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Fix long type for big numbers #201

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merged 6 commits into from
Jul 27, 2023
Merged

Fix long type for big numbers #201

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87db9f0
fix(long): change int to float
thanh-nguyen-dang Jun 29, 2023
ab6cb89
fix(test): add test
thanh-nguyen-dang Jul 10, 2023
5ed57df
fix(test): fix test failed
thanh-nguyen-dang Jul 11, 2023
27259d6
fix(data): rollback to old value
thanh-nguyen-dang Jul 21, 2023
2c61a3a
rename the test
thanh-nguyen-dang Jul 27, 2023
8425187
remove submitted_unaligned_reads
thanh-nguyen-dang Jul 27, 2023
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6 changes: 3 additions & 3 deletions peregrine/resources/submission/graphql/node.py
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Original file line number Diff line number Diff line change
Expand Up @@ -525,7 +525,7 @@ def lookup_graphql_type(T):
return {
bool: graphene.Boolean,
float: graphene.Float,
int: graphene.Int,
int: graphene.Float,
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list: graphene.List(graphene.String),
}.get(T, graphene.String)

Expand Down Expand Up @@ -580,7 +580,7 @@ def get_node_interface_args():
of_type=graphene.List(graphene.String),
project_id=graphene.String(),
category=graphene.String(),
)
),
)


Expand Down Expand Up @@ -990,7 +990,7 @@ def get_withpathto_type():
for cls in psqlgraph.Node.get_subclasses()
]
for k, v in cls_attrs.items()
}
},
),
)

Expand Down
4 changes: 2 additions & 2 deletions tests/graphql/data/bulk1.json
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Original file line number Diff line number Diff line change
Expand Up @@ -30,12 +30,12 @@
"doc_format": "JSON"
},
{
"doc": "{\"file_name\": \"C500.CGCI-file1.bam\", \"md5sum\": \"35b39360cc41a7b635980159aef265ba\", \"submitter_id\": \"CGCI-file-1\", \"aliquots\": {\"submitter_id\": \"BLGSP-71-06-00005-99A-01D\"}, \"file_size\": 5962718282, \"type\": \"file\"}",
"doc": "{\"file_name\": \"C500.CGCI-file1.bam\", \"md5sum\": \"35b39360cc41a7b635980159aef265ba\", \"submitter_id\": \"CGCI-file-1\", \"aliquots\": {\"submitter_id\": \"BLGSP-71-06-00005-99A-01D\"}, \"file_size\": 5962718282, \"type\": \"file\"}",
"name": "CGCI-file-1.json",
"doc_format": "JSON"
},
{
"doc": "{\"file_name\": \"C500.CGCI-file2.bam\", \"md5sum\": \"35980159aef265ba35b39360cc41a7b6\", \"submitter_id\": \"CGCI-file-2\", \"aliquots\": {\"submitter_id\": \"BLGSP-71-06-00005-99A-01D\"}, \"file_size\": 5962718282, \"type\": \"file\"}",
"doc": "{\"file_name\": \"C500.CGCI-file2.bam\", \"md5sum\": \"35980159aef265ba35b39360cc41a7b6\", \"submitter_id\": \"CGCI-file-2\", \"aliquots\": {\"submitter_id\": \"BLGSP-71-06-00005-99A-01D\"}, \"file_size\": 5962718282, \"type\": \"file\"}",
"name": "CGCI-file-2.json",
"doc_format": "JSON"
},
Expand Down
2 changes: 1 addition & 1 deletion tests/graphql/data/read_group.json
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Expand Up @@ -10,6 +10,6 @@
"library_strategy": "WXS",
"library_name": "library1",
"is_paired_end": false,
"read_length": 12345,
"read_length": 59627182820,
"read_group_name": "readgroup-1"
}
2 changes: 1 addition & 1 deletion tests/graphql/data/submitted_unaligned_reads.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
},
"submitter_id": "CGCI-file-2",
"data_format": "BAM",
"file_size": 5962718282,
"file_size": 59627182820,
"file_name": "C500.CGCI-file1.bam",
"md5sum": "35b39360cc41a7b635980159aef265ba",
"experimental_strategy": "WGS",
Expand Down
29 changes: 29 additions & 0 deletions tests/graphql/test_graphql.py
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Expand Up @@ -1270,6 +1270,35 @@ def test_without_path_order(client, submitter, pg_driver_clean, cgci_blgsp):
}, r.data


def test_long_as_float_type(client, submitter, pg_driver_clean, cgci_blgsp):
"""Assert the long type is working as float"""
post_example_entities_together(client, pg_driver_clean, submitter)

r = client.post(
path,
headers=submitter,
data=json.dumps(
{
"query": """
query Test {
read_group (
order_by_desc: "read_length",
)
{ submitter_id, read_length }
}
"""
}
),
)
assert r.json == {
"data": {
"read_group": [
{"submitter_id": "test-readgroup-1", "read_length": 59627182820.0},
]
}
}, r.data


def test_read_group_with_path_to_case(client, submitter, pg_driver_clean, cgci_blgsp):
"""Regression for incorrect counts"""
put_example_entities_together(client, pg_driver_clean, submitter)
Expand Down
1 change: 1 addition & 0 deletions tests/graphql/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
"diagnosis.json",
"exposure.json",
"treatment.json",
"read_group.json",
]

PATH = "/v0/submission/graphql"
Expand Down