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faridseififaridseifi
authored
487 handle error when scaffolds batch csv command ran with a folder that does not have the required data (#489)
* Updating tests * added error handling if there is an issue at startup. For example missing input files.
1 parent 7f3f6d4 commit cf13bd4

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6 files changed

+123
-123
lines changed

6 files changed

+123
-123
lines changed

‎scaffold/startup.py‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@
2626
columns=["subject", "preference.json"], index=["subject"]
2727
)
2828
history: pd.DataFrame = pd.DataFrame(
29-
columns=["subject", "period.start","period.end", "history.json"], index=["subject"]
29+
columns=["subject", "period.start", "period.end", "history.json"], index=["subject"]
3030
)
3131
# performance_data = pd.DataFrame()
3232
performance_measure_report = pd.DataFrame()
@@ -88,18 +88,18 @@ def startup(performance_data_path: pathlib.Path = None, performance_m: str = "")
8888
performance_measure_report = pd.read_csv(
8989
os.path.join(performance_data_path, "PerformanceMeasureReport.csv"),
9090
parse_dates=["period.start", "period.end"],
91-
dtype={"subject": str}
91+
dtype={"subject": str},
9292
)
9393
comparator_measure_report = pd.read_csv(
9494
os.path.join(performance_data_path, "ComparatorMeasureReport.csv"),
9595
parse_dates=["period.start", "period.end"],
9696
)
9797
practitioner_role = pd.read_csv(
9898
os.path.join(performance_data_path, "PractitionerRole.csv"),
99-
dtype={"PractitionerRole.identifier": str}
99+
dtype={"PractitionerRole.identifier": str},
100100
)
101101
config = json.load(open(os.path.join(performance_data_path, "config.json")))
102-
102+
103103
if settings.use_preferences:
104104
preferences_file = os.path.join(performance_data_path, "Preference.csv")
105105
if os.path.exists(preferences_file):
@@ -124,8 +124,8 @@ def startup(performance_data_path: pathlib.Path = None, performance_m: str = "")
124124
performance_month = performance_m
125125

126126
except Exception as e:
127-
print("Startup aborted, see traceback:")
128-
raise e
127+
print("Startup aborted:", e)
128+
exit(0)
129129

130130

131131
### read csv file to a dictionary

‎tests/bitstomach/test_achievements.py‎

Lines changed: 18 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -42,18 +42,18 @@ def comparator_data() -> pd.DataFrame:
4242
"measureScore.rate",
4343
"group.code",
4444
],
45-
["BP01", "2022-08-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
46-
["BP01", "2022-08-01", 88.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
47-
["BP01", "2022-08-01", 90.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
48-
["BP01", "2022-08-01", 99.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
49-
["BP01", "2022-09-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
50-
["BP01", "2022-09-01", 89.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
51-
["BP01", "2022-09-01", 91.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
52-
["BP01", "2022-09-01", 100.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
53-
["BP01", "2022-10-01", 80.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
54-
["BP01", "2022-10-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
55-
["BP01", "2022-10-01", 90.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
56-
["BP01", "2022-10-01", 95.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
45+
["BP01", "2022-08-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000126"],
46+
["BP01", "2022-08-01", 0.88, "http://purl.obolibrary.org/obo/PSDO_0000128"],
47+
["BP01", "2022-08-01", 0.90, "http://purl.obolibrary.org/obo/PSDO_0000129"],
48+
["BP01", "2022-08-01", 0.99, "http://purl.obolibrary.org/obo/PSDO_0000094"],
49+
["BP01", "2022-09-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000126"],
50+
["BP01", "2022-09-01", 0.89, "http://purl.obolibrary.org/obo/PSDO_0000128"],
51+
["BP01", "2022-09-01", 0.91, "http://purl.obolibrary.org/obo/PSDO_0000129"],
52+
["BP01", "2022-09-01", 1.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
53+
["BP01", "2022-10-01", 0.80, "http://purl.obolibrary.org/obo/PSDO_0000126"],
54+
["BP01", "2022-10-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000128"],
55+
["BP01", "2022-10-01", 0.90, "http://purl.obolibrary.org/obo/PSDO_0000129"],
56+
["BP01", "2022-10-01", 0.95, "http://purl.obolibrary.org/obo/PSDO_0000094"],
5757
]
5858
comparator_df = pd.DataFrame(comparator_data[1:], columns=comparator_data[0])
5959

@@ -146,7 +146,7 @@ def test_signal_properties(perf_data, comparator_data):
146146
perf_level_test_set = [
147147
(
148148
[0.67, 0.79, 0.97],
149-
[80.0, 85.0, 90.0, 95.0],
149+
[0.80, 0.85, 0.90, 0.95],
150150
{
151151
PSDO.peer_90th_percentile_benchmark,
152152
PSDO.peer_75th_percentile_benchmark,
@@ -157,7 +157,7 @@ def test_signal_properties(perf_data, comparator_data):
157157
),
158158
(
159159
[0.67, 0.95, 0.99],
160-
[80.0, 96.0, 98.0, 97.0],
160+
[0.80, 0.96, 0.98, 0.97],
161161
{
162162
PSDO.peer_90th_percentile_benchmark,
163163
PSDO.peer_75th_percentile_benchmark,
@@ -167,15 +167,15 @@ def test_signal_properties(perf_data, comparator_data):
167167
),
168168
(
169169
[0.67, 0.96, 0.97],
170-
[80.0, 95.0, 96.5, 95.0],
170+
[0.80, 0.95, 0.965, 0.95],
171171
{
172172
PSDO.peer_90th_percentile_benchmark,
173173
},
174174
"last month negative gap for 90 percentile",
175175
),
176176
(
177177
[0.67, 0.98, 0.97],
178-
[80.0, 95.0, 96.5, 95.0],
178+
[0.80, 0.95, 0.965, 0.95],
179179
set(),
180180
"no trend",
181181
),
@@ -217,7 +217,7 @@ def test_detect(perf_data, comparator_data):
217217
new_row_comp = pd.DataFrame(
218218
{
219219
"period.start": "2022-07-01",
220-
"measureScore.rate": [90.0],
220+
"measureScore.rate": [0.9],
221221
"group.code": "http://purl.obolibrary.org/obo/PSDO_0000129",
222222
}
223223
)
@@ -236,7 +236,7 @@ def test_detect(perf_data, comparator_data):
236236
new_row_comp = pd.DataFrame(
237237
{
238238
"period.start": "2022-06-01",
239-
"measureScore.rate": [90.0],
239+
"measureScore.rate": [0.90],
240240
"group.code": "http://purl.obolibrary.org/obo/PSDO_0000129",
241241
}
242242
)

‎tests/bitstomach/test_achievements_over_periods.py‎

Lines changed: 24 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -100,18 +100,18 @@ def comparator_data() -> pd.DataFrame:
100100
"measureScore.rate",
101101
"group.code",
102102
],
103-
["BP01", "2022-08-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
104-
["BP01", "2022-08-01", 88.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
105-
["BP01", "2022-08-01", 90.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
106-
["BP01", "2022-08-01", 99.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
107-
["BP01", "2022-09-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
108-
["BP01", "2022-09-01", 89.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
109-
["BP01", "2022-09-01", 91.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
110-
["BP01", "2022-09-01", 100.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
111-
["BP01", "2022-10-01", 80.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
112-
["BP01", "2022-10-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
113-
["BP01", "2022-10-01", 90.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
114-
["BP01", "2022-10-01", 95.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
103+
["BP01", "2022-08-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000126"],
104+
["BP01", "2022-08-01", 0.88, "http://purl.obolibrary.org/obo/PSDO_0000128"],
105+
["BP01", "2022-08-01", 0.90, "http://purl.obolibrary.org/obo/PSDO_0000129"],
106+
["BP01", "2022-08-01", 0.99, "http://purl.obolibrary.org/obo/PSDO_0000094"],
107+
["BP01", "2022-09-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000126"],
108+
["BP01", "2022-09-01", 0.89, "http://purl.obolibrary.org/obo/PSDO_0000128"],
109+
["BP01", "2022-09-01", 0.91, "http://purl.obolibrary.org/obo/PSDO_0000129"],
110+
["BP01", "2022-09-01", 1.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
111+
["BP01", "2022-10-01", 0.80, "http://purl.obolibrary.org/obo/PSDO_0000126"],
112+
["BP01", "2022-10-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000128"],
113+
["BP01", "2022-10-01", 0.90, "http://purl.obolibrary.org/obo/PSDO_0000129"],
114+
["BP01", "2022-10-01", 0.95, "http://purl.obolibrary.org/obo/PSDO_0000094"],
115115
]
116116
comparator_df = pd.DataFrame(comparator_data[1:], columns=comparator_data[0])
117117

@@ -127,18 +127,18 @@ def comparator_data_quarterly() -> pd.DataFrame:
127127
"measureScore.rate",
128128
"group.code",
129129
],
130-
["BP01", "2022-04-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
131-
["BP01", "2022-04-01", 88.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
132-
["BP01", "2022-04-01", 90.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
133-
["BP01", "2022-04-01", 99.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
134-
["BP01", "2022-07-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
135-
["BP01", "2022-07-01", 89.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
136-
["BP01", "2022-07-01", 91.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
137-
["BP01", "2022-07-01", 100.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
138-
["BP01", "2022-10-01", 80.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
139-
["BP01", "2022-10-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
140-
["BP01", "2022-10-01", 90.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
141-
["BP01", "2022-10-01", 95.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
130+
["BP01", "2022-04-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000126"],
131+
["BP01", "2022-04-01", 0.88, "http://purl.obolibrary.org/obo/PSDO_0000128"],
132+
["BP01", "2022-04-01", 0.90, "http://purl.obolibrary.org/obo/PSDO_0000129"],
133+
["BP01", "2022-04-01", 0.99, "http://purl.obolibrary.org/obo/PSDO_0000094"],
134+
["BP01", "2022-07-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000126"],
135+
["BP01", "2022-07-01", 0.89, "http://purl.obolibrary.org/obo/PSDO_0000128"],
136+
["BP01", "2022-07-01", 0.91, "http://purl.obolibrary.org/obo/PSDO_0000129"],
137+
["BP01", "2022-07-01", 1.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
138+
["BP01", "2022-10-01", 0.80, "http://purl.obolibrary.org/obo/PSDO_0000126"],
139+
["BP01", "2022-10-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000128"],
140+
["BP01", "2022-10-01", 0.90, "http://purl.obolibrary.org/obo/PSDO_0000129"],
141+
["BP01", "2022-10-01", 0.95, "http://purl.obolibrary.org/obo/PSDO_0000094"],
142142
]
143143
comparator_df = pd.DataFrame(comparator_data[1:], columns=comparator_data[0])
144144

‎tests/bitstomach/test_comparisons.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -46,14 +46,14 @@ def comparator_data() -> pd.DataFrame:
4646
"measureScore.rate",
4747
"group.code",
4848
],
49-
["BP01", "2022-08-01", 84.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
50-
["BP01", "2022-08-01", 88.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
51-
["BP01", "2022-08-01", 90.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
52-
["BP01", "2022-08-01", 99.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
53-
["BP01", "2022-09-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
54-
["BP01", "2022-09-01", 89.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
55-
["BP01", "2022-09-01", 91.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
56-
["BP01", "2022-09-01", 100.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
49+
["BP01", "2022-08-01", 0.84, "http://purl.obolibrary.org/obo/PSDO_0000126"],
50+
["BP01", "2022-08-01", 0.88, "http://purl.obolibrary.org/obo/PSDO_0000128"],
51+
["BP01", "2022-08-01", 0.90, "http://purl.obolibrary.org/obo/PSDO_0000129"],
52+
["BP01", "2022-08-01", 0.99, "http://purl.obolibrary.org/obo/PSDO_0000094"],
53+
["BP01", "2022-09-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000126"],
54+
["BP01", "2022-09-01", 0.89, "http://purl.obolibrary.org/obo/PSDO_0000128"],
55+
["BP01", "2022-09-01", 0.91, "http://purl.obolibrary.org/obo/PSDO_0000129"],
56+
["BP01", "2022-09-01", 1.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
5757
]
5858
comparator_df = pd.DataFrame(comparator_data[1:], columns=comparator_data[0])
5959

‎tests/bitstomach/test_loss.py‎

Lines changed: 19 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -41,18 +41,18 @@ def comparator_data() -> pd.DataFrame:
4141
"measureScore.rate",
4242
"group.code",
4343
],
44-
["BP01", "2022-08-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
45-
["BP01", "2022-08-01", 88.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
46-
["BP01", "2022-08-01", 90.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
47-
["BP01", "2022-08-01", 95.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
48-
["BP01", "2022-09-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
49-
["BP01", "2022-09-01", 89.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
50-
["BP01", "2022-09-01", 91.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
51-
["BP01", "2022-09-01", 95.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
52-
["BP01", "2022-10-01", 80.0, "http://purl.obolibrary.org/obo/PSDO_0000126"],
53-
["BP01", "2022-10-01", 85.0, "http://purl.obolibrary.org/obo/PSDO_0000128"],
54-
["BP01", "2022-10-01", 90.0, "http://purl.obolibrary.org/obo/PSDO_0000129"],
55-
["BP01", "2022-10-01", 95.0, "http://purl.obolibrary.org/obo/PSDO_0000094"],
44+
["BP01", "2022-08-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000126"],
45+
["BP01", "2022-08-01", 0.88, "http://purl.obolibrary.org/obo/PSDO_0000128"],
46+
["BP01", "2022-08-01", 0.90, "http://purl.obolibrary.org/obo/PSDO_0000129"],
47+
["BP01", "2022-08-01", 0.95, "http://purl.obolibrary.org/obo/PSDO_0000094"],
48+
["BP01", "2022-09-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000126"],
49+
["BP01", "2022-09-01", 0.89, "http://purl.obolibrary.org/obo/PSDO_0000128"],
50+
["BP01", "2022-09-01", 0.91, "http://purl.obolibrary.org/obo/PSDO_0000129"],
51+
["BP01", "2022-09-01", 0.95, "http://purl.obolibrary.org/obo/PSDO_0000094"],
52+
["BP01", "2022-10-01", 0.80, "http://purl.obolibrary.org/obo/PSDO_0000126"],
53+
["BP01", "2022-10-01", 0.85, "http://purl.obolibrary.org/obo/PSDO_0000128"],
54+
["BP01", "2022-10-01", 0.90, "http://purl.obolibrary.org/obo/PSDO_0000129"],
55+
["BP01", "2022-10-01", 0.95, "http://purl.obolibrary.org/obo/PSDO_0000094"],
5656
]
5757
comparator_df = pd.DataFrame(comparator_data[1:], columns=comparator_data[0])
5858

@@ -137,7 +137,7 @@ def test_signal_properties(perf_data, comparator_data):
137137
perf_level_test_set = [
138138
(
139139
[0.97, 0.96, 0.67],
140-
[80.0, 85.0, 90.0, 95.0],
140+
[0.80, 0.85, 0.90, 0.95],
141141
{
142142
PSDO.peer_average_comparator,
143143
PSDO.peer_75th_percentile_benchmark,
@@ -148,7 +148,7 @@ def test_signal_properties(perf_data, comparator_data):
148148
),
149149
(
150150
[0.99, 0.98, 0.67],
151-
[95.0, 96.0, 99.0, 97.0],
151+
[0.95, 0.96, 0.99, 0.97],
152152
{
153153
PSDO.peer_average_comparator,
154154
PSDO.peer_75th_percentile_benchmark,
@@ -158,15 +158,15 @@ def test_signal_properties(perf_data, comparator_data):
158158
),
159159
(
160160
[0.97, 0.90, 0.67],
161-
[80.0, 94.0, 96.5, 95.0],
161+
[0.80, 0.94, 0.96, 0.95],
162162
{
163163
PSDO.peer_average_comparator,
164164
},
165165
"last month positive gap for peer_average_comparator",
166166
),
167167
(
168168
[0.97, 0.95, 0.81],
169-
[80.0, 94.0, 96.5, 95.0],
169+
[0.80, 0.94, 0.965, 0.95],
170170
{
171171
PSDO.peer_75th_percentile_benchmark,
172172
PSDO.goal_comparator_content,
@@ -175,7 +175,7 @@ def test_signal_properties(perf_data, comparator_data):
175175
),
176176
(
177177
[0.67, 0.98, 0.97],
178-
[80.0, 94.0, 96.5, 95.0],
178+
[0.80, 0.94, 0.965, 0.95],
179179
set(),
180180
"no trend",
181181
),
@@ -214,7 +214,7 @@ def test_detect(perf_data, comparator_data):
214214
new_row_comp = pd.DataFrame(
215215
{
216216
"period.start": "2022-07-01",
217-
"measureScore.rate": [95.0],
217+
"measureScore.rate": [0.95],
218218
"group.code": "http://purl.obolibrary.org/obo/PSDO_0000094",
219219
}
220220
)
@@ -230,7 +230,7 @@ def test_detect(perf_data, comparator_data):
230230
new_row_comp = pd.DataFrame(
231231
{
232232
"period.start": "2022-06-01",
233-
"measureScore.rate": [95.0],
233+
"measureScore.rate": [0.95],
234234
"group.code": "http://purl.obolibrary.org/obo/PSDO_0000094",
235235
}
236236
)

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