Cluster the cluster data #18
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ialarmedalien
commented
Aug 18, 2020
| _CLUSTER_BASE = os.path.join(configuration['ROOT_DATA_PATH'], 'cluster_data') | ||
| configuration['_CLUSTER_PATHS'] = { | ||
| 'cluster_I2': os.path.join( | ||
| 'markov_i2': os.path.join( |
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rename these to something more informative
ialarmedalien
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Aug 18, 2020
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| self.check_deltas(edge_data=edge_data, node_metadata=node_metadata, cluster_data=clusters) | ||
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| def check_deltas(self, edge_data={}, node_metadata={}, cluster_data={}): |
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brief dataset summary for sanity checking
ialarmedalien
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Aug 18, 2020
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| for data_structure in [edge_data, expected]: | ||
| for k in data_structure.keys(): | ||
| data_structure[k] = sorted(data_structure[k], key=lambda n: n['_key']) |
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order data as it won't necessarily be sorted when coming out of the parser
ialarmedalien
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Aug 18, 2020
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| clusters: | ||
| type: array | ||
| title: Clusters | ||
| description: Clusters to which the node has been assigned | ||
| items: | ||
| type: string | ||
| format: regex | ||
| pattern: ^\w+:\d+$ | ||
| examples: [["markov_i2:1", "markov_i4:5"], ["markov_i6:3"]] |
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The important bit
ialarmedalien
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Aug 18, 2020
| # nodes are represented as a list of node[_key] | ||
| # edges are objects with keys _to, _from, edge_type and score | ||
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| def test_fetch_phenotypes_no_results(self): |
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the queries with no results have been merged in with the other tests
Update parser and tests accordingly
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jayrbolton
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Aug 19, 2020
| title: Cluster IDs | ||
| description: Cluster IDs, in the form "clustering_system_name:cluster_id" | ||
| items: {type: string} | ||
| examples: [['markov_i2:5', 'markov_i6:2'],['markov_i6:1']] |
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Should this be an object so we don't have to parse these entries?
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I guess if the client is using string parameters like "markov_i2:5" then it doesn't matter
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Part 1 of the changes in this old PR in the relation_engine_spec repo.
Merge all
clusterfields in thedjornl_nodecollection into a single field.Update parser and tests accordingly.