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updated code for the output function trying to detect entries that ar…
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…e empty, especially in the dataset section
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@stuchalk
stuchalk committed Dec 18, 2023
1 parent 836fb98 commit 4f5bbf5
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Showing 2 changed files with 79 additions and 61 deletions.
10 changes: 5 additions & 5 deletions examples/example.py
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Original file line number Diff line number Diff line change
Expand Up @@ -300,12 +300,10 @@ def create_scidata():

# add rights
holder = (
'Chalk Research Group, ',
'Department of Chemistry, ',
'University of North Florida'
'Chalk Research Group, Department of Chemistry, Univ. of North Florida'
)
lic = 'https://creativecommons.org/licenses/by-nc-nd/4.0/'
example.rights([holder, lic])
example.rights([{'holder': holder, 'license': lic}])

packet = [{
"aspects":
Expand Down Expand Up @@ -357,6 +355,8 @@ def create_scidata():
"dataset": [
{"@id": "datapoint",
"@type": "sdo:datapoint",
"empty_entry": "",
"some_entry": "some",
"data": [
{"@id": "datum",
"@type": "sdo:exptdata",
Expand All @@ -365,7 +365,7 @@ def create_scidata():
"12.300000000000000000000000000000",
"units": "uM"}]}]}]

example.scidatapacket(packet)
example.scidatapackage(packet)

# print(json.dumps(example.output, ensure_ascii=False))
print(json.dumps(example.output, indent=4, ensure_ascii=False))
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130 changes: 74 additions & 56 deletions scidatalib/scidata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,8 @@ def __init__(self, uid: str):
"dataset": {
"@id": "dataset/",
"@type": "sdo:dataset",
"dataseries": [], # def dataseries
"datagroup": [], # def datagroup
"datapoint": [], # def datapoint OR def scidatapacket
"scope": ""}, # def scope
},
Expand Down Expand Up @@ -1060,7 +1062,7 @@ def enumuid(uidstr):
def output(self) -> dict:
"""
Completes and cleans a Scidata Object (instance of this class)
before its output.
before it is output.
"""

# add the generatedAt date
Expand All @@ -1076,83 +1078,99 @@ def output(self) -> dict:
# clean scidata
for key in list(self.meta['@graph']['scidata']):
value = self.meta['@graph']['scidata'][key]
if not value or value == "":
if not value:
del self.meta['@graph']['scidata'][key]

# clean methodology, if exists
if 'methodology' in self.meta['@graph']['scidata']:
methodology = self.meta['@graph']['scidata']['methodology']

if methodology.get('aspects', False):
for key in list(methodology):
if not methodology[key] or methodology[key] == "":
del methodology[key]
# check if aspects is set or not in methodology
if 'aspects' in self.meta['@graph']['scidata']['methodology'].keys():
# check if aspects has data
if self.meta['@graph']['scidata']['methodology']['aspects']:
for key in list(self.meta['@graph']['scidata']['methodology']):
if not self.meta['@graph']['scidata']['methodology'][key]:
del self.meta['@graph']['scidata']['methodology'][key]
else:
# as 'aspects' is present but empty, delete the methodology section
del self.meta['@graph']['scidata']['methodology']
else:
# as 'aspects' is empty, delete the methodology section
del methodology
# as 'aspects' is not present, delete the methodology section
del self.meta['@graph']['scidata']['methodology']

# clean system, if exists
# clean system, if exists
if 'system' in self.meta['@graph']['scidata']:
system = self.meta['@graph']['scidata']['system']
if system.get('facets', False):
for key in list(system):
if not system[key] or system[key] == "":
del system[key]
if 'facets' in self.meta['@graph']['scidata']['system'].keys():
# check if aspects has data
if self.meta['@graph']['scidata']['system']['facets']:
for key in list(self.meta['@graph']['scidata']['system']):
if not self.meta['@graph']['scidata']['system'][key]:
del self.meta['@graph']['scidata']['system'][key]
else:
# as 'aspects' is present but empty, delete the methodology section
del self.meta['@graph']['scidata']['system']
else:
# as 'facets' is empty, delete the system section
del system
# as 'facets' is not present, delete the system section
del self.meta['@graph']['scidata']['system']

# remove data set if not data
# remove dataset if no data
if 'dataset' in self.meta['@graph']['scidata']:
dataset = self.meta['@graph']['scidata']['dataset']
if not dataset.get('dataseries', False):
if not dataset.get('datagroups', False):
if not dataset.get('datapoints', False):
del dataset
if not self.meta['@graph']['scidata']['dataset']['dataseries']:
if not self.meta['@graph']['scidata']['dataset']['datagroup']:
if not self.meta['@graph']['scidata']['dataset']['datapoint']:
del self.meta['@graph']['scidata']['dataset']

# clean dataset, if exists
if 'dataset' in self.meta['@graph']['scidata']:
dataset = self.meta['@graph']['scidata']['dataset']
if dataset:
for key in list(dataset):
if not dataset[key] or dataset[key] == "":
del dataset[key]
# if dataset exists and is not empty
if self.meta['@graph']['scidata']['dataset']:
# check each key of the dictionary
for key in list(self.meta['@graph']['scidata']['dataset']):
if not self.meta['@graph']['scidata']['dataset'][key]:
# if the key section is empty, delete the key section
del self.meta['@graph']['scidata']['dataset'][key]

# clean dataseries
if 'dataseries' in dataset.keys():
if dataset.get('dataseries', False):
dataseries = dataset["dataseries"]
for seridx, series in enumerate(dataseries):
for key in list(series):
if not series[key]:
del dataseries[seridx][key]
if 'dataseries' in list(self.meta['@graph']['scidata']['dataset']):
if self.meta['@graph']['scidata']['dataset']['dataseries']:
# look at each series in the list
for seridx in range(len(self.meta['@graph']['scidata']['dataset']['dataseries'])):
for key in list(self.meta['@graph']['scidata']['dataset']['dataseries'][seridx]):
# if the dictionary entry is empty, delete the dictionary entry
if not self.meta['@graph']['scidata']['dataset']['dataseries'][seridx][key]:
del self.meta['@graph']['scidata']['dataset']['dataseries'][seridx][key]
else:
# delete if present but empty
del dataseries
# delete if dataseries is present but empty
del self.meta['@graph']['scidata']['dataset']['dataseries']

# clean datagroups
if 'datagroups' in dataset.keys():
if dataset.get('datagroups', False):
datagroups = dataset["datagroups"]
for grpidx, series in enumerate(datagroups):
for key in list(series):
if not series[key]:
del datagroups[grpidx][key]
if 'datagroup' in list(self.meta['@graph']['scidata']['dataset']):
if self.meta['@graph']['scidata']['dataset']['datagroup']:
# look at each series in the list
for grpidx in range(len(self.meta['@graph']['scidata']['dataset']['datagroup'])):
for key in list(self.meta['@graph']['scidata']['dataset']['datagroup'][grpidx]):
# if the dictionary entry is empty, delete the dictionary entry
if not self.meta['@graph']['scidata']['dataset']['datagroup'][grpidx][key]:
del self.meta['@graph']['scidata']['dataset']['datagroup'][grpidx][key]
else:
# delete if present but empty
del datagroups
# delete if datagroup is present but empty
del self.meta['@graph']['scidata']['dataset']['datagroup']

# clean datapoints
if 'datapoints' in dataset.keys():
if dataset.get('datapoints', False):
datapoints = dataset["datapoints"]
for pntidx, series in enumerate(datapoints):
for key in list(series):
if not series[key]:
del datapoints[pntidx][key]
if 'datapoint' in list(self.meta['@graph']['scidata']['dataset']):
if self.meta['@graph']['scidata']['dataset']['datapoint']:
# look at each series in the list
for pntidx in range(len(self.meta['@graph']['scidata']['dataset']['datapoint'])):
for key in list(self.meta['@graph']['scidata']['dataset']['datapoint'][pntidx]):
# if the dictionary entry is empty, delete the dictionary entry
if not self.meta['@graph']['scidata']['dataset']['datapoint'][pntidx][key]:
del self.meta['@graph']['scidata']['dataset']['datapoint'][pntidx][key]
else:
# delete if present but empty
del datapoints
# delete if datapoint is present but empty
del self.meta['@graph']['scidata']['dataset']['datapoint']

else:
# dataset exists but is empty
del self.meta['@graph']['scidata']['dataset']

# add the toc to the output
self.__addtoc()
Expand Down

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