 
@@ -951,11 +951,11 @@ class Otter(Database):
         assert (
             len(data[pd.isna(data.ra)].name.unique()) == 0
         ), "Missing some RA and Decs, please check the input files!"
-        if phot is not None:
-            for name in meta.name:
-                assert len(data[data.name == name]) == len(
-                    phot[phot.name == name]
-                ), f"failed on {name}"
+        # if phot is not None:
+        #    for name in meta.name:
+        #        assert len(data[data.name == name]) == len(
+        #            phot[phot.name == name]
+        #        ), f"failed on {name}"
 
         # actually do the data conversion to OTTER
         all_jsons = []
@@ -1084,7 +1084,7 @@ class Otter(Database):
             # skip the photometry code if there is no photometry file
             # if there is a photometry file then we want to convert it below
             phot_sources = []
-            if phot is not None:
+            if phot is not None and not np.all(pd.isna(tde["flux"])):
                 tde["obs_type"] = [
                     freq_to_obstype(vv * u.Unit(uu))
                     for vv, uu in zip(
@@ -1531,7 +1531,7 @@ class Otter(Database):
             all_jsons.append(Transient(json))
 
         if db is None:
-            db = Otter(datadir=local_outpath)
+            db = Otter(datadir=local_outpath, gen_summary=True)
         else:
             db.DATADIR = local_outpath
 

{astro_otter-0.3.5 → astro_otter-0.4.1}/src/otter/io/transient.py

@@ -432,6 +432,16 @@ class Transient(MutableMapping):
         if "host" in self:
             max_hosts = min([max_hosts, len(self["host"])])
             for h in self["host"][:max_hosts]:
+                # only return hosts with their ra and dec stored
+                if (
+                    "host_ra" not in h
+                    or "host_dec" not in h
+                    or "host_ra_units" not in h
+                    or "host_dec_units" not in h
+                ):
+                    continue
+
+                # now we can construct a host object from this
                 host.append(Host(transient_name=self.default_name, **dict(h)))
 
         # then try BLAST

{astro_otter-0.3.5 → astro_otter-0.4.1}/tests/test_data_finder.py

@@ -98,7 +98,7 @@ def test_query_simbad():
     df1 = construct_data_finder()
     res = df1.query_simbad()
 
-    assert len(res) == 3
+    assert len(res) == 1
 
 
 def test_query_vizier():

{astro_otter-0.3.5 → astro_otter-0.4.1}/tests/test_otter.py

@@ -23,6 +23,18 @@ def test_otter_constructor():
     db = Otter(url=OTTER_URL, password=OTTER_TEST_PASSWORD)
     assert isinstance(db, Otter)
 
+    # and using a custom local directory
+    otter_test_dir = os.path.join(os.getcwd(), "otter-test")
+    db = Otter(
+        url=OTTER_URL,
+        password=OTTER_TEST_PASSWORD,
+        datadir=otter_test_dir,
+        gen_summary=True,
+    )
+
+    assert os.path.exists(otter_test_dir)  # make sure it was created
+    assert isinstance(db, Otter)
+
 
 def test_get_meta():
     """
@@ -87,7 +99,7 @@ def test_get_phot():
         "reference",
     ]
 
-    names = ["2018hyz", "2018zr", "ASASSN-14li"]
+    names = ["2018hyz", "2018zr", "ASASSN-14li", "2016fnl", "J123715"]
 
     # first with returning an astropy table (the default)
     allphot = db.get_phot(names=names)
@@ -107,6 +119,10 @@ def test_get_phot():
     with pytest.raises(FailedQueryError):
         db.get_phot(names="foo")
 
+    # some other random tests
+    with pytest.raises(OSError):
+        db.get_phot(names="ASASSN-14li", return_type="foobar")
+
 
 def test_query():
     """
@@ -135,3 +151,53 @@ def test_query():
     # test hasphot and hasspec
     assert len(db.query(hasspec=True)) == 0
     assert "ASASSN-20il" not in {t["name/default_name"] for t in db.query(hasphot=True)}
+
+    # test has_*_phot
+    assert len(db.query(has_radio_phot=True)) >= 92
+    assert len(db.query(has_xray_phot=True)) >= 35
+    assert len(db.query(has_uvoir_phot=True)) >= 120
+    assert len(db.query(has_radio_phot=True, has_xray_phot=True)) < len(
+        db.query(has_radio_phot=True)
+    )
+
+    # test classification related queries
+    assert len(db.query(spec_classed=True)) > 140
+    assert len(db.query(unambiguous=True)) > 190
+    assert len(db.query(classification="SLSN")) >= 1
+
+    # check that querying based on references works
+    fake_test_bibcodes = ["'tasdfasdf...lkjsfd'", "'asfd...kjasdf...lkjs'"]
+    assert len(db.query(refs=fake_test_bibcodes)) == 0
+    assert len(db.query(refs=fake_test_bibcodes[0])) == 0
+
+    # try querying with the fake "private" data
+    db2 = Otter(
+        url=OTTER_URL,
+        password=OTTER_TEST_PASSWORD,
+        datadir=os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), "private_otter_data"
+        ),
+        gen_summary=True,
+    )
+    res = db2.query(names="2018hyz", query_private=True)
+    assert res[0].default_name == "2018hyz"
+
+    # check that some errors are thrown when appropriate
+    with pytest.raises(Exception):
+        db.query(names=10)
+        db.query(refs=10)
+
+
+def test_from_csvs():
+    """
+    This tests the "from_csvs" method which allows for interaction with locally
+    stored datasets
+    """
+
+    metapath = os.path.join(os.path.dirname(os.path.abspath(__file__)), "meta-test.csv")
+    photpath = os.path.join(os.path.dirname(os.path.abspath(__file__)), "phot-test.csv")
+    outpath = os.path.join(os.path.dirname(os.path.abspath(__file__)), "from-csvs-out")
+
+    db = Otter.from_csvs(metafile=metapath, photfile=photpath, local_outpath=outpath)
+
+    assert isinstance(db, Otter)

{astro_otter-0.3.5 → astro_otter-0.4.1}/tests/test_transient.py

@@ -31,6 +31,13 @@ def test_transient_constructor():
     assert t.srcmap["2012MNRAS.421.1942W"] == "Wiersema et al. (2012)", srcmap_msg
     assert t.srcmap["2011ApJ...737..103S"] == "Schlafly & Finkbeiner (2011)", srcmap_msg
 
+    with pytest.raises(AttributeError):
+        Transient(d={"name": {"default": "foo"}})
+
+    del test_json["name"]
+    t = Transient(test_json, name="SwJ1644+57")
+    assert t.default_name == "SwJ1644+57", "default_name is incorrect!"
+
 
 def test_getitem():
     """
@@ -131,6 +138,10 @@ def test_iter():
     """
     Test that my __iter__ overwrite works
     """
+    t = Transient({"test1": {"mytest": "nothing to see here", "other": 1}})
+
+    assert list(iter(t)) == list(iter(t.data))
+
     true_vals = [
         {"value": "Sw J1644+57", "reference": ["Swift"]},
         {"value": "GRB 110328A", "reference": [["2011Sci...333..203B"]]},