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Fix #42 Bug with Install Instructions / Requirements #43

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Fix #42 Bug with Install Instructions / Requirements #43

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a4079ff
Fix #42 Bug with Install Instructions / Requirements
RyanJField Aug 29, 2024
7e5e030
Update tests, add full stop to message
RyanJField Aug 30, 2024
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19 changes: 16 additions & 3 deletions fuji_server/data/repodois.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ ardcx.curtin: https://doi.org/10.17616/R3WM02
ardcx.griffith: https://doi.org/10.17616/R3FG92
ardcx.usq: https://doi.org/10.17616/R36Q18
arfm.ufzdrp: https://doi.org/10.17616/R31NJN1M
awsod.roda: https://doi.org/10.17616/R3M91V
awzy.fednnv: https://doi.org/10.17616/R3PM1K
bamf.bamf: https://doi.org/10.17616/R31NJMZ5
bf.discover: https://doi.org/10.17616/R31NJMN0
Expand Down Expand Up @@ -48,6 +49,7 @@ bl.ukda: https://doi.org/10.17616/R3088K
bmbf.hirzqt: https://doi.org/10.17616/R3CK9G
brown.bdr: https://doi.org/10.17616/R3193B
brvz.rdr: https://doi.org/10.17616/R31NJN5S
bvbw.dhbqgy: https://doi.org/10.17616/R3H35C
caltech.data: https://doi.org/10.17616/R3SW99
carl.frdr: https://doi.org/10.17616/R3X50W
cbg.datasets: https://doi.org/10.17616/R3PP7J
Expand Down Expand Up @@ -90,6 +92,7 @@ dkrz.wdcc: https://doi.org/10.17616/R3989R
dryad.dryad: https://doi.org/10.17616/R34S33
dzhw.fdz-dzhw: https://doi.org/10.17616/R3BR0G
elsevier.md: https://doi.org/10.17616/R3DD11
epua.rdcrki: https://doi.org/10.17616/R3K31G
esdis.ornl: https://doi.org/10.17616/R3SG61
estdoi.keel: https://doi.org/10.17616/R3P636
estdoi.qdb: https://doi.org/10.17616/R31NJMVF
Expand Down Expand Up @@ -131,8 +134,8 @@ gesis.dezim: https://doi.org/10.17616/R31NJMNK
gesis.gesis: https://doi.org/10.17616/R3BB70
gesis.icpsr: https://doi.org/10.17616/R3BC8Q
gesis.indepth: https://doi.org/10.17616/R3432T
gesis.iqb: https://doi.org/10.17616/R3M30D
gesis.neps: https://doi.org/10.17616/R35P7W
gesis.rki: https://doi.org/10.17616/R3K31G
gesis.share: https://doi.org/10.17616/R3BK5N
gesis.sodanet: https://doi.org/10.17616/R38G7R
gesis.srda: https://doi.org/10.17616/R31NJMLA
Expand All @@ -141,6 +144,7 @@ gesis.zpid: https://doi.org/10.17616/R3FS48
hain.njltcl: https://doi.org/10.17616/R31NJNAM
heliophy.spdf: https://doi.org/10.17616/R3P301
hlqc.znxeli: https://doi.org/10.17616/R31NJMJP
hyfx.gqlzxo: https://doi.org/10.17616/R31NJNDH
ieee.dataport: https://doi.org/10.17616/R3H77H
iiasa.dare: https://doi.org/10.17616/R31NJMH0
illinois.databank: https://doi.org/10.17616/R3C93F
Expand All @@ -150,7 +154,7 @@ inist.humanum: https://doi.org/10.17616/R3JM1B
inist.ifremer: https://doi.org/10.17616/R31NJMHX
inist.ifsttar: https://doi.org/10.17616/R31NJMKM
inist.ill: https://doi.org/10.17616/R33H18
inist.inra: https://doi.org/10.17616/R3DJ4J
inist.osuna: https://doi.org/10.17616/R31NJNKA
inist.otelo: https://doi.org/10.17616/R3F19K
inist.resif: https://doi.org/10.17616/R37Q06
iris.iris: https://doi.org/10.17616/R3X607
Expand All @@ -161,6 +165,7 @@ jbru.bbees: https://doi.org/10.17616/R31NJNEN
jcvi.eivbwb: https://doi.org/10.17616/R30P93
jcvi.gxpwaq: https://doi.org/10.17616/R3S634
kaggle.kaggle: https://doi.org/10.17616/R32N5V
kim.colabfit: https://doi.org/10.17616/R31NJNJL
kim.openkim: https://doi.org/10.17616/R3SK8T
kmot.rdr: https://doi.org/10.17616/R31NJMN6
ktsw.aezvvv: https://doi.org/10.17616/R31NJMVX
Expand All @@ -173,6 +178,7 @@ mdw.repository: https://doi.org/10.17616/R30M00
mit.physio: https://doi.org/10.17616/R3D06S
mlbs.skuxgs: https://doi.org/10.17616/R3ZP8D
nasapds.nasapds: https://doi.org/10.17616/R37593
nbqj.daks: https://doi.org/10.17616/R31NJMZS
nkn.nkn: https://doi.org/10.17616/R3JK91
nlqq.xoncsf: https://doi.org/10.17616/R31NJMYB
noaa.ncei: https://doi.org/10.17616/R3362J
Expand All @@ -192,8 +198,13 @@ psu.datacom: https://doi.org/10.17616/R31NJMGV
psu.scholar: https://doi.org/10.17616/R34W4H
pu.dataspace: https://doi.org/10.17616/R33B6F
purdue.purduelib: https://doi.org/10.17616/R3V90N
rdg.prod: https://doi.org/10.17616/R31NJN8R
repod.dbuw: https://doi.org/10.17616/R31NJNHR
repod.mxrdr: https://doi.org/10.17616/R31NJMYU
repod.rds: https://doi.org/10.17616/R31NJMYP
rg.rg: https://doi.org/10.17616/R36H16
rice.kinder: https://doi.org/10.17616/R3GB90
rpak.zvrzin: https://doi.org/10.17616/R31NJNLV
sagebio.synapse: https://doi.org/10.17616/R3B934
si.cda: https://doi.org/10.17616/R3201S
si.si: https://doi.org/10.17616/R3W49N
Expand Down Expand Up @@ -224,9 +235,11 @@ tib.kit4radar: https://doi.org/10.17616/R31NJMVU
tib.ldeo: https://doi.org/10.17616/R3PV10
tib.luis: https://doi.org/10.17616/R3C519
tib.radar: https://doi.org/10.17616/R3ZX96
tib.repod: https://doi.org/10.17616/R3JS93
tib.tuhh: https://doi.org/10.17616/R31NJML0
tib.ub-hro: https://doi.org/10.17616/R31NJMQH
tib.ubbs: https://doi.org/10.17616/R31NJMTU
tib.ubmr: https://doi.org/10.17616/R31NJMTD
tib.ukon: https://doi.org/10.17616/R3M024
tib.zih: https://doi.org/10.17616/R31NJMHY
tuw.tethys: https://doi.org/10.17616/R31NJMU0
Expand All @@ -237,7 +250,7 @@ umn.drum: https://doi.org/10.17616/R30D19
umn.ipums: https://doi.org/10.17616/R3ZS59
undr.undr: https://doi.org/10.17616/R31NJN9K
unimelb.repo1: https://doi.org/10.17616/R3HH10
unm.dataone: https://doi.org/10.17616/R3101G
unisalzb.anc: https://doi.org/10.17616/R31NJNKJ
usda.usda: https://doi.org/10.17616/R3G051
usgs.prod: https://doi.org/10.17616/R33S3S
uva.libra: https://doi.org/10.17616/R3TS86
Expand Down
3 changes: 2 additions & 1 deletion fuji_server/data/software_file.json
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,8 @@
],
"parse": "file_name",
"pattern": [
"requirements\\.txt"
"requirements\\.txt",
"pyproject\\.toml"
]
},
"docs_directory": {
Expand Down
10 changes: 7 additions & 3 deletions fuji_server/evaluators/fair_evaluator_requirements.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ def nestedDataContainsKeyword(self, data, key):
)
for d in values:
if isinstance(d, bytes):
d = d.decode("utf-8")
d = d.decode("utf-8", errors="replace")
if isinstance(d, str):
if key in d.lower():
return True
Expand Down Expand Up @@ -88,13 +88,17 @@ def scanForKeywords(self, keywords, locations):
content = self.fuji.github_data.get(location)
if content is not None:
if isinstance(content, bytes):
content = content.decode("utf-8")
content = content.decode("utf-8", errors="replace")
if isinstance(content, str):
if k in content.lower():
hit_dict[k] = True # found keyword in location
keys_to_check.remove(k) # stop looking, have found something for this key
else:
hit_dict[k] = self.nestedDataContainsKeyword(content, k)
if hit_dict[k] is True:
keys_to_check.remove(k) # Need to also stop looking
self.logger.info(
f"{self.metric_identifier} : Found {k} in {location}."
) # Info message for specific keys
return hit_dict

def testInstructions(self):
Expand Down
3 changes: 2 additions & 1 deletion fuji_server/yaml/metrics_v0.7_software.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -356,6 +356,7 @@ metrics:
required:
dependency_file:
- requirements.txt
- pyproject.toml
- target: https://f-uji.net/vocab/metadata/standards
modality: all
required:
Expand All @@ -367,7 +368,7 @@ metrics:
- deploy
created_by: FAIR4RS
date_created: 2024-01-18
date_updated: 2024-01-18
date_updated: 2024-08-28
version: 0.1
total_score: 2
- metric_identifier: FRSM-14-R1
Expand Down
4 changes: 2 additions & 2 deletions tests/functional/cassettes/test_evaluation/test_evaluation_software.yaml
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54 changes: 27 additions & 27 deletions tests/functional/test_evaluation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -176,13 +176,13 @@ def test_evaluation_software(client: FlaskClient) -> None:
response = client.post(valid_url, json=payload, headers=headers)
assert response.status_code == HTTP_200_OK

# these are the results from 2024-05-03
# these are the results from 2024-08-30
expected = {
"score_earned": {
"A": 0,
"F": 0,
"I": 0,
"R": 4,
"R": 5,
"A1": 0,
"F1": 0,
"F1.1": 0,
Expand All @@ -192,10 +192,10 @@ def test_evaluation_software(client: FlaskClient) -> None:
"F4": 0,
"I1": 0,
"I2": 0,
"R1": 0,
"R1": 1,
"R1.1": 4,
"R1.2": 0,
"FAIR": 4.0,
"FAIR": 5,
},
"score_total": {
"A": 2,
Expand All @@ -214,26 +214,26 @@ def test_evaluation_software(client: FlaskClient) -> None:
"R1": 8,
"R1.1": 5,
"R1.2": 3,
"FAIR": 45.0,
"FAIR": 45,
},
"score_percent": {
"A": 0.0,
"F": 0.0,
"I": 0.0,
"R": 25.0,
"A1": 0.0,
"F1": 0.0,
"F1.1": 0.0,
"F1.2": 0.0,
"F2": 0.0,
"F3": 0.0,
"F4": 0.0,
"I1": 0.0,
"I2": 0.0,
"R1": 0.0,
"R1.1": 80.0,
"R1.2": 0.0,
"FAIR": 8.89,
"A": 0,
"F": 0,
"I": 0,
"R": 31.25,
"A1": 0,
"F1": 0,
"F1.1": 0,
"F1.2": 0,
"F2": 0,
"F3": 0,
"F4": 0,
"I1": 0,
"I2": 0,
"R1": 12.5,
"R1.1": 80,
"R1.2": 0,
"FAIR": 11.11,
},
"status_total": {
"A1": 1,
Expand Down Expand Up @@ -264,14 +264,14 @@ def test_evaluation_software(client: FlaskClient) -> None:
"F4": 0,
"I1": 0,
"I2": 0,
"R1": 0,
"R1": 1,
"R1.1": 2,
"R1.2": 0,
"A": 0,
"F": 0,
"I": 0,
"R": 2,
"FAIR": 2,
"R": 3,
"FAIR": 3,
},
"maturity": {
"A": 0,
Expand All @@ -287,10 +287,10 @@ def test_evaluation_software(client: FlaskClient) -> None:
"F4": 0,
"I1": 0,
"I2": 0,
"R1": 0,
"R1": 1,
"R1.1": 3,
"R1.2": 0,
"FAIR": 1.0,
"FAIR": 1,
},
}
response_json = response.json()
Expand Down