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‎samples/lineage_example.py‎

Lines changed: 118 additions & 52 deletions
Original file line numberDiff line numberDiff line change
@@ -10,67 +10,128 @@
1010
###################
1111
# Create a data class domain
1212
###################
13-
simple_molecules_domain = api.domain.create({
14-
"kind": "DataClass",
15-
"domainDesign": {
16-
"name": "SimpleMolecules",
17-
"fields": [
18-
{"name": "formula", "label": "Chemical Formula", "rangeURI": "string"},
19-
{"name": "molarMass", "label": "Molar Mass (g/mol)", "rangeURI": "double"},
20-
]
13+
simple_molecules_domain = api.domain.create(
14+
{
15+
"kind": "DataClass",
16+
"domainDesign": {
17+
"name": "SimpleMolecules",
18+
"fields": [
19+
{"name": "formula", "label": "Chemical Formula", "rangeURI": "string"},
20+
{"name": "molarMass", "label": "Molar Mass (g/mol)", "rangeURI": "double"},
21+
],
22+
},
2123
}
22-
})
24+
)
2325

24-
api.query.insert_rows("exp.data", "SimpleMolecules", [
25-
{"name": "Water", "formula": "H20", "molarMass": 18.01528},
26-
{"name": "Salt", "formula": "NaCl", "molarMass": 58.443}
27-
])
26+
api.query.insert_rows(
27+
"exp.data",
28+
"SimpleMolecules",
29+
[
30+
{"name": "Water", "formula": "H20", "molarMass": 18.01528},
31+
{"name": "Salt", "formula": "NaCl", "molarMass": 58.443},
32+
],
33+
)
2834

2935
###################
3036
# Create a second data class domain
3137
###################
32-
substances_domain = api.domain.create({
33-
"kind": "DataClass",
34-
"domainDesign": {
35-
"name": "Substances",
36-
"fields": [
37-
{"name": "type", "rangeURI": "string"},
38-
{"name": "fromNature", "rangeURI": "boolean"},
39-
]
38+
substances_domain = api.domain.create(
39+
{
40+
"kind": "DataClass",
41+
"domainDesign": {
42+
"name": "Substances",
43+
"fields": [
44+
{"name": "type", "rangeURI": "string"},
45+
{"name": "fromNature", "rangeURI": "boolean"},
46+
],
47+
},
4048
}
41-
})
42-
43-
api.query.insert_rows("exp.data", "Substances", [
44-
{"name": "Ocean Water", "type": "liquid", "fromNature": True, "DataInputs/SimpleMolecules": "Water, Salt"},
45-
{"name": "Bath Water", "type": "liquid", "fromNature": False, "DataInputs/SimpleMolecules": "Water"}
46-
])
49+
)
50+
51+
api.query.insert_rows(
52+
"exp.data",
53+
"Substances",
54+
[
55+
{
56+
"name": "Ocean Water",
57+
"type": "liquid",
58+
"fromNature": True,
59+
"DataInputs/SimpleMolecules": "Water, Salt",
60+
},
61+
{
62+
"name": "Bath Water",
63+
"type": "liquid",
64+
"fromNature": False,
65+
"DataInputs/SimpleMolecules": "Water",
66+
},
67+
],
68+
)
4769

4870
###################
4971
# Create a sample type domain
5072
###################
51-
field_samples_domain = api.domain.create({
52-
"kind": "SampleSet",
53-
"domainDesign": {
54-
"name": "FieldSamples",
55-
"fields": [
56-
{"name": "name", "rangeURI": "string"},
57-
{"name": "receivedDate", "rangeURI": "dateTime"},
58-
{"name": "volume_mL", "rangeURI": "int"},
59-
]
73+
field_samples_domain = api.domain.create(
74+
{
75+
"kind": "SampleSet",
76+
"domainDesign": {
77+
"name": "FieldSamples",
78+
"fields": [
79+
{"name": "name", "rangeURI": "string"},
80+
{"name": "receivedDate", "rangeURI": "dateTime"},
81+
{"name": "volume_mL", "rangeURI": "int"},
82+
],
83+
},
6084
}
61-
})
62-
63-
api.query.insert_rows("samples", "FieldSamples", [
64-
{"name": "OC-1", "receivedDate": "05/12/2025", "volume_mL": 400, "DataInputs/Substances": "Ocean Water"},
65-
{"name": "OC-2", "receivedDate": "05/13/2025", "volume_mL": 600, "DataInputs/Substances": "Ocean Water"},
66-
{"name": "OC-3", "receivedDate": "05/14/2025", "volume_mL": 800, "DataInputs/Substances": "Ocean Water"},
67-
68-
{"name": "BW-1", "receivedDate": "05/12/2025", "volume_mL": 400, "DataInputs/Substances": "Bath Water"},
69-
{"name": "BW-2", "receivedDate": "05/13/2025", "volume_mL": 600, "DataInputs/Substances": "Bath Water"},
70-
{"name": "BW-3", "receivedDate": "05/14/2025", "volume_mL": 800, "DataInputs/Substances": "Bath Water"},
71-
72-
{"name": "Mixed-1", "receivedDate": "05/18/2025", "volume_mL": 50, "DataInputs/Substances": "\"Bath Water\", \"Ocean Water\""},
73-
])
85+
)
86+
87+
api.query.insert_rows(
88+
"samples",
89+
"FieldSamples",
90+
[
91+
{
92+
"name": "OC-1",
93+
"receivedDate": "05/12/2025",
94+
"volume_mL": 400,
95+
"DataInputs/Substances": "Ocean Water",
96+
},
97+
{
98+
"name": "OC-2",
99+
"receivedDate": "05/13/2025",
100+
"volume_mL": 600,
101+
"DataInputs/Substances": "Ocean Water",
102+
},
103+
{
104+
"name": "OC-3",
105+
"receivedDate": "05/14/2025",
106+
"volume_mL": 800,
107+
"DataInputs/Substances": "Ocean Water",
108+
},
109+
{
110+
"name": "BW-1",
111+
"receivedDate": "05/12/2025",
112+
"volume_mL": 400,
113+
"DataInputs/Substances": "Bath Water",
114+
},
115+
{
116+
"name": "BW-2",
117+
"receivedDate": "05/13/2025",
118+
"volume_mL": 600,
119+
"DataInputs/Substances": "Bath Water",
120+
},
121+
{
122+
"name": "BW-3",
123+
"receivedDate": "05/14/2025",
124+
"volume_mL": 800,
125+
"DataInputs/Substances": "Bath Water",
126+
},
127+
{
128+
"name": "Mixed-1",
129+
"receivedDate": "05/18/2025",
130+
"volume_mL": 50,
131+
"DataInputs/Substances": '"Bath Water", "Ocean Water"',
132+
},
133+
],
134+
)
74135

75136
###################
76137
# Query the lineage
@@ -82,7 +143,9 @@
82143
entity_name = "Ocean Water"
83144

84145
# Fetch the LSID of the "seed" for the lineage request. In this case, we'll query for the "Ocean Water" entity in Substances.
85-
result = api.query.select_rows(schema_name, query_name, columns="Name, LSID", filter_array=[QueryFilter("name", entity_name)])
146+
result = api.query.select_rows(
147+
schema_name, query_name, columns="Name, LSID", filter_array=[QueryFilter("name", entity_name)]
148+
)
86149
seed_lsid = result["rows"][0]["LSID"]
87150

88151
# Lineage results includes the following:
@@ -94,6 +157,7 @@
94157
# "children": An aray of objects representing edges in the graph to nodes to which this node refers.
95158
lineage_result = api.experiment.lineage([seed_lsid], depth=10)
96159

160+
97161
###################
98162
# Traverse the lineage
99163
###################
@@ -114,9 +178,11 @@ def process_edges(edges, offset):
114178
for edge in edges:
115179
related_lsid = edge["lsid"]
116180
related_node = lineage_result["nodes"][related_lsid]
117-
nodes_by_depth[new_depth].add(related_node['name'])
181+
nodes_by_depth[new_depth].add(related_node["name"])
118182

119-
traverse_lineage(related_lsid, lineage_result, new_depth, visited.copy(), nodes_by_depth)
183+
traverse_lineage(
184+
related_lsid, lineage_result, new_depth, visited.copy(), nodes_by_depth
185+
)
120186

121187
process_edges(node.get("parents", []), -1)
122188
process_edges(node.get("children", []), 1)

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