rossmounce / checkmydois Goto Github PK
View Code? Open in Web Editor NEWCode to check the DOIs of your own authored research outputs (not just articles!)
License: MIT License
checkmydois's People
Contributors
Stargazers
Watchers
checkmydois's Issues
hanging?
when I try this (one of my DOIs) it seems to hang a long time. Do we need a timeout?
http_status(GET("http://doi.org/10.1016/j.neuropharm.2015.07.027"))$message
The paper works ok though when I visit the DOI in a browser.
Set cron job from R?
Investigate cronR https://github.com/bnosac/cronR
suggested by Thomas https://twitter.com/thomasingalls/status/826437598713294849
Document TravisCI setup [FUTURE ENHANCEMENT]
Once we have this working, and easily configurable, I would put something like this in the README file?
- Fork the repository on GitHub
- Turn on TravisCI testing for the forked repository
- Change the TravisCI settings to:
- Only test is
.travis.ymlis present (not essential) - Set the
$ORCIDenvironment variable to your own (see #5) - Turn on a weekly cron test of the master branch (otherwise only runs tests if code is updated)
If and when the master fork (i.e. Ross' GItHub repository) is updated, then the user may wish to update their forked copy to get the latest changes
Warning message: In rm(vec) : object 'vec' not found
Running locally the output seems overly verbose:
$ Rscript checkmydois.R ; echo "Return code $?"
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
[1] "http://doi.org/10.1111/evo.12884"
[2] "http://doi.org/10.7287/peerj.preprints.773v1"
[3] "http://doi.org/10.3897/rio.1.e7547"
[4] "http://doi.org/10.5334/ban"
[5] "http://doi.org/10.1045/november14-murray-rust"
[6] "http://doi.org/10.3897/bdj.2.e1125"
[7] "http://doi.org/10.4033/iee.2013.6b.14.f"
[8] "http://doi.org/10.1002/bult.2013.1720390406"
[9] "http://doi.org/10.5061/dryad.h6pf365t"
[10] "http://doi.org/10.1186/1756-0500-5-574"
[11] "http://doi.org/10.1038/nature10266"
[12] "http://doi.org/10.1038/npre.2011.6048"
Warning message:
In rm(vec) : object 'vec' not found
matrix.unlist.vec.. uniquedois
1 Success: (200) OK http://doi.org/10.1111/evo.12884
2 Success: (200) OK http://doi.org/10.7287/peerj.preprints.773v1
3 Success: (200) OK http://doi.org/10.3897/rio.1.e7547
4 Success: (200) OK http://doi.org/10.5334/ban
5 Success: (200) OK http://doi.org/10.1045/november14-murray-rust
6 Success: (200) OK http://doi.org/10.3897/bdj.2.e1125
7 Success: (200) OK http://doi.org/10.4033/iee.2013.6b.14.f
8 Success: (200) OK http://doi.org/10.1002/bult.2013.1720390406
9 Success: (200) OK http://doi.org/10.5061/dryad.h6pf365t
10 Success: (200) OK http://doi.org/10.1186/1756-0500-5-574
11 Success: (200) OK http://doi.org/10.1038/nature10266
12 Success: (200) OK http://doi.org/10.1038/npre.2011.6048
Return code 0
In particular, removing this warning would be nice:
Warning message:
In rm(vec) : object 'vec' not found
This was using R version 3.3.2 under Linux.
Cryptic failure, Error in curl::curl_fetch_memory(url, handle = handle)
I've tried running this on my own ORCID,
$ git diff
diff --git a/checkmydois.R b/checkmydois.R
index c5ff9b6..bcf45c8 100644
--- a/checkmydois.R
+++ b/checkmydois.R
@@ -7,7 +7,7 @@ library(dplyr)
library(httr)
#Put your ORCID ID below
-your.ORCID.ID <- "0000-0002-3520-2046"
+your.ORCID.ID <- "0000-0001-9513-9993"
#This gets your list of works with identifiers from ORCID
#Thanks to Scott Chamberlain for this step https://github.com/ropensci/rorcid/issues/31
I know that many of these papers are paywalled, so perhaps this is not unexpected - but the error message is cryptic:
$ Rscript checkmydois.R ; echo "Return code $?"
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
[1] "http://doi.org/10.1111/mpp.12280"
... <snip> ...
Warning message:
In rm(vec) : object 'vec' not found
Error in curl::curl_fetch_memory(url, handle = handle) :
Failure when receiving data from the peer
Calls: http_status ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Return code 1
Configurable ORCID or list of DOIs to check? [ENHANCEMENT]
Currently the script has the ORCID ID hard coded. It would be great to have this as a command line option, or via an environment variable (perhaps defaulting to the current value for testing).
(I can see how this might then be used via a continuous integration service like TravisCI where the user can put in their own ORCID to the TravisCI settings, without having to modify the code in git)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.