Make report on unswered issues and try to respond

[matentzn]

Using Github API maybe

[matentzn]

Hey @gouttegd I am assigning you here only since you are already working on API stuff.

Basically it would be great to have a small script that generates a markdown table like:

Issue	Person	Uberon team?	Assignee
Close all issues that have not seen activity in last 3 years	@matentzn	Yes	@gouttegd
incorrect classification of bone surfaces under 'surface structure'	@dosumis	Yes	@megbalk
eyestalk	@ANiknejad	No

• Open issues
• That have not been commented on in the last 6 months.
• For the Uberon team flag, you check whether its one of:

@dosumis @cmungall @megbalk @gouttegd @paolaroncaglia @nicolevasilevsky (.... fill in other names)

[gouttegd]

I have a first draft that does most of the job. It gives issues that were last updated more than 180 days ago (truncated here to the first 50 such issues).

For now, the author of an issue is considered to be part of the "Uberon team" if that user either is a member of the Obophenotype organization (member) or has been invited to contribute to the repository (collaborator). This is the easiest way to do it, but it’s not really suitable for Uberon given that several contributors are effectively considered part of the team even though they are not formally members or collaborators from GitHub’s point of view. I’ll add a check against an externally-maintained list of contributors later.

Issue	Author	Uberon team?	Assignee(s)
consistency in tooth terms	@megbalk	No
UBERON:0006871 embryonic footplate - change synonym scope	@paola-scibite	No
EHDAA2:0001090 medulla oblongata alar plate (human), wrong part_of relationship	@ANiknejad	No
Xrefs without prefixes in OBO export	@cthoyt	No
UBERON:4200132 tuber	@paola-scibite	No
UBERON:7500041 tip of digit	@paola-scibite	No
UBERON:4200179 manual claw	@paola-scibite	No
UBERON:0018306 bulge and UBERON:0010188 protuberance	@paola-scibite	No
Some "buccal" terms missing part_of parent	@paola-scibite	No
Typo in synonym of UBERON:0018133 monotreme bill	@paola-scibite	No
Typo in def of UBERON:0011933 vibrissa unit	@paola-scibite	No
Mapping external references	@computationdoc	No
"anatomical collection" in Uberon and "anatomical set" in FMA	@ChristianKleineidam	No
developing anatomical structure missing parent	@pgaudet	No
Add TC UBERON:0002542 'scale' never in Homo sapiens?	@paola-scibite	No
NTR: right gastric artery	@paola-scibite	No
NTRs: greater + lesser palatine foramen	@paola-scibite	No
NTR: Tenon capsule	@paola-scibite	No
anatomical projection and incorrect FMA link	@ChristianKleineidam	No
NTR: periosteum of orbit	@paola-scibite	No
NTR: epitrochlear lymph node	@paola-scibite	No
Missing textual definitions	@paola-scibite	No
Some definitions don't start with uppercase and don't end with a period	@paola-scibite	No
NTR: ganglion impar	@paola-scibite	No
NTR: glomus coccygeum	@paola-scibite	No
Typo in label of UBERON:0008989 submocosal esophageal gland	@paola-scibite	No
Typo in definition of several "epithelium" terms	@paola-scibite	No
Def of UBERON:0000444 'lymphoid follicle' contains "." only	@paola-scibite	No
Incorrect UMLS Xref for UBERON:0004016	@pecan88	No
Lack of consistency in use of kidney vs. renal in preferred terms [Typo/Bug]	@rich-brennan	No
Experiment: materialize phylo-specific uberon classes	@cmungall	Yes
standardize on creation date property	@cmungall	Yes
Incorporate ICDOT mappings	@cmungall	Yes
parent of 'life cycle stage' unclear	@johnwjudkins	No
human-view.owl should remove contextual axioms in final release	@dosumis	Yes	@cmungall
Bad URI for image depiction	@balhoff	Yes
Request for comments: model anatomical spaces as material entities, consistent with GO	@cmungall	Yes
UBERON:0018241 prime adult stage	@ANiknejad	No	@nicolevasilevsky
Adding a whole bunch of species-specific terms	@stevevanhooser	No
NTR: endodontium	@paola-scibite	No
uberon uses a 'contains process' relation that has a non-existing IRI	@cmungall	Yes
Invalid Xrefs in human-view.obo	@rpwagner	No
Why doesn't adventitia subclass connective tissue?	@ChristianKleineidam	No
Ligament and Ligament organ	@ChristianKleineidam	No
nested logical definitions	@ramonawalls	No
import BSPO terms	@ramonawalls	No
NTR: oral fluid	@cmrn-rhi	No
lacrimal apparatus function?	@drseb	Yes
Add perioral region?	@drseb	Yes
Make part relationship for tracheobronchial epithelium to tracheobronchial tree	@mkeays	Yes

[matentzn]

No, I think you are doing the right thing - this is perfect. Let's make this all a bit more organised:

All people that are part of the wider Uberon team should be in
https://github.com/orgs/obophenotype/teams/uberon-curators

I have sent out some invites. Check only that team - if you are listed in there (and only then), you are considered core team. I will update the list when I see the names coming in - maybe you can send me a list of all github handles you see outside that list and I can update.

[paolaroncaglia]

Hi @gouttegd and @matentzn ,
I have followed up on all tickets above opened by my alter ego paola-scibite. She won't join obophenotype for now ;-) (notifications go to yet another email account, I'd rather keep everything in one place...). Thanks for your work on this!

[gouttegd]

@matentzn The script will be available in this repo.

It's in a very rough shape for now, but it already works (for some definition of "works", anyway: for example there's absolutely no error checking of any kind) for what you want to do.

If you want to try it to get the list you want:

1. Create an access token.
2. Create a configuration file named ~/Library/Application Support/grainyhead/config with the following:

[default]
user: obophenotype
repo: oberon
token: <your access token>

3. From the cloned repo:

$ PYTHONPATH=. python fbcam/grainyhead/main.py issues --older-than 180 --team obophenotype/uberon-cl-curators > old-issues.md

You'll need the click, click-shell, ghapi, and ipython packages from PyPI.

Alternatively you can already install the package in your per-user Python environment (which would then install the grh command in your PATH — this would also take care of downloading the dependencies), but I'd say it's probably a bit premature for now.

Warning: I make no promise that I will not change the format of the configuration file or the syntax of the command line.

[matentzn]

This is amazing! Will come back to this next week - now I am on vacation ;) supper cooool.

[matentzn]

Awesome thank you @gouttegd; Currently I get:

[email protected]:~/ws/grainyhead (master) $ cat ~/Library/Application\ Support/grainyhead/config 
[default]
user: obophenotype
repo: uberon
token: IHAVEADDEDMYTOKENHERE
[email protected]:~/ws/grainyhead (master) $ PYTHONPATH=. python fbcam/grainyhead/main.py issues --older-than 180 --team obophenotype/uberon-cl-curators > old-issues.md
Traceback (most recent call last):
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/configparser.py", line 789, in get
    value = d[option]
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/collections/__init__.py", line 898, in __getitem__
    return self.__missing__(key)            # support subclasses that define __missing__
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/collections/__init__.py", line 890, in __missing__
    raise KeyError(key)
KeyError: 'repository'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "fbcam/grainyhead/main.py", line 250, in <module>
    grh()
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/site-packages/click_shell/core.py", line 164, in invoke
    ret = super(Shell, self).invoke(ctx)
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/site-packages/click/decorators.py", line 33, in new_func
    return f(get_current_context().obj, *args, **kwargs)
  File "fbcam/grainyhead/main.py", line 133, in list_issues
    repo = grh.repository
  File "fbcam/grainyhead/main.py", line 82, in repository
    repo_url = self._config.get(self._name, 'repository')
  File "/Users/matentzn/opt/anaconda3/lib/python3.8/configparser.py", line 792, in get
    raise NoOptionError(option, section)
configparser.NoOptionError: No option 'repository' in section: 'default'
[email protected]:~/ws/grainyhead (master) $ 

[gouttegd]

Told you I don't promise the interface wouldn't change. :D The comment above is already obsolete, this weekend I replace the user and repo options with a single repository option, for simplicity's sake.

The config file should now be like:

[default]
repository: obophenotype/uberon
token: <your access token>

[matentzn]

Update to command:

PYTHONPATH=. python fbcam/grainyhead/main.py issues --older-than 180 --team uberon-cl-curators > old-issues.md

I will close this issue now, as its all done! Thank you @gouttegd