G-Node / G-Node/python-odml

Cumbersome usage of terminology

未关闭
#74 1 条评论 0 个 reaction 已指派 0 人 在 GitHub 查看
terminology
主要语言
Python
星标
25
派生
30
PR 合并指标
30 天内没有已合并 PR

描述

While preparing the new documentation I stumbled upon the functionality of terminology for Document and Section objects. Let me demonstrate the cumbersome aspects of the repository functionality for integrating terminologies via the following example (performed in odml v1.2):

```python
import odml

# define the G-Node repo
repo_doc = 'http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml'

# doc1 should be the Document I would like to create by using terminologies of the G-Node repo
doc1 = odml.Document('WantedDoc', repository=repo_doc)

# doc1 is now an empty Document with the G-Node repository
print(doc1)
# output: None by WantedDoc (0 sections)>

# to actually use the terminologies provided via the repository,
# to include an Event section with the provided terminology
# I now have to generate secondary objects

# A: for example, via another Document
doc2 = doc1.get_terminology_equivalent()
# output: Document containing all Sections that are provided as terminologies via the G-Node repo
#
# (note that this will currently give a lot of warnings,
# since the terminologies are not yet updated to the recent changes of odML)
doc1.append(odml.Section('MyEvent1', type='whatever'))
doc1.sections['MyEvent1'].merge(doc2.sections['Event'])

# B: via creating and appending a Section which has a type equivalent terminology in the G-Node repo
doc1.append(odml.Section('MyEvent2', type='event'))
ev_sec_a = doc1.sections['MyEvent2'].get_terminology_equivalent()
# output: first Section (with children) occurring in the term. of the G-Node repo with Section type 'event'
#
doc1.sections['MyEvent2'].merge(ev_sec_a)

# NOTE:
# that for A the Section type is irrelevant, because the user actively selects a Section
# from the complete terminology tree of the given repo
# for B, the terminology of the wanted Section is AUTOMATICALLY extracted from the repo
# by matching the Section types

# B also works for a standalone Section, but defining a Section specific repo is only indirectly possible:
repo_sec = 'http://portal.g-node.org/odml/terminologies/v1.0/event/event.xml'
# my_ev_sec = odml.Section('MyEvent3', type='event', repository=repo_sec)
# -> will give a TypeError: __init__() got an unexpected keyword argument 'repository'
# but the following is possible:
my_ev_sec = odml.Section('MyEvent3', type='event')
my_ev_sec.repository = repo_sec
# and then follow B to use the repository functionality
ev_sec_b = my_ev_sec.get_terminology_equivalent()
doc1.append(ev_sec_b.clone())
# will append a clone of the Section with the extracted terminology to doc1
```

贡献指南

打开贡献指南

评估

这个 Issue 还没有评估数据。

把新 issue 发到你的邮箱

精选适合新手参与的 GitHub issue 摘要。