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SciDataLib-85 Using SciData.output irreversibly deletes json attributes
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added local copy of self.meta as self.temp in output function so data is not removed from self.meta
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@stuchalk
stuchalk committed Dec 18, 2023
1 parent 7fd8448 commit 1ff8547
Showing 1 changed file with 61 additions and 56 deletions.
117 changes: 61 additions & 56 deletions scidatalib/scidata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,7 @@ def __init__(self, uid: str):
self.baseurl = {}
self.meta['@graph']['uid'] = uid
self.uidindex = []
self.temp = {}

# public class methods
def context(self, context: [str, list], replace=False) -> list:
Expand Down Expand Up @@ -1101,114 +1102,118 @@ def output(self) -> dict:
before it is output.
"""

# copy current data to temp variable
# the rest of the code works on the copy so no data is lost in meta
self.temp = self.meta.copy()

# add the generatedAt date
today = datetime.today()
self.meta['generatedAt'] = today.strftime("%m-%d-%y %H:%M:%S")
self.temp['generatedAt'] = today.strftime("%m-%d-%y %H:%M:%S")

# clean @graph
for key in list(self.meta['@graph']):
if not self.meta['@graph'][key]:
for key in list(self.temp['@graph']):
if not self.temp['@graph'][key]:
if key != 'toc':
del self.meta['@graph'][key]
del self.temp['@graph'][key]

# clean scidata
for key in list(self.meta['@graph']['scidata']):
value = self.meta['@graph']['scidata'][key]
for key in list(self.temp['@graph']['scidata']):
value = self.temp['@graph']['scidata'][key]
if not value:
del self.meta['@graph']['scidata'][key]
del self.temp['@graph']['scidata'][key]

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

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

# remove dataset if no data
if 'dataset' in self.meta['@graph']['scidata']:
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']
if 'dataset' in self.temp['@graph']['scidata']:
if not self.temp['@graph']['scidata']['dataset']['dataseries']:
if not self.temp['@graph']['scidata']['dataset']['datagroup']:
if not self.temp['@graph']['scidata']['dataset']['datapoint']:
del self.temp['@graph']['scidata']['dataset']

# clean dataset, if exists
if 'dataset' in self.meta['@graph']['scidata']:
if 'dataset' in self.temp['@graph']['scidata']:
# if dataset exists and is not empty
if self.meta['@graph']['scidata']['dataset']:
if self.temp['@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]:
for key in list(self.temp['@graph']['scidata']['dataset']):
if not self.temp['@graph']['scidata']['dataset'][key]:
# if the key section is empty, delete the key section
del self.meta['@graph']['scidata']['dataset'][key]
del self.temp['@graph']['scidata']['dataset'][key]

# clean dataseries
if 'dataseries' in list(self.meta['@graph']['scidata']['dataset']):
if self.meta['@graph']['scidata']['dataset']['dataseries']:
if 'dataseries' in list(self.temp['@graph']['scidata']['dataset']):
if self.temp['@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]):
for seridx in range(len(self.temp['@graph']['scidata']['dataset']['dataseries'])):
for key in list(self.temp['@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]
if not self.temp['@graph']['scidata']['dataset']['dataseries'][seridx][key]:
del self.temp['@graph']['scidata']['dataset']['dataseries'][seridx][key]
else:
# delete if dataseries is present but empty
del self.meta['@graph']['scidata']['dataset']['dataseries']
del self.temp['@graph']['scidata']['dataset']['dataseries']

# clean datagroups
if 'datagroup' in list(self.meta['@graph']['scidata']['dataset']):
if self.meta['@graph']['scidata']['dataset']['datagroup']:
if 'datagroup' in list(self.temp['@graph']['scidata']['dataset']):
if self.temp['@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]):
for grpidx in range(len(self.temp['@graph']['scidata']['dataset']['datagroup'])):
for key in list(self.temp['@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]
if not self.temp['@graph']['scidata']['dataset']['datagroup'][grpidx][key]:
del self.temp['@graph']['scidata']['dataset']['datagroup'][grpidx][key]
else:
# delete if datagroup is present but empty
del self.meta['@graph']['scidata']['dataset']['datagroup']
del self.temp['@graph']['scidata']['dataset']['datagroup']

# clean datapoints
if 'datapoint' in list(self.meta['@graph']['scidata']['dataset']):
if self.meta['@graph']['scidata']['dataset']['datapoint']:
if 'datapoint' in list(self.temp['@graph']['scidata']['dataset']):
if self.temp['@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]):
for pntidx in range(len(self.temp['@graph']['scidata']['dataset']['datapoint'])):
for key in list(self.temp['@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]
if not self.temp['@graph']['scidata']['dataset']['datapoint'][pntidx][key]:
del self.temp['@graph']['scidata']['dataset']['datapoint'][pntidx][key]
else:
# delete if datapoint is present but empty
del self.meta['@graph']['scidata']['dataset']['datapoint']
del self.temp['@graph']['scidata']['dataset']['datapoint']

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

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

return self.meta
return self.temp

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