Skip to content

Add CompTox webtest_query()#251

Closed
andschar wants to merge 200 commits intoropensci:masterfrom
andschar:dev_comptox
Closed

Add CompTox webtest_query()#251
andschar wants to merge 200 commits intoropensci:masterfrom
andschar:dev_comptox

Conversation

@andschar
Copy link
Copy Markdown
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