Add new tests

tests/edge/test_nanopubstore_start_dates.py

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+#!/usr/bin/env python
+
+# from bel.Config import config
+# import bel.edge.edges
+# import json
+
+
+# def test_get_start_dates():
+
+#     doc = bel.edge.edges.get_start_dates()
+#     print(doc)
+#     assert doc['_key'] == 'nanopubstore_start_dt'
+#     assert 'start_dates' in doc
+
+
+# def test_update_start_dates():
+
+#     bel.edge.pipeline.put_start_dates('https://nanopubstore.demo.biodati.com', '2018-02-21T01:01:30.000Z')
+#     doc = bel.edge.pipeline.get_start_dates()
+#     print(f'Doc1: {json.dumps(doc, indent=4)}')
+#     assert '2018-02-21T01:01:30.000Z' == [start_date for start_date in doc['start_dates'] if start_date['nanopubstore_url'] == 'https://nanopubstore.demo.biodati.com'][0]['start_dt']
+
+#     bel.edge.pipeline.put_start_dates('https://nanopubstore.test.biodati.com', '2018-01-21T01:01:30.000Z')
+#     doc = bel.edge.pipeline.get_start_dates()
+#     print(f'Doc2: {json.dumps(doc, indent=4)}')
+#     assert '2018-01-21T01:01:30.000Z' == [start_date for start_date in doc['start_dates'] if start_date['nanopubstore_url'] == 'https://nanopubstore.test.biodati.com'][0]['start_dt']
+
+#     bel.edge.pipeline.put_start_dates('https://nanopubstore.demo.biodati.com', '2018-02-30T01:01:30.000Z')
+#     doc = bel.edge.pipeline.get_start_dates()
+#     print(f'Doc3: {json.dumps(doc, indent=4)}')
+#     assert '2018-02-30T01:01:30.000Z' == [start_date for start_date in doc['start_dates'] if start_date['nanopubstore_url'] == 'https://nanopubstore.demo.biodati.com'][0]['start_dt']
+
+

tests/lang/test_migrate12.py

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+import bel.lang.migrate_1_2
+
+
+def test_migrate():
+
+    # No migration examples
+    bel1 = 'sec(a(CHEBI:"3-hydroxybutyrate"))'
+    bel2 = 'sec(a(CHEBI:"3-hydroxybutyrate"))'
+
+    assert bel.lang.migrate_1_2.migrate(bel1) == bel2
+
+    # kin() -> activity()
+    # bel1 = 'p(HGNC:BRAF,sub(V,599,E)) directlyIncreases kin(p(HGNC:BRAF))'
+    # bel2 = 'p(HGNC:BRAF, var("p.599V>E")) directlyIncreases act(p(HGNC:BRAF), ma(kin))'
+
+    bel1 = 'kin(p(HGNC:BRAF))'
+    bel2 = 'act(p(HGNC:BRAF), ma(kin))'
+
+    assert bel.lang.migrate_1_2.migrate(bel1) == bel2
+
+    # cat() -> act()
+    bel1 = 'cat(p(RGD:Sod1))'
+    bel2 = 'act(p(RGD:Sod1), ma(cat))'
+
+    assert bel.lang.migrate_1_2.migrate(bel1) == bel2
+
+    # sub() -> var()
+
+    # p(HGNC:CFTR, var(p.Gly576Ala))  # substitution using 3 or 1 letter amino acid code, *=stop codon
+    # p(HGNC:CFTR, var(p.C65* ))  # truncation at residue 65
+    # r(HGNC:CFTR), var(r.243a>u)  # [a, g, c, u]
+    # g(HGNC:CFTR), var(c.243A>T)  # [A, G, C, T]  (g.* prefix is for genomic sequence)
+
+    bel1 = 'p(HGNC:PIK3CA, sub(E, 545, K))'
+    bel2 = 'p(HGNC:PIK3CA, var("p.Glu545Lys"))'
+
+    assert bel.lang.migrate_1_2.migrate(bel1) == bel2
+
+    # trunc() -> var()
+    bel1 = 'p(HGNC:ABCA1, trunc(1851))'
+    bel2 = 'p(HGNC:ABCA1, var("truncated at 1851"))'
+
+    assert bel.lang.migrate_1_2.migrate(bel1) == bel2
+
+    # fus()
+    bel1 = 'r(HGNC:BCR, fus(HGNC:JAK2, 1875, 2626), pmod(P))'
+    bel2 = 'r(fus(HGNC:BCR, "r.1_1875", HGNC:JAK2, "r.2626_?"), pmod(Ph))'
+
+    assert bel.lang.migrate_1_2.migrate(bel1) == bel2
+
+    bel1 = 'p(HGNC:BCR, fus(HGNC:JAK2))'
+    bel2 = 'p(fus(HGNC:BCR, ?, HGNC:JAK2, ?))'
+
+    assert bel.lang.migrate_1_2.migrate(bel1) == bel2
+
+    # pmod() - updating modtype
+    bel1 = 'p(HGNC:MAPK1, pmod(P, Thr, 185))'
+    bel2 = 'p(HGNC:MAPK1, pmod(Ph, Thr, 185))'
+
+    assert bel.lang.migrate_1_2.migrate(bel1) == bel2
+
+    # tloc()
+    bel1 = 'tloc(p(HGNC:EGFR), MESHCL:Cytoplasm, MESHCL:"Cell Nucleus")'
+    bel2 = 'tloc(p(HGNC:EGFR), fromLoc(MESHCL:Cytoplasm), toLoc(MESHCL:"Cell Nucleus"))'
+
+    assert bel.lang.migrate_1_2.migrate(bel1) == bel2

tests/lang/test_partialparse.py

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+import bel.lang.partialparse
+
+
+def test_parse():
+
+    bel_version = '2.0.0'
+    belstr = 'sec(a(CHEBI:"3-hydroxybutyrate"))'
+    ast = bel.lang.partialparse.get_ast_obj(belstr, bel_version)
+
+    print(ast.to_string())
+
+    assert False