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authorMuriithi Frederick Muriuki2021-08-17 08:47:11 +0300
committerArun Isaac2021-08-18 08:47:34 +0000
commitfc233942e9118a341001f3357a5d2b1c65187736 (patch)
treefe2a707bbffd1d3b4ec1cdba083cf31f9ea2ccd1 /gn3/computations
parent0fbbfa9181229a89da566adcf4bed24281da1e80 (diff)
downloadgenenetwork3-fc233942e9118a341001f3357a5d2b1c65187736.tar.gz
Add tests and fix errors caught with tests
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: fix errors * tests/unit/computations/test_heatmap.py: new tests Add new tests with the expected source data format, and expected results. Fix all errors that were caught by running the tests
Diffstat (limited to 'gn3/computations')
-rw-r--r--gn3/computations/heatmap.py18
1 files changed, 9 insertions, 9 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
index a0e778a..8a86fe8 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/computations/heatmap.py
@@ -34,11 +34,11 @@ def export_trait_data(
"""
def __export_all_types(tdata, strain):
sample_data = []
- if tdata[strain]["val"]:
- sample_data.append(tdata[strain]["val"])
+ if tdata[strain]["value"]:
+ sample_data.append(tdata[strain]["value"])
if var_exists:
- if tdata[strain].var:
- sample_data.append(tdata[strain]["var"])
+ if tdata[strain]["variance"]:
+ sample_data.append(tdata[strain]["variance"])
else:
sample_data.append(None)
if n_exists:
@@ -58,15 +58,15 @@ def export_trait_data(
def __exporter(accumulator, strain):
# pylint: disable=[R0911]
- if trait_data.has_key(strain):
+ if strain in trait_data["data"]:
if dtype == "val":
- return accumulator + (trait_data[strain]["val"], )
+ return accumulator + (trait_data["data"][strain]["value"], )
if dtype == "var":
- return accumulator + (trait_data[strain]["var"], )
+ return accumulator + (trait_data["data"][strain]["variance"], )
if dtype == "N":
- return trait_data[strain]["ndata"]
+ return accumulator + (trait_data["data"][strain]["ndata"], )
if dtype == "all":
- return accumulator + __export_all_types(trait_data, strain)
+ return accumulator + __export_all_types(trait_data["data"], strain)
raise KeyError("Type `%s` is incorrect" % dtype)
if var_exists and n_exists:
return accumulator + (None, None, None)