Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add CompTox webtest_query() #251

Closed
wants to merge 200 commits into from
Closed

Add CompTox webtest_query() #251

wants to merge 200 commits into from

Conversation

andschar
Copy link
Contributor

@andschar andschar commented May 7, 2020 •
edited
Loading

Another PR that is connected to AcTOR #247 somehow. If I understand it correctly, AcTOR is the underlying data warehouse for CompTox, which provides many different kinds of toxicity-relevant data on chemicals. CompTox by itself doesn't have a web service, at least to my current understanding. But, there is one web service for a specific feature in CompTox, namely the calculation of QSAR values named webTEST. For this web service I have written the function webtest_query().

Some more thoughts:

  • AS @stitam showed in Add AcTOR query and img function #247 there is also an AcTOR web service. Yet I think it doesn't provide the webTEST data.
  • The whole EPA chemicals, toxicity web services ecosystem seem currently quite opaque. Probably they are also currently rebuilding stuff. I also don't see how old the AcTOR web service is.
  • The script file is named comptox.R and the function webtest_query() - a bit confusing, as is there web service ecosystem currently.

PR task list:

  • Update NEWS
  • Add tests (if appropriate)
  • Update documentation with devtools::document()
  • Check package passed

stitam and others added 30 commits April 16, 2020 09:48
@stitam
Add functions to customize communication with PubChem REST-API
119fcc1
@stitam
Merge remote-tracking branch 'upstream/master' into i206
76249f3
@stitam
New functions for the PubChem PUG-REST API
419c692
@stitam
Updates documentation for pc_pugrest
c13b7e1
@stitam
Multiple ways to post http requests
8735236
@stitam
Merge remote-tracking branch 'upstream/master' into i206
5058dc5
@stitam
Remove pc_pugrest, pc_validate, add get_sid
407f272
@stitam
Add ... argument to get_sid documentation
575e59f
@stitam
Tests to check examples in article
34ac653
@stitam
Merge remote-tracking branch 'upstream/master' into article
0e5824c
@stitam
Increase version number
7d629a3
@stitam
Revert "Increase version number"
a10646a 
This reverts commit 7d629a3.
@stitam
Remove cas.etox_basic() from extractors.R
394adcc
@stitam
Add new function cs_image()
1f910eb
@stitam
Merge remote-tracking branch 'upstream/master' into i206
d891a9c
@stitam
Update get_cid() to handle complex queries
30bcfa7
@stitam
Export get_sid() and fix some tests
ec60d27
@stitam
Include article tests in test files
4d76660
@stitam
Fix conflict in test-chebi.R
feba94e
@stitam
Updates to articles tests
e6b7fb5
@stitam
Small fixes in tests
b467673
@stitam
Merge remote-tracking branch 'upstream/master' into article
252d70c
@stitam
Fix some tests in test-chemspider.R
94c5665
@stitam
Merge remote-tracking branch 'upstream/master' into chemspider
c8941ce
@stitam
Updates to cs_image()
356bc1c
@Aariq
changes to tests including: replacing expect_is with expect_s3_class …
d501eb1 
…or expect_type, removing context(), moving skip_*() functions into test_that() blocks so they work, adding skip_on_travis() to chempsider tests, adding skip statements for ping_*() functions
@Aariq
added codecov.yml
26696e9
@Aariq
changed email to tamas instead of eduard
c4f8000
@Aariq
added codecov
0a53d26
@Aariq
travis should now run tests because it's NOT_CRAN
9b6c8be
Aariq and others added 27 commits June 27, 2020 14:00
@Aariq
addressing review of PR
7c3a889
@Aariq
add skips for integration function tests.
e29b476
@Aariq
change pan example, update a test.
76c32a8
@Aariq
lintr suggestions
99b5284
@stitam
Updates badges, Put databases in alphabetical order
f93a85d
@stitam
Generate codemeta.json
fb78a71
@stitam
Remove reference to the polite package
76b31cb
@stitam
Add guideline for functions that retrieve images
a6a4370
@stitam
Ping webservices in test files
44f1d15
@stitam
Add rOpenSci Code of Conduct
27736fd
@stitam
Fix Issue 269
37bd2f0
@stitam
Update URL encoding, unskip tests
73b8c26
@stitam
Update URL encoding to include reverse = TRUE
7808a3f
@Aariq
change autotranslate to with_cts and make unexported. Re-run document…
fdf6547 
…ation.
@Aariq
changed function name from has_entry to find_db. Other minor changes …
19ba9d1 
…to appease check()
@stitam
Merge pull request ropensci#264 from Aariq/integration
f33a964 
Check coverage across webchem. Closes ropensci#262, ropensci#263.
@stitam
Merge remote-tracking branch 'upstream/master' into documentation
5e2e82e
@stitam
Merge pull request ropensci#267 from stitam/documentation
12c6c9f 
Updates to the documentation
@stitam
Merge remote-tracking branch 'upstream/master' into bugs
8cc11a4
@stitam
Add tests for handling special characters in SMILES
2d637ac
@stitam
Fix failing test
8b5b18a
@stitam
Add a line to news and a note to contributing
4b0ed71
@Aariq
Merge pull request ropensci#270 from stitam/bugs
4712e9c 
Handling special characters in SMILES strings
@andschar
added webtest_query()
50bad3c
@andschar
chenged to testthat::expect_s3_class()
2d9d64d
@andschar
bug
5a0d2e6
@andschar
bug
d8165a3 
Merge branch 'dev_comptox' of github.com:andschar/webchem into dev_comptox

# Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/comptox.R
@andschar andschar closed this Jul 14, 2020
@andschar andschar deleted the dev_comptox branch July 14, 2020 16:24
@andschar andschar mentioned this pull request Jul 14, 2020
Draft
4 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@Aariq Aariq Aariq approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@andschar @Aariq @stitam