Skip to content

Commit

Permalink
Merge pull request #55 from ChalkLab/use-pytest-fixture
Browse files Browse the repository at this point in the history 
Switches to fixture in tests, added attributes method, and added common iterate function
  • Loading branch information
@JohnsonDylan
JohnsonDylan committed Apr 27, 2021
2 parents 5902f07 + 6c13bb5 commit 79801a7
Show file tree
Hide file tree
Showing 2 changed files with 198 additions and 153 deletions.
233 changes: 114 additions & 119 deletions scidatalib/scidata.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -417,48 +417,15 @@ def aspects(self, aspects: list) -> list:
"""Add to or replace the aspects of the file"""
cnt_index = {}

def iterateaspects(it, level):
""" iterateaspects function """
if isinstance(it, str):
self.__addid(it)
return it
elif '@id' in it:
category = it['@id']
else:
category = 'undefined'
if category in cnt_index:
cnt_index[category] += 1
else:
cnt_index[category] = 1
cat_index.update({level: category})
uid = ''
for cat in cat_index.values():
uid += cat + '/' + str(cnt_index[category]) + '/'
temp: dict = {'@id': uid, '@type': 'sdo:' + category}
for k in it.keys():
if k != '@id':
if isinstance(it[k], list):
level += 1
for i, y in enumerate(it[k]):
it[k][i] = iterateaspects(y, level)
temp[k] = it[k]
level -= 1
elif isinstance(it[k], dict):
level += 1
temp[k] = iterateaspects(it[k], level)
level -= 1
else:
temp[k] = it[k]
self.__addid(it[k])
return temp

scidata: dict = self.meta['@graph']['scidata']
meth: dict = scidata['methodology']
curr_aspects: list = meth['aspects']

for item in aspects:
cat_index = {}
item = iterateaspects(item, 1)
item, category, count, cat_index = self.__iterate_function(
item, 1, cnt_index, cat_index)
cnt_index[category] = count
curr_aspects.append(item)

meth['aspects'] = curr_aspects
Expand All @@ -471,50 +438,15 @@ def facets(self, facets: list) -> list:
"""Add to or replace the facets of the file"""
cnt_index = {}

def iteratefacets(it, level):
""" iteratefacets function """
if isinstance(it, str):
self.__addid(it)
return it
elif '@id' in it:
category = it['@id']
elif 'descriptors' in it or 'identifiers' in it:
category = 'compound'
else:
category = 'undefined'
if category in cnt_index:
cnt_index[category] += 1
else:
cnt_index[category] = 1
cat_index.update({level: category})
uid = ''
for cat in cat_index.values():
uid += cat + '/' + str(cnt_index[category]) + '/'
temp: dict = {'@id': uid, '@type': 'sdo:' + category}
for k in it.keys():
if k != '@id':
if isinstance(it[k], list):
level += 1
for i, y in enumerate(it[k]):
it[k][i] = iteratefacets(y, level)
temp[k] = it[k]
level -= 1
elif isinstance(it[k], dict):
level += 1
temp[k] = iteratefacets(it[k], level)
level -= 1
else:
temp[k] = it[k]
self.__addid(it[k])
return temp

scidata: dict = self.meta['@graph']['scidata']
system: dict = scidata['system']
curr_facets: list = system['facets']

for item in facets:
cat_index = {}
item = iteratefacets(item, 1)
item, category, count, cat_index = self.__iterate_function(
item, 1, cnt_index, cat_index)
cnt_index[category] = count
curr_facets.append(item)

system['facets'] = curr_facets
Expand All @@ -538,45 +470,34 @@ def scope(self, scope: [str, list]) -> str:
self.meta['@graph']['scidata']['dataset']['scope'] = scope
return self.meta['@graph']['scidata']['dataset']['scope']

def attribute(self, attributes: list) -> list:
"""Add one or more attributes"""
cnt_index = {}

scidata: dict = self.meta['@graph']['scidata']
dataset: dict = scidata['dataset']
if 'attribute' in dataset.keys():
curr_attributes: list = dataset['attribute']
else:
curr_attributes = []

for item in attributes:
cat_index = {}
cnt_index = {'attribute': len(curr_attributes)}
item, category, count, cat_index = self.__iterate_function(
item, 1, cnt_index, cat_index)
cnt_index[category] = count
curr_attributes.append(item)

dataset['attribute'] = curr_attributes
scidata['dataset'] = dataset
self.meta['@graph']['scidata'] = scidata
return curr_attributes

def datapoint(self, points: list) -> list:
"""Add one or more datapoints"""
cnt_index = {}

def iteratedatapoint(it, level):
""" iteratedatapoint function """
if isinstance(it, str):
self.__addid(it)
return it
elif '@id' in it:
category = it['@id']
else:
category = 'undefined'
if category in cnt_index:
cnt_index[category] += 1
else:
cnt_index[category] = 1
cat_index.update({level: category})
uid = ''
for cat in cat_index.values():
uid += cat + '/' + str(cnt_index[cat]) + '/'
temp: dict = {'@id': uid, '@type': 'sdo:' + category}
for k in it.keys():
if k != '@id':
if isinstance(it[k], list):
level += 1
for i, y in enumerate(it[k]):
it[k][i] = iteratedatapoint(y, level)
temp[k] = it[k]
level -= 1
elif isinstance(it[k], dict):
level += 1
temp[k] = iteratedatapoint(it[k], level)
level -= 1
else:
temp[k] = it[k]
self.__addid(it[k])
return temp

scidata: dict = self.meta['@graph']['scidata']
dataset: dict = scidata['dataset']
if 'datapoint' in dataset.keys():
Expand All @@ -587,7 +508,9 @@ def iteratedatapoint(it, level):
for item in points:
cat_index = {}
cnt_index = {'datapoint': len(curr_points)}
item = iteratedatapoint(item, 1)
item, category, count, cat_index = self.__iterate_function(
item, 1, cnt_index, cat_index)
cnt_index[category] = count
curr_points.append(item)

dataset['datapoint'] = curr_points
Expand Down Expand Up @@ -619,16 +542,28 @@ def iteratedatagroup(it, level):
temp: dict = {'@id': uid, '@type': 'sdo:' + category}
if 'source' in it:
temp.update({'source': it['source']})

dset = self.meta['@graph']['scidata']['dataset']
pointlist = []
for x in it['datapoints']:
dset = self.meta['@graph']['scidata']['dataset']
if 'datapoint' in dset:
cnt = len(dset['datapoint'])
else:
cnt = 0
pointlist.append('datapoint/' + str(cnt + 1) + '/')
self.datapoint([x])
temp['datapoints'] = pointlist
if 'datapoints' in it:
for x in it['datapoints']:
if 'datapoint' in dset:
cnt = len(dset['datapoint'])
else:
cnt = 0
pointlist.append('datapoint/' + str(cnt + 1) + '/')
self.datapoint([x])
temp['datapoints'] = pointlist
if 'attribute' in it:
for x in it['attribute']:
if 'attribute' in dset:
cnt = len(dset['attribute'])
else:
cnt = 0
pointlist.append('attribute/' + str(cnt + 1) + '/')
self.attribute([x])
temp['attribute'] = pointlist

return temp

scidata: dict = self.meta['@graph']['scidata']
Expand Down Expand Up @@ -757,6 +692,66 @@ def __make_context(self) -> dict:
self.meta["@context"] = c + [n, b]
return self.meta["@context"]

def __iterate_function(self, it, level, cnt_index, cat_index):
"""
Recursive function to iteratively update @id, @type, and categories
for a sub-section
:param it: string or list of objects to iterate over
:param level: current level of sub-section
:param cnt_index: dict to keep the count of a repeated category
:param cat_index: dict to keep the category level
:return: Tuple of [
updated object in the iterated listcategory,
category of object,
count of the given repeated category,
update cat_index
]
"""
new_cat_index = cat_index.copy()

if isinstance(it, str):
self.__addid(it)
return it, 1, cnt_index, cat_index

if '@id' in it:
category = it['@id']
elif 'descriptors' in it or 'identifiers' in it:
category = 'compound'
else:
category = 'undefined'

count = 1
if category in cnt_index:
count = cnt_index[category] + 1

new_cat_index.update({level: category})

uid = ''
for cat in list(new_cat_index.values()):
uid += cat + '/' + str(count) + '/'
temp: dict = {'@id': uid, '@type': 'sdo:' + category}
for k in it.keys():
if k != '@id':
if isinstance(it[k], list):
level += 1
for i, y in enumerate(it[k]):
it[k][i], category, count, new_cat_index = \
self.__iterate_function(
y, level, cnt_index, new_cat_index)
temp[k] = it[k]
level -= 1
elif isinstance(it[k], dict):
level += 1
temp[k], category, count, new_cat_index = \
self.__iterate_function(
it[k], level, cnt_index, new_cat_index)
level -= 1
else:
temp[k] = it[k]
self.__addid(it[k])
return temp, category, count, new_cat_index

@property
def output(self) -> dict:
"""
Expand Down

0 comments on commit 79801a7

Please sign in to comment.