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How to use create_cluster method in localstack

Best Python code snippet using localstack_python

test_formation.py

Source:test_formation.py

...12class TestCreation(unittest.TestCase):13    def test_creation_empty(self):14        assert creator([]) == []15    def test_creation_single(self):16        created = creator([create_cluster(3, 8, 71, 76, 'a')])17        print(created)18        assert len(created) == 119        assert created[0].location == FeatureLocation(3, 76)20        assert created[0].kind == CandidateCluster.kinds.SINGLE21    def test_creation_neighbours(self):22        cluster = create_cluster(3, 8, 71, 76, 'a')23        extra_cluster = create_cluster(50, 100, 120, 170, 'b')24        created = creator([cluster, extra_cluster])25        print(created)26        assert len(created) == 327        expected_location = FeatureLocation(cluster.location.start,28                                            extra_cluster.location.end)29        assert created[0].kind == CandidateCluster.kinds.NEIGHBOURING and created[0].location == expected_location30        assert created[1].kind == CandidateCluster.kinds.SINGLE and created[1].location == cluster.location31        assert created[2].kind == CandidateCluster.kinds.SINGLE and created[2].location == extra_cluster.location32    def test_creation_coreoverlap(self):33        cluster = create_cluster(3, 8, 71, 76, 'a')34        extra_cluster = create_cluster(50, 60, 120, 170, 'b')35        # create a CDS within both clusters that has a product from only one cluster36        cds = create_cds(60, 65, ["a"])37        cluster.add_cds(cds)38        extra_cluster.add_cds(cds)39        created = creator([cluster, extra_cluster])40        print(created)41        assert len(created) == 142        candidate_cluster = created[0]43        assert candidate_cluster.kind == CandidateCluster.kinds.INTERLEAVED44        assert candidate_cluster.location == FeatureLocation(3, 170)45    def test_creation_hybrid(self):46        cluster = create_cluster(3, 8, 71, 76, 'a')47        hybrid_cluster = create_cluster(50, 60, 120, 170, 'b')48        # insert the cds that will cause the hybrid call49        cds_ab = create_cds(60, 65, ["a", "b"])50        cluster.add_cds(cds_ab)51        hybrid_cluster.add_cds(cds_ab)52        created = creator([cluster, hybrid_cluster])53        print(created)54        assert len(created) == 155        candidate_cluster = created[0]56        assert candidate_cluster.kind == CandidateCluster.kinds.CHEMICAL_HYBRID57        assert candidate_cluster.location == FeatureLocation(3, 170)58    def test_creation_mixed(self):59        cluster = create_cluster(3, 8, 71, 76, 'a')60        hybrid_cluster = create_cluster(50, 60, 120, 170, 'b')61        overlap_cluster = create_cluster(80, 90, 130, 180, 'o')62        neighbour_cluster = create_cluster(50, 210, 260, 270, 'a')63        isolated_cluster = create_cluster(450, 500, 550, 600, 'alone')64        # insert the cds that will cause the hybrid call65        cds_ab = create_cds(60, 65, ["a", "b"])66        cluster.add_cds(cds_ab)67        hybrid_cluster.add_cds(cds_ab)68        created = creator([cluster, hybrid_cluster, overlap_cluster, neighbour_cluster, isolated_cluster])69        print(created)70        assert len(created) == 571        assert created[0].location == FeatureLocation(3, 270)72        assert created[0].kind == CandidateCluster.kinds.NEIGHBOURING73        assert created[0].protoclusters == (cluster, neighbour_cluster, hybrid_cluster, overlap_cluster)74        assert created[1].location == FeatureLocation(3, 180)75        assert created[1].kind == CandidateCluster.kinds.INTERLEAVED76        assert created[1].protoclusters == (cluster, hybrid_cluster, overlap_cluster)77        assert created[2].location == FeatureLocation(3, 170)78        assert created[2].kind == CandidateCluster.kinds.CHEMICAL_HYBRID79        assert created[2].protoclusters == (cluster, hybrid_cluster)80        assert created[3].location == FeatureLocation(50, 270)81        assert created[3].kind == CandidateCluster.kinds.SINGLE82        assert created[3].protoclusters == (neighbour_cluster,)83        assert created[4].location == FeatureLocation(450, 600)84        assert created[4].kind == CandidateCluster.kinds.SINGLE85        assert created[4].protoclusters == (isolated_cluster,)86    def test_hybrid_interactions(self):87        cluster = create_cluster(3, 8, 171, 176, "a")88        hybrid = create_cluster(3, 8, 50, 55, "b")89        contained = create_cluster(80, 90, 100, 110, "c")  # will form part of hybrid90        hybrid_cds = create_cds(8, 50, ["a", "b"])91        cluster.add_cds(hybrid_cds)92        hybrid.add_cds(hybrid_cds)93        for overlapping in [create_cluster(120, 130, 200, 250, "d"),94                            create_cluster(60, 70, 200, 250, "d")]:95            created = creator([cluster, hybrid, contained, overlapping])96            assert len(created) == 297            assert created[0].location == FeatureLocation(3, 250)98            assert created[0].kind == CandidateCluster.kinds.INTERLEAVED99            assert created[0].protoclusters == tuple(sorted([cluster, hybrid, contained, overlapping]))100            assert created[1].location == FeatureLocation(3, 176)101            assert created[1].kind == CandidateCluster.kinds.CHEMICAL_HYBRID102            assert created[1].protoclusters == (cluster, hybrid, contained)103    def test_interleaving(self):104        # these first two hybrid clumps should be interleaved105        first_hybrid_clusters = [create_cluster(30, 60, 120, 150, "a"),106                                 create_cluster(60, 90, 150, 180, "b")]107        cds = create_cds(90, 120, ["a", "b"])108        for cluster in first_hybrid_clusters:109            cluster.add_cds(cds)110        second_hybrid_clusters = [create_cluster(90, 120, 250, 280, "c"),111                                  create_cluster(190, 220, 280, 310, "d")]112        cds = create_cds(220, 250, ["c", "d"])113        for cluster in second_hybrid_clusters:114            cluster.add_cds(cds)115        # this non-hybrid should also be included in the interleaved116        single = create_cluster(230, 250, 410, 430, "e")117        # this hybrid should not118        standalone = [create_cluster(1000, 1100, 1400, 1500, "f"),119                      create_cluster(1100, 1200, 1500, 1600, "g")]120        cds = create_cds(1300, 1400, ["f", "g"])121        for cluster in standalone:122            cluster.add_cds(cds)123        created = creator(first_hybrid_clusters + second_hybrid_clusters + [single] + standalone)124        assert len(created) == 4125        assert created[0].location == FeatureLocation(30, 430)126        assert created[0].core_location == FeatureLocation(60, 410)127        assert created[0].kind == CandidateCluster.kinds.INTERLEAVED128        assert created[0].protoclusters == tuple(first_hybrid_clusters + second_hybrid_clusters + [single])129        assert created[1].location == FeatureLocation(30, 180)130        assert created[1].protoclusters == tuple(first_hybrid_clusters)131        assert created[2].location == FeatureLocation(90, 310)132        assert created[2].protoclusters == tuple(second_hybrid_clusters)133        for cand in created[1:3]:134            assert cand.kind == CandidateCluster.kinds.CHEMICAL_HYBRID135        assert created[3].location == FeatureLocation(1000, 1600)136        assert created[3].kind == CandidateCluster.kinds.CHEMICAL_HYBRID137    def test_interleaving_order(self):138        clusters = [create_cluster(1000, 1100, 1400, 1500, "a"),139                    create_cluster(1050, 2000, 3000, 4000, "b"), # sorts second due to neighbouring140                    create_cluster(1100, 1200, 1500, 1600, "c")]141        assert sorted(clusters) == clusters142        created = creator(clusters)143        assert len(created) == 3144        assert created[0].kind == CandidateCluster.kinds.NEIGHBOURING145        assert created[0].location == FeatureLocation(1000, 4000)146        assert created[1].kind == CandidateCluster.kinds.INTERLEAVED147        assert created[1].location == FeatureLocation(1000, 1600)148        assert created[2].kind == CandidateCluster.kinds.SINGLE149        assert created[2].location == FeatureLocation(1050, 4000)150    def test_contained_neighbours(self):151        big = create_cluster(0, 100, 130, 230, "a")152        small = create_cluster(10, 20, 30, 40, "b")153        created = creator([big, small])154        assert len(created) == 2155        assert created[0].kind == CandidateCluster.kinds.NEIGHBOURING156        assert created[0].location == big.location157        assert created[1].kind == CandidateCluster.kinds.SINGLE158        assert created[1].location == small.location159    def test_multiple_contained_in_hybrid(self):160        clusters = [161            create_cluster(142916, 162916, 191227, 209850, "a"),  # covers whole region162            create_cluster(142916, 162916, 169708, 189708, "b"),  # causes chem hybrid163            create_cluster(154261, 174261, 175881, 195881, "c"),  # interleaved164            create_cluster(160464, 180464, 183155, 203155, "d"),  # interleaved165        ]166        cds = create_cds(162916, 169708, ["a", "b"])167        clusters[0].add_cds(cds)168        clusters[1].add_cds(cds)169        created = creator(clusters)170        assert len(created) == 1171        assert created[0].kind == CandidateCluster.kinds.CHEMICAL_HYBRID...

test_cluster_prediction.py

Source:test_cluster_prediction.py

...19        irrelevant = rule_parser.DetectionRule("irrelevant", 10, 10, DummyConditions())20        self.rules_by_name = {rule.name: rule for rule in [superior, inferior, irrelevant]}21    def remove(self, clusters):22        return cluster_prediction.remove_redundant_clusters(clusters, self.rules_by_name)23    def create_cluster(self, rule_name, start, end):24        rule = self.rules_by_name[rule_name]25        core = FeatureLocation(start, end)26        surrounds = FeatureLocation(max(0, start - rule.extent), end + rule.extent)27        return Cluster(core, surrounds, tool="testing", cutoff=rule.cutoff,28                       neighbourhood_range=rule.extent, product=rule_name,29                       detection_rule="rule text")30    def test_alone(self):31        clusters = [self.create_cluster("inferior", 101, 110)]32        assert clusters == self.remove(clusters)33    def test_non_overlap(self):34        clusters = [self.create_cluster("inferior", 101, 110),35                    self.create_cluster("superior", 200, 210)]36        assert clusters == self.remove(clusters)37    def test_not_relevant_equal(self):38        clusters = [self.create_cluster("inferior", 101, 110),39                    self.create_cluster("irrelevant", 101, 110)]40        assert clusters == self.remove(clusters)41    def test_not_relevant_contained(self):42        clusters = [self.create_cluster("inferior", 105, 108),43                    self.create_cluster("irrelevant", 101, 110)]44        assert clusters == self.remove(clusters)45    def test_not_relevant_larger(self):46        clusters = [self.create_cluster("inferior", 101, 110),47                    self.create_cluster("irrelevant", 105, 108)]48        assert clusters == self.remove(clusters)49    def test_contained(self):50        clusters = [self.create_cluster("inferior", 110, 210),51                    self.create_cluster("superior", 101, 310)]52        assert self.remove(clusters) == [clusters[1]]53    def test_equal(self):54        clusters = [self.create_cluster("inferior", 101, 110),55                    self.create_cluster("superior", 101, 110)]56        assert self.remove(clusters) == [clusters[1]]57    def test_larger(self):58        clusters = [self.create_cluster("inferior", 101, 110),59                    self.create_cluster("superior", 102, 109)]60        print("testing clusters:", clusters)61        assert self.remove(clusters) == clusters62    def test_extents_dont_matter(self):63        extent = self.rules_by_name["superior"].extent64        for new_extent in [extent - 10, extent + 10]:65            self.rules_by_name["inferior"].extent = new_extent66            self.test_larger()67            self.test_equal()68            self.test_contained()69    def test_cutoffs_dont_matter(self):70        cutoff = self.rules_by_name["superior"].cutoff71        for new_cutoff in [cutoff - 10, cutoff + 10]:72            self.rules_by_name["inferior"].cutoff = new_cutoff73            self.test_larger()...

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