vfbquery 0.2.6__py3-none-any.whl → 0.2.8__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- test/term_info_queries_test.py +50 -45
- vfbquery/vfb_queries.py +728 -163
- vfbquery-0.2.8.dist-info/METADATA +1168 -0
- vfbquery-0.2.8.dist-info/RECORD +10 -0
- {vfbquery-0.2.6.dist-info → vfbquery-0.2.8.dist-info}/WHEEL +1 -1
- vfbquery-0.2.6.dist-info/METADATA +0 -1512
- vfbquery-0.2.6.dist-info/RECORD +0 -10
- {vfbquery-0.2.6.dist-info → vfbquery-0.2.8.dist-info}/LICENSE +0 -0
- {vfbquery-0.2.6.dist-info → vfbquery-0.2.8.dist-info}/top_level.txt +0 -0
test/term_info_queries_test.py
CHANGED
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@@ -59,11 +59,11 @@ class TermInfoQueriesTest(unittest.TestCase):
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self.assertEqual(0, len(terminfo.xrefs))
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self.assertEqual(
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self.assertEqual(5, len(terminfo.pub_syn))
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# TODO: XXX check vfb_connect version
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# self.assertEqual("labellar taste bristle mechanosensitive neuron", terminfo.pub_syn[0].synonym.label)
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self.
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self.assertTrue("labellar taste bristle mechanosensory neuron" == terminfo.pub_syn[0].synonym.label or "labellar hMSN" == terminfo.pub_syn[0].synonym.label, "not matching synonym")
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self.assertEqual("Unattributed", terminfo.pub_syn[0].pub.core.short_form)
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self.assertEqual("", terminfo.pub_syn[0].pub.PubMed)
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@@ -92,7 +92,7 @@ class TermInfoQueriesTest(unittest.TestCase):
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self.assertTrue("Classification" in serialized)
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self.assertEqual(2, len(serialized["Classification"]))
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self.
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self.assertTrue("[expression pattern fragment](VFBext_0000004)" == serialized["Classification"][0] or "[adult DPMpl1 lineage neuron](FBbt_00050031)" == serialized["Classification"][0], "Classification not matched")
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self.assertTrue("relationships" in serialized)
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self.assertEqual(6, len(serialized["relationships"]))
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@@ -111,7 +111,7 @@ class TermInfoQueriesTest(unittest.TestCase):
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'format': 'PNG',
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'name': 'fru-F-500075',
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'reference': 'VFB_00010001'} in serialized["thumbnail"])
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self.assertTrue({'data': 'https://www.virtualflybrain.org/data/VFB/i/0001/0001/thumbnailT.png',
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self.assertTrue({'data': 'https://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00017894/thumbnailT.png',
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'format': 'PNG',
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'name': 'fru-F-500075 [adult brain template JFRC2]',
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'reference': '[VFB_00017894,VFB_00010001]'} in serialized["thumbnail"])
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@@ -121,7 +121,7 @@ class TermInfoQueriesTest(unittest.TestCase):
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self.assertFalse("targetingNeurons" in serialized)
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self.assertTrue("downloads_label" in serialized)
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self.assertEqual("
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self.assertEqual("JRC2018Unisex", serialized["downloads_label"])
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self.assertTrue("downloads" in serialized)
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self.assertEqual(5, len(serialized["downloads"]))
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self.assertTrue("[my_id_pointCloud.obj](/data/VFB/i/0001/0001/VFB_00101567/volume.obj)" in serialized["downloads"])
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@@ -224,33 +224,33 @@ class TermInfoQueriesTest(unittest.TestCase):
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self.assertTrue("Classification" in serialized)
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self.assertEqual(2, len(serialized["Classification"]))
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self.
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self.assertTrue("[adult neuron](FBbt_00047095)" == serialized["Classification"][0] or "[Drosulfakinin neuron](FBbt_00048998)" == serialized["Classification"][0], "Classification not matched")
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self.assertFalse("relationships" in serialized)
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self.assertFalse("related_individuals" in serialized)
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self.assertFalse("xrefs" in serialized)
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self.assertTrue("examples" in serialized)
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self.assertEqual(10, len(serialized["examples"]))
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self.
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self.assertTrue({'data': 'https://www.virtualflybrain.org/data/VFB/i/jrch/jti6/VFB_00101567/thumbnailT.png',
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'format': 'PNG',
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'name': 'DSKMP3_R (FlyEM-HB:327937328)',
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'reference': 'VFB_jrchjti6'}
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self.
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'reference': 'VFB_jrchjti6'} in serialized["examples"])
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self.assertTrue({'data': 'https://www.virtualflybrain.org/data/VFB/i/jrch/jti3/VFB_00101567/thumbnailT.png',
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'format': 'PNG',
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'name': 'DSKMP1A(PVM02)_L (FlyEM-HB:1260833150)',
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'reference': 'VFB_jrchjti3'}
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self.
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'reference': 'VFB_jrchjti3'} in serialized["examples"])
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self.assertTrue({'data': 'https://www.virtualflybrain.org/data/VFB/i/jrch/jti7/VFB_00101567/thumbnailT.png',
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'format': 'PNG',
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'name': 'DSKMP3_R (FlyEM-HB:328559607)',
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'reference': 'VFB_jrchjti7'}
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self.
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self.
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'reference': 'VFB_jrchjti7'} in serialized["examples"])
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# self.assertTrue({'data': 'https://www.virtualflybrain.org/data/VFB/i/jrch/jti2/VFB_00101567/thumbnailT.png',
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# 'format': 'PNG',
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# 'name': 'DSKMP1A_R (FlyEM-HB:1135837629)',
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# 'reference': 'VFB_jrchjti2'} in serialized["examples"])
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self.assertTrue({'data': 'https://www.virtualflybrain.org/data/VFB/i/jrch/jti5/VFB_00101567/thumbnailT.png',
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'format': 'PNG',
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'name': 'DSKMP1B(PVM02)_L (FlyEM-HB:1011184205)',
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'reference': 'VFB_jrchjti5'}
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'reference': 'VFB_jrchjti5'} in serialized["examples"])
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self.assertFalse("thumbnail" in serialized)
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self.assertTrue("references" in serialized)
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@@ -283,9 +283,7 @@ class TermInfoQueriesTest(unittest.TestCase):
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self.assertEqual(8, len(serialized["types"]))
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self.assertTrue("Neuron" in serialized["types"])
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self.assertTrue("Cholinergic" in serialized["types"])
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self.assertEqual("Small field neuron of the central complex with dendritic and axonal arbors in the inner, outer and posterior layers of either a half or a full ellipsoid body (EB) slice (wedge), and axon terminals in the dorsal or ventral gall and a single protocerebral bridge glomerulus (excluding glomerulus 9) (Lin et al., 2013; Wolff et al., 2015). Neurons that target odd or even numbered protocerebral bridge glomeruli target the dorsal or ventral gall, respectively (Lin et al., 2013; Wolff et al., 2015). These neurons receive inhibitory input from delta 7 (PB 18 glomeruli) neurons and they are cholinergic (Turner-Evans et al., 2020). These cells output to P-EN1 neurons and P-EG neurons of the same glomerulus in the protocerebral bridge, and form less specific 'hyper-local' feedback loops with P-EN1 neurons in the EB (Turner-Evans et al., 2020). It also receives input from R4d ring neurons and P-EN2 neurons in the EB (Turner-Evans et al., 2020). "
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"\n Based on images/diagrams in Lin et al. (2013), Wolff et al. (2015) and Turner-Evans et al. (2020), these appear to innervate the ipsilateral PB and contralateral gall, but could not find confirmation of this [FBC:CP]."
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"\n([Lin et al., 2013](FBrf0221742), [Wolff and Rubin, 2018](FBrf0240744), [Wolff et al., 2015](FBrf0227801), [Turner-Evans et al., 2020](FBrf0246945))", serialized["description"])
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self.assertEqual("Small field neuron of the central complex with dendritic and axonal arbors in the inner, outer and posterior layers of either a half or a full ellipsoid body (EB) slice (wedge), and axon terminals in the dorsal or ventral gall and a single protocerebral bridge glomerulus (excluding glomerulus 9) (Lin et al., 2013; Wolff et al., 2015). Neurons that target odd or even numbered protocerebral bridge glomeruli target the dorsal or ventral gall, respectively (Lin et al., 2013; Wolff et al., 2015). These neurons receive inhibitory input from delta 7 (PB 18 glomeruli) neurons and they are cholinergic (Turner-Evans et al., 2020). These cells output to P-EN1 neurons and P-EG neurons of the same glomerulus in the protocerebral bridge, and form less specific 'hyper-local' feedback loops with P-EN1 neurons in the EB (Turner-Evans et al., 2020). It also receives input from R4d ring neurons and P-EN2 neurons in the EB (Turner-Evans et al., 2020).", serialized["description"])
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self.assertTrue("synonyms" in serialized)
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self.assertEqual(8, len(serialized["synonyms"]))
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print(serialized["synonyms"][0])
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self.assertTrue("relationships" in serialized)
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self.assertEqual(2, len(serialized["relationships"]))
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self.
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self.assertTrue(serialized["relationships"][0] == "has hemidriver [P{VT043927-GAL4.DBD}](FBtp0124468)" or serialized["relationships"][0] == "has hemidriver [P{VT017491-p65.AD}](FBtp0133404)", "Hemidriver Missing")
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self.assertFalse("related_individuals" in serialized)
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self.assertTrue("xrefs" in serialized)
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@@ -397,7 +395,7 @@ class TermInfoQueriesTest(unittest.TestCase):
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self.assertFalse("logo" in serialized)
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self.assertTrue("link" in serialized)
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self.assertEqual("[http://flybase.org/reports/FBrf0221438.html](http://flybase.org/reports/FBrf0221438.html)", serialized["link"])
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self.assertEqual(
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self.assertEqual(3, len(serialized["types"]))
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self.assertTrue("DataSet" in serialized["types"])
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self.assertEqual("An exhaustive set of lineage clones covering the adult brain from Kei Ito's lab.", serialized["description"])
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self.assertFalse("synonyms" in serialized)
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self.assertFalse("xrefs" in serialized)
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self.assertTrue("examples" in serialized)
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self.assertEqual(10, len(serialized["examples"]))
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expected = [
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{'name': 'VPNp&v1 clone of Ito 2013',
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'data': 'https://www.virtualflybrain.org/data/VFB/i/0002/0254/VFB_00101567/thumbnailT.png',
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'reference': 'VFB_00020254',
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'format': 'PNG'},
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{'data': 'https://www.virtualflybrain.org/data/VFB/i/0002/0206/VFB_00101567/thumbnailT.png',
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'format': 'PNG',
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'name': 'PSa1 clone of Ito 2013',
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'reference': 'VFB_00020206'},
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{'data': 'https://www.virtualflybrain.org/data/VFB/i/0002/0248/VFB_00101567/thumbnailT.png',
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'format': 'PNG',
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'name': 'VLPl2 clone of Ito 2013',
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'reference': 'VFB_00020248'},
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{'data': 'https://www.virtualflybrain.org/data/VFB/i/0002/0209/VFB_00101567/thumbnailT.png',
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'format': 'PNG',
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'name': 'LALv1 clone of Ito 2013',
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'reference': 'VFB_00020209'},
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{'data': 'https://www.virtualflybrain.org/data/VFB/i/0002/0202/VFB_00101567/thumbnailT.png',
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'format': 'PNG',
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'name': 'DM4 clone of Ito 2013',
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'reference': 'VFB_00020202'}
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]
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expected_set = set(frozenset(d.items()) for d in expected)
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result_set = set(frozenset(d.items()) for d in serialized["examples"])
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self.assertEqual(expected_set, result_set)
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self.assertFalse("thumbnail" in serialized)
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self.assertFalse("link" in serialized)
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self.assertEqual(8, len(serialized["types"]))
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self.assertTrue("Template" in serialized["types"])
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self.
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self.assertTrue("description" in serialized)
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self.assertFalse("synonyms" in serialized)
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self.
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self.assertTrue("source" in serialized)
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self.assertTrue("license" in serialized)
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self.assertEqual(1, len(serialized["license"]))
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self.assertEqual({'icon': 'http://mirrors.creativecommons.org/presskit/buttons/88x31/png/by-nc-sa.png',
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