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Add CIR Image function #250

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119fcc1
Add functions to customize communication with PubChem REST-API
stitam Apr 16, 2020
76249f3
Merge remote-tracking branch 'upstream/master' into i206
stitam Apr 16, 2020
419c692
New functions for the PubChem PUG-REST API
stitam Apr 16, 2020
c13b7e1
Updates documentation for pc_pugrest
stitam Apr 16, 2020
8735236
Multiple ways to post http requests
stitam Apr 16, 2020
5058dc5
Merge remote-tracking branch 'upstream/master' into i206
stitam Apr 17, 2020
407f272
Remove pc_pugrest, pc_validate, add get_sid
stitam Apr 18, 2020
575e59f
Add ... argument to get_sid documentation
stitam Apr 19, 2020
34ac653
Tests to check examples in article
stitam Apr 23, 2020
0e5824c
Merge remote-tracking branch 'upstream/master' into article
stitam Apr 23, 2020
7d629a3
Increase version number
stitam Apr 23, 2020
a10646a
Revert "Increase version number"
stitam Apr 23, 2020
394adcc
Remove cas.etox_basic() from extractors.R
stitam Apr 23, 2020
d891a9c
Merge remote-tracking branch 'upstream/master' into i206
stitam Apr 28, 2020
30bcfa7
Update get_cid() to handle complex queries
stitam Apr 29, 2020
ec60d27
Export get_sid() and fix some tests
stitam Apr 29, 2020
4d76660
Include article tests in test files
stitam Apr 30, 2020
feba94e
Fix conflict in test-chebi.R
stitam Apr 30, 2020
e6b7fb5
Updates to articles tests
stitam Apr 30, 2020
b467673
Small fixes in tests
stitam Apr 30, 2020
252d70c
Merge remote-tracking branch 'upstream/master' into article
stitam Apr 30, 2020
94c5665
Fix some tests in test-chemspider.R
stitam Apr 30, 2020
d501eb1
changes to tests including: replacing expect_is with expect_s3_class …
Aariq May 4, 2020
26696e9
added codecov.yml
Aariq May 4, 2020
c4f8000
changed email to tamas instead of eduard
Aariq May 4, 2020
0a53d26
added codecov
Aariq May 4, 2020
9b6c8be
travis should now run tests because it's NOT_CRAN
Aariq May 4, 2020
1db4a3f
added codecov
Aariq May 4, 2020
1cc2d93
changed codecov badge to master branch since we're not using test bra…
Aariq May 4, 2020
9176cda
changed codecov badge to master branch since we don't use test branch…
Aariq May 4, 2020
cbd929e
skip tests if service is down
Aariq May 5, 2020
226f1dc
just skip some tests for now so I can get a passing build
Aariq May 5, 2020
6e37e43
change email
Aariq May 5, 2020
fbb6d67
fix merge
Aariq May 5, 2020
93d729c
rearranged tests by service rather than function.
Aariq May 5, 2020
b5ea772
properly deprecate first=TRUE
Aariq May 5, 2020
24a7d2b
check if services are down before testing
Aariq May 5, 2020
1314044
Fix merge conflict
stitam May 5, 2020
b3e5982
used queries with more unique results to better test cs_control(). o…
Aariq May 5, 2020
58db4bc
CORRECTLY deprecated first=
Aariq May 5, 2020
ec5c54b
fixing expect_ functions
Aariq May 5, 2020
3781efe
skip failing tests for now to test codecov
Aariq May 5, 2020
52bf304
try installing r-cran-rjava to deal with error in test-utils.R on lib…
Aariq May 5, 2020
283d686
skip failing tests for now to check codecov
Aariq May 5, 2020
7230cc7
try adding rcdk to Suggests instead. (facepalm)
Aariq May 5, 2020
224bfa9
set appveyor to run as NOT_CRAN
Aariq May 5, 2020
532c3d7
attempt to get appveyor to load rcdk correctly using suggestion here:…
Aariq May 5, 2020
c300992
one more try to get 64 bit build to work with rJava
Aariq May 5, 2020
f29f8ac
push logs as artifact upon failure
Aariq May 5, 2020
8a750a2
change email to tamas
Aariq May 5, 2020
a0bc643
unskip failing tests
Aariq May 5, 2020
3c05b8c
added cir_img()
andschar May 6, 2020
93d17f3
added ping_*() functions to aid in testing. Closes #118.
Aariq May 6, 2020
5d730ec
molecular weights of two compound are equal so order is fine like this.
Aariq May 6, 2020
18fbdb0
moved ping_()s outside of tests so only pings service once.
Aariq May 6, 2020
5cf42d8
skiped a test that only seems to fail on R CMD check
Aariq May 6, 2020
6a2714d
update cir_img()
andschar May 7, 2020
406ba3b
Update R/cir.R
andschar May 7, 2020
680ab27
wrote a single exported ping_service function.
Aariq May 8, 2020
69a3cc2
changed tests to use new ping_service() function
Aariq May 8, 2020
7ddf680
CHEMID is back up and most of the tests are failing. Seems like it's…
Aariq May 8, 2020
79fe8fe
really having problems with chemid, so just skipping everything for now.
Aariq May 8, 2020
ce79d1b
minor edits to tests
Aariq May 8, 2020
7b7d56e
changed to match travis.yml
Aariq May 8, 2020
0803bea
Merge pull request #248 from Aariq/codecov
stitam May 9, 2020
2fc70eb
Fix merge conflicts
stitam May 11, 2020
3b4af6c
minor changes + tests
andschar May 12, 2020
5233e61
Merge remote-tracking branch 'upstream/master' into i206
stitam May 13, 2020
125f840
Add NEWS.md
Aariq May 13, 2020
32e05ec
switch NEWS to .md file
Aariq May 13, 2020
60f3fb7
severely reduced README length
Aariq May 13, 2020
2c1c106
added vignette for "getting started"
Aariq May 13, 2020
77463fb
added pkgdown config
Aariq May 13, 2020
2ff71bd
added instructions for previewing pkgdown site
Aariq May 13, 2020
5363ace
Update get_cid() to query substance and assay domains as well
stitam May 14, 2020
d3bc549
Fix failed tests
stitam May 14, 2020
3cc6ad3
Minor fix in pubchem tests
stitam May 14, 2020
25eea87
Add URLencoding and uncomment a failed test
stitam May 15, 2020
786d074
Merge pull request #239 from stitam/i206
stitam May 15, 2020
8ee6cf1
Fix get_cid() etc. related tests
stitam May 15, 2020
92a489a
Small fix for unused connections in scrapers
stitam May 15, 2020
3a790a9
Skip some tests when ChemSpider is down
stitam May 16, 2020
5396e1e
Make PubChem tests less sensitive to web service updates
stitam May 16, 2020
984c343
Trigger retest
stitam May 16, 2020
7d89a4f
Trigger retest
stitam May 16, 2020
d97dff8
Trigger retest
stitam May 17, 2020
552e033
Remove tests that might take a long time
stitam May 17, 2020
000d110
Remove handle from PubChem requests
stitam May 17, 2020
a1c3be0
Trigger retest
stitam May 17, 2020
757b00d
fixed typos
Aariq May 18, 2020
5a7d1f9
reverted changes to related projects, added link to survey at top.
Aariq May 18, 2020
20021a0
update from master
Aariq May 18, 2020
acb42e4
relaxed testing condition.
Aariq May 18, 2020
409a888
fixed pkgdown build error
Aariq May 19, 2020
cd14385
added ChemPhys CRAN task view
Aariq May 19, 2020
14b4deb
try switching to open ssl for curl backend.
Aariq May 19, 2020
51fb6b2
tried using GET rather than fromJSON directly. Not sure if this will…
Aariq May 19, 2020
95c4d0a
Merge pull request #256 from Aariq/gh-pages
stitam May 19, 2020
437684f
Trigger retest
stitam May 19, 2020
7ed0c9f
Update AppVeyor badge
stitam May 19, 2020
5325778
Merge pull request #243 from stitam/article
stitam May 19, 2020
d746658
fixing bugs related to NAs. May have fixed some other bugs by accident.
Aariq May 14, 2020
e3ef522
Revert "added instructions for previewing pkgdown site"
Aariq May 14, 2020
35579f6
Changed default behavior of extractors to error rather than guessing.…
Aariq May 14, 2020
fcc5fcd
give opsin query a class
Aariq May 24, 2020
ed15fac
removed tests for cts since it returns a named vector not a list.
Aariq May 24, 2020
6e3d9bf
switched cts tests to chemical name since inchikey translations are b…
Aariq May 24, 2020
87e1e9d
minor changes
Aariq May 24, 2020
e8b15f1
Merge pull request #259 from Aariq/aariq-nas
stitam May 25, 2020
fd71d9b
dir stop clause
andschar May 26, 2020
e35c8cc
tests
andschar May 26, 2020
ff77ce3
added cir_img()
andschar May 6, 2020
28cb09f
update cir_img()
andschar May 7, 2020
17676d5
Update R/cir.R
andschar May 7, 2020
349ee7a
minor changes + tests
andschar May 12, 2020
398fc3d
dir stop clause
andschar May 26, 2020
7a983ec
tests
andschar May 26, 2020
04f1834
manual
andschar May 26, 2020
191e9dd
fixing merge conflicts + examples
andschar May 26, 2020
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minor changes + tests
andschar committed May 26, 2020
commit 349ee7a22a224fa166107cfae30c0e66503f6fcc
13 changes: 7 additions & 6 deletions R/cir.R
Original file line number Diff line number Diff line change
@@ -370,13 +370,14 @@ cir_img <- function(query,
)
if (inherits(h, "try-error")) {
warning("Problem with web service encountered... Returning NA.")
return(NA)
return(data.frame(query = query, stringsAsFactors = FALSE))
} else {
# return paths data.frame
data.frame(query = query,
path = path,
url = qurl,
stringsAsFactors = FALSE)
}
# return paths data.frame
data.frame(query = query,
path = path,
url = qurl,
stringsAsFactors = FALSE)
}
out <- lapply(query,
foo,
11 changes: 11 additions & 0 deletions tests/testthat/test-cir.R
Original file line number Diff line number Diff line change
@@ -23,3 +23,14 @@ test_that("cir_query() doesn't mistake NA for sodium", {

expect_true(is.na(cir_query(as.character(NA), 'cas')))
})

test_that("cir_img()", {
skip_on_cran()

Sys.sleep(5)




})