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Submission: rtika #191

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goodmansasha opened this issue Jan 31, 2018 · 38 comments

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@goodmansasha
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commented Jan 31, 2018

Summary

  • What does this package do? (explain in 50 words or less):

Extract text or metadata from over a thousand file types. This is an R interface to Apache Tika, a content and metadata extraction tool. Tika is written in Java and is maintained by the Apache Software Foundation since 2007.

  • Paste the full DESCRIPTION file inside a code block below:
Package: rtika
Type: Package
Title: R Interface to 'Apache Tika' 
Version: 0.1.2
Author: Sasha Goodman <goodmansasha@gmail.com>[aut], The Apache Software Foundation [aut,cph]
Maintainer: Sasha Goodman <goodmansasha@gmail.com>
Suggests: 
    sys,
    jsonlite,
    xml2,
    data.table,
    curl,
    testthat,
    knitr,
    rmarkdown,
    covr,
    Matrix
License: Apache License 2.0 | file LICENSE
SystemRequirements: Java (>=7) | openjdk-7-jre (via apt) | java-1.7.0-openjdk (via yum) | openjdk-8-jre (via apt) | java-1.8.0-openjdk (via yum) 
Description: Extract text or metadata from over a thousand file types. Get either plain text or structured XHTML. This R interface includes the Tika software. Its source is available at https://github.com/apache/tika. 
Depends: R (>= 3.1.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
URL: http://github.com/predict-r/rtika
BugReports: http://github.com/predict-r/rtika/issues
VignetteBuilder: knitr

  • URL for the package (the development repository, not a stylized html page):

https://github.com/predict-r/rtika

  • Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

It fits into data extraction, especially text extraction. This package helps extract either a plain text or XHTML rendition of most common file types, without leaving R. It includes parsers for Microsoft Office (both the old and new formats), OpenOffice, iWorks, WordPerfect, PDF, ePub, rtf, HTML, XML, and Mbox email.

The hours of labor spent on these parsers is unbelievable. I recall Tika was intended to prevent duplicate work at Apache, and has since became a foundational library for Apache search engine projects.

Tika also detects metadata from over a thousand file formats. These include basic features like Content-Encoding and mime type sniffing. Beyond that, there are specialized extractors for scientific formats (ISA-Tab, Matlab), geospatial formats (GDAL, ISO-19139), image Exif data from tiff or jpeg, and many more.

The long list of formats is here: https://tika.apache.org/1.17/formats.html

  • Who is the target audience and what are scientific applications of this package?

Computational social scientists, digital humanities scholars, historians, or any person that works with large digital archives filled with possibly unpredictable file formats.

For example, consider a social scientist studying the California state legislature, as I am. The legislature publishes a database that includes, among other things, Microsoft Word documents created over the past decades. These are at http://leginfo.legislature.ca.gov/.

I've used Tika to automatically extract text from decades of Word documents, even if I don't know the particular version of Word beforehand. Further, with the XHTML output option, I can preserve tables inside each Word document.

There are specialized parsers for several of the file types Tika processes, such as antiword for older Microsoft Word documents. Overlap is going to be inevitable. I have used antiword and it worked well, except that some of my files did not have a file type affix (e.g. .docx or .doc), and could be in either format, and so it took some trial and error to get it working. It turned out antiword does not process the modern XML based Word formats. It also does not render the Word document into XHTML, which could preserve tables from the Word document.

Listing all the document parsers that Tika overlaps with would take an enormous amount of space, since it processes over a thousand file types. In general, however, Tika's aims to streamline text extraction within large archives. Archives often contain heterogeneous and unpredictable file formats. Tika handles most of what I throw at it.

The other package I found that interfaces with Apache Tika is tikaR, released in September of 2017 (See: https://github.com/kyusque/tikaR). It provides only XHMTL renditions of documents, and uses the rJava package to interface with Tika.

I was a Java developer and implemented a rJava interface with Tika in 2012, when I was considering my first package for R (the project is empty, but I set up a repository on r-forge back then: https://r-forge.r-project.org/projects/r-tika/). My rJava code worked, but I concluded at the time that the Apache Tika command line interface (CLI) was sufficient for myself and most people. I ended up just crafting some specialized system calls to the command line for my own work. The r-forge repository remains empty because I didn't want to maintain a complex Java codebase.

Recently, the Tika project came out with a very nice batch processor in their command line that I found to be the most efficient method to handle tens of thousands of documents. It was too good to keep to myself.

Unlike the rJava functions used by tikaR, I essentially send Tika a file list to process, and then craft a specialized call to the command line to invoke the batch processor. Retrieving the converted results is pretty straightforward. The code is simple and easy to maintain.

Unlike tikaR, I've included a variety of tests and keep track of test coverage, and anticipate that maintaining this package will be fairly simple, even without Java knowledge. There are also more features implemented in my package than tikaR, such as the ability to use multiple threads.

  • If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

Requirements

Confirm each of the following by checking the box. This package:

  • does not violate the Terms of Service of any service it interacts with.
  • has a CRAN and OSI accepted license.
  • contains a README with instructions for installing the development version.
  • includes documentation with examples for all functions.
  • contains a vignette with examples of its essential functions and uses.
  • has a test suite.
  • has continuous integration, including reporting of test coverage, using services such as Travis CI, Coveralls and/or CodeCov.
  • I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Publication options

  • Do you intend for this package to go on CRAN?
  • Do you wish to automatically submit to the Journal of Open Source Software? If so:
    • The package has an obvious research application according to JOSS's definition.
    • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
    • The package is deposited in a long-term repository with the DOI:
    • (Do not submit your package separately to JOSS)
  • Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
    • The package is novel and will be of interest to the broad readership of the journal.
    • The manuscript describing the package is no longer than 3000 words.
    • You intend to archive the code for the package in a long-term repository which meets the requirements of the journal.
    • (Please do not submit your package separately to Methods in Ecology and Evolution)

Detail

  • Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

  • Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:

  • If this is a resubmission following rejection, please explain the change in circumstances:

  • If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:

Jeroen Ooms has worked on text file parsers and I respect his work immensely.

@karthik karthik added the package label Jan 31, 2018

@goodmansasha

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commented Feb 8, 2018

Following up on this, is there anything I can do to help, like suggest additional reviewers?

@noamross

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commented Feb 9, 2018

Editor checks:

  • Fit: The package meets criteria for fit and overlap
  • Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
  • License: The package has a CRAN or OSI accepted license
  • Repository: The repository link resolves correctly
  • Archive (JOSS only, may be post-review): The repository DOI resolves correctly
  • Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

Editor comments

Thanks for your submission @predict-r! And sorry for the slow reply, this fell through the cracks for a week. This is a good fit and I'll go ahead and find reviewers.

Here are the results of our automated tests via goodpractice::gp(). You have good code coverage (100% not required, but this helps rviewers see where they might look for edge cases that need coverage.) Most of the other stuff should be straightforward and I'll go ahead and look for reviewers. You can make those changes either before or after you get your first-round reviews.

I suspect you'll have trouble getting a >50MB .jar file onto CRAN. I'll leave this until we have a review from Java-experienced reviewer, but I suspect you may have to pursue an approach such as packaging the .jar file in a separate package and listing it as a dependency (see CRAN polices), file or having a function like install_tika() in the package that downloads the file before the package is functional.

── GP rtika ─────────────────────────────────────

It is good practice to

  ✖ write unit tests for all functions, and all package code in general. 92% of code lines are covered by test cases.

    R/tika_html.R:12:NA
    R/tika_json.R:17:NA
    R/tika_text.R:13:NA
    R/tika_xml.R:13:NA
    R/tika.R:128:NA
    ... and 7 more lines

  ✖ use '<-' for assignment instead of '='. '<-' is the standard, and R users and developers are used it and it is easier to read your code for them if you use '<-'.

    inst/doc/text_processing.R:121:11

  ✖ avoid long code lines, it is bad for readability. Also, many people prefer editor windows that are about 80 characters wide. Try make your lines shorter than 80 characters

    inst/doc/text_processing.R:12:1
    inst/doc/text_processing.R:58:1
    inst/doc/text_processing.R:62:1
    inst/doc/text_processing.R:84:1
    inst/doc/text_processing.R:106:1
    ... and 56 more lines

  ✖ omit trailing semicolons from code lines. They are not needed and most R coding standards forbid them

    inst/doc/text_processing.R:36:66

  ✖ avoid sapply(), it is not type safe. It might return a vector, or a list, depending on the input data. Consider using vapply() instead.

    R/tika.R:185:18

  ✖ not use exportPattern in NAMESPACE. It can lead to exporting functions unintendedly. Instead, export functions that constitute the external API of your package.
  ✖ fix this R CMD check NOTE: installed size is 53.3Mb sub-directories of 1Mb or more: java 53.1Mb
─────────────────────────────────────────────

Reviewers: @juliasilge @davidgohel
Due date: 2018-03-05

@noamross

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commented Feb 10, 2018

Thank you @juliasilge and @davidgohel for agreeing to review! Reviews will be due 2018-03-05.

@noamross

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commented Feb 10, 2018

@predict-r You can add the review badge to your README now if you wish. It will auto-update with review status:

[![](https://badges.ropensci.org/191_status.svg)](https://github.com/ropensci/onboarding/issues/191)
@goodmansasha

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commented Feb 11, 2018

Thanks! I'll go ahead and add the badge then. I'll patch some of the goodpractice issues listed above.

Thanks for pointing out the CRAN situation. I can create another repository with the Jar, and call it 'tikajar' . That package won't update often, so maybe CRAN will accept it. If not, the package can be left on github and downloaded with devtools.

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commented Feb 15, 2018

Okay, I removed the .jar file. It is in a new package on github called 'tikajar' (see: https://github.com/predict-r/tikajar ). Since its a key part of 'rtika', I added the review badge to tikajar as well. Let me know if that's an issue.

@davidgohel

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commented Feb 21, 2018

Hi, here is my review:

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

  • As the reviewer I confirm that there are no conflicts of interest for me to review this work.

Documentation

The package includes all the following forms of documentation:

  • A statement of need clearly stating problems the software is designed to solve and its target audience in README
  • Installation instructions: for the development version of package and any non-standard dependencies in README
  • Vignette(s) demonstrating major functionality that runs successfully locally
  • Function Documentation: for all exported functions in R help
  • Examples for all exported functions in R Help that run successfully locally
  • Community guidelines including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

  • Installation: Installation succeeds as documented.
  • Functionality: Any functional claims of the software been confirmed.
  • Performance: Any performance claims of the software been confirmed.

davidgohel: I tested with 1204 documents (my admin folder). I got 20.354 sec. with 8 threads
and 36.376 with 1 threads. This is really good (it tooks 20 second to get my whole admin
directory scanned and returned as an R object).

I was expecting a faster execution with 8 threads (not 8 times faster but at
least twice minimum). I used the profiling tools of RStudio and could see that the
function spent 1/3 of time executing .rtika_readFile() and 1/3 executing enc2utf8().
I think that starting JVM with arg -Dfile.encoding=UTF-8 instead of using enc2utf8
could be a solution (not tested here, but was the solution in past experiences...).

  • Automated tests: Unit tests cover essential functions of the package
    and a reasonable range of inputs and conditions. All tests pass on the local machine.
  • Packaging guidelines: The package conforms to the rOpenSci packaging guidelines

davidgohel:

  • There is no Code of conduct (but it is only recommanded in the guidelines)

  • Authorship: in field Author I recommand you the format with Authors@R: c(person(...).
    One benefit for example is you will ensure programmatically that the roles are correct.

  • Package dependencies: in R/tika.R (l179), you are using utils but it is not in Suggests.
    Package stats is used in R/tika.R (l130) and should be declared in Imports.
    The way you are using Suggests and requireNamespace instead of Imports
    is unconventional to me but I think it is valid.

  • SystemRequirements: I don't think it will be accepted as is. (2 months ago, R Core Team
    standardized java value), it should be java (>= 7). Also CRAN is asking to double check the
    version of java - something like:

.onLoad= function(libname, pkgname){

  .jpackage( pkgname, lib.loc = libname )

  jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
  reg <- "([0-9]+)\\.([0-9]+)\\.(.*)"
  majorv <- as.integer(gsub(reg, "\\1", jv))
  minorv <- as.integer(gsub(reg, "\\2", jv))
  if(majorv == 1 ){
    if( minorv < 7 ) {
      stop("java version should be at minimum version 7 (>=1.7)")
    }
  }
}
  • The run examples are too long to be executed (when checking the package).
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
tika      11.477  0.636   8.347
tika_text  5.786  0.328   3.875
tika_json  5.582  0.313   4.163
tika_xml   5.387  0.299   2.787
tika_html  5.224  0.308   2.812

As the unit tests are there and cover almost
100%, I suggest you use \donttest{} for the 5 examples.

  • R CMD check did not succeed (via RStudio ckeck button).
    I am running R 3.4.3 on OSX High Sierra 10.13.3.
    Some tests are failling:
OK: 49 SKIPPED: 0 FAILED: 5
1. Error: tika parses multiple local files (@test_tika.R#58) 
2. Error: tika outputs NA with a path to nowhere in right order (@test_tika.R#86) 
3. Error: tika outputs parsable xml (@test_tika.R#119) 
4. Error: tika outputs parsable html (@test_tika.R#135) 
5. Error: tika outputs parsable json (@test_tika.R#152) 

The fun fact is that these are sucessful when launched via RStudio test button... Maybe
that's because of my environment. You can use that bit of code to check the package
with R for OSX on travis:

https://github.com/davidgohel/gdtools/blob/master/.travis.yml#L5

Final approval (post-review)

  • The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 4


Review Comments

Congratulations for that package, it brings someting new
and really useful in the R data importation ecosystem.

It works well and is simple to use.
I appreciated the help files. Vignettes are giving
lot of examples and shows how to use the results.

A minor modification might be necessary: starting JVM with option -Djava.awt.headless=true,
this should ensure it will run on a server with no graphical environment.

More a wish than a comment... I would have used rJava API in order to avoid system calls.
I believe this could cause troubles in corporate environments where IT teams are sometimes
using tools that deny access to command line for some users.
I don't know tika but the rJava call should be something like:

.jcall("org.apache.tika.wrongbatchclassname","V","main",.jarray(list(...), "java/lang/String")

About the size of the jar file, I did not read anything that says it's an
issue (it will be if often updated) but you could ask to CRAN-submissions@R-project.org
or r-package-devel@r-project.org what is the recommanded strategy.

Hope you will find that review useful :)

David

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commented Feb 22, 2018

Thank you David for the very helpful comments. I've attempted to address your concerns in the 0.1.5 version, and hope they meet your approval. I'm happy that the batch speed was good, and have sped up the package a bit more this time.

I got 20.354 sec. with 8 threads and 36.376 with 1 threads.

Yes, I wish there was a better improvement in speed with that many threads. It seems like the speed per thread shows sharply diminishing returns, unfortunately (perhaps this is because of file system read speed maxing out, but that is just a guess). Your experience had led me to increase the default number of threads to two. Tika's default is the number of processors minus one, according to the batch processor config file. If you think I should use that instead, I will.

I used the profiling tools of RStudio and could see that the function spent 1/3 of time executing .rtika_readFile() and 1/3 executing enc2utf8().

This was very helpful. Your comment led me to read the Tika source code more carefully. I am happy to report that Tika outputs UTF-8 now. It was not immediately apparent, because the original Tika used UTF-16. However, the newer batch processor's FSOutputStreamFactory defaults to UTF-8. There is no need to create a special config file or anything, so I removed the offending enc2utf8(). This will speed up the package quite a bit! Thanks.

There is no Code of conduct

Thank you for reminding me. I've added one.

Authorship formatting

I've updated the authorship to use 'person' functions, as you suggested.

Package dependencies: in R/tika.R (l179), you are using utils but it is not in Suggests.
Package stats is used in R/tika.R (l130) and should be declared in Imports.

The utils and stats packages are now declared in Imports.

Java SystemRequirements

I've updated the Java declaration to use the standard CRAN version style you mentioned. I've also included an .onLoad() function to verify that java is available and is the appropriate version.

The run examples are too long to be executed

These have been stopped using \donttest{} statements. I also made a change to the tests to speed them up, that you may or may not approve of. Instead of downloading files for the test each time, which took fifteen seconds or so, I moved a few different files into the test directory and now test on those.

R CMD check did not succeed

After several hours, this has been fixed on both linux and OS X. On my OS X laptop, I was able to replicate the error by using the system2 command to invoke java. The problem was that system2 stops Tika from finishing in some cases, terminating the process in the middle. The problem was intermittent. It did affect the same tests as you reported. By making the 'sys' package a requirement instead of suggestion, and using sys::exec_wait, the issue is fixed on my end. The .travis.yml is updated to test on both osx and linux now, and is passing. As a side effect, sys::exec_wait speeds up rtika by up to five seconds on my laptop.

A minor modification might be necessary: starting JVM with option -Djava.awt.headless=true,
this should ensure it will run on a server with no graphical environment.

Thank you for this, and it has been implemented.

More a wish than a comment... I would have used rJava API

Thank you for letting me know. I agree that the rJava package could help with certain security issues. It would definitely bring speed benefits over repeated command line invocations. However, it would take time to to dive into the Tika codebase, implement it and test it. Perhaps my main issue is that I've had a some recurring frustration over the years installing rJava. While I'm not opposed to rJava, I would prefer not to add the extra complexity in this first version. If the rtika package is popular at all, I will add rJava.

About the size of the jar file, I did not read anything that says it's an
issue (it will be if often updated) but you could ask to CRAN-submissions@R-project.org
or r-package-devel@r-project.org what is the recommended strategy.

Thank you, I will look into the .jar size issue next!

I hope I've addressed your questions and comments, to your satisfaction.

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commented Feb 22, 2018

Awesome, thank you.

There are 2 NOTE(s) left that could be suppressed:

https://travis-ci.org/predict-r/rtika/jobs/344591725#L349

  • The first one is because you don't need to keep rtika.pdf, R will built it from the man/ directory.
  • the second one is because you are using packageStartupMessage() that should not be called from .onLoad(), using warning() instead should solve that.
@noamross

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commented Feb 22, 2018

Thanks for your thorough review, @davidgohel!

@goodmansasha

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commented Feb 22, 2018

David, I fixed the issue with the two NOTES.

@davidgohel

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commented Feb 22, 2018

Thank you Sasha

@juliasilge

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commented Feb 24, 2018

Hello! Here is my review. 🙂

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

  • As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

  • A statement of need clearly stating problems the software is designed to solve and its target audience in README
  • Installation instructions: for the development version of package and any non-standard dependencies in README
  • Vignette(s) demonstrating major functionality that runs successfully locally
  • Function Documentation: for all exported functions in R help
  • Examples for all exported functions in R Help that run successfully locally
  • Community guidelines including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

  • Installation: Installation succeeds as documented.
  • Functionality: Any functional claims of the software been confirmed.
  • Performance: Any performance claims of the software been confirmed.
  • Automated tests: Unit tests cover essential functions of the package
    and a reasonable range of inputs and conditions. All tests pass on the local machine.
  • Packaging guidelines: The package conforms to the rOpenSci packaging guidelines

Final approval (post-review)

  • The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 3


Review Comments

I have had HORRIBLE EXPERIENCES with installation and usage for Java-dependent R packages 😱😱😱 so I was full of dread I was asked to review this package. However, I am very happy to report that I was able to install and use this package without any trouble at all. Great job on this package, its test coverage, and usability!

library(rtika)
library(tidyverse)
library(tidytext)

my_path <- "~/Documents/Very Ancient Stuff/Teaching & Astronomy/"

batch <- paste0(my_path, list.files(path = my_path))

text <-  
    batch %>%
    tika_text() 

tidy_df <-
    data_frame(file = batch,
               text = text) %>%
    unnest_tokens(word, text) %>%
    count(file, word, sort = TRUE) %>%
    anti_join(get_stopwords())
## Joining, by = "word"
tidy_df
## # A tibble: 3,652 x 3
##    file                                                     word         n
##    <chr>                                                    <chr>    <int>
##  1 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/phy… students   116
##  2 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/phy… writing     68
##  3 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/phy… physics     60
##  4 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/Uni… universe    57
##  5 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/Uni… galaxies    45
##  6 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/Spe… science     43
##  7 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/phy… assignm…    40
##  8 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/phy… class       40
##  9 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/Uni… http        36
## 10 ~/Documents/Very Ancient Stuff/Teaching & Astronomy/Spe… god         33
## # ... with 3,642 more rows
metadata <- 
    data_frame(raw = batch %>%
                           tika_json()) %>%
    filter(!is.na(raw)) %>%
    mutate(JSON = map(raw, jsonlite::fromJSON, flatten = TRUE)) %>%
    pull(JSON) %>%
    map_df(function(x) { x[1:4] %>% head(1) })

metadata
##       Application-Name                 Author         Company
## 1 Microsoft PowerPoint           Robert Silge    Robert Silge
## 2      Microsoft Excel           Robert Silge                
## 3 Microsoft PowerPoint           Robert Silge UT Southwestern
## 4                 <NA>                   tech            <NA>
## 5 Microsoft PowerPoint Information Technology  Calvin College
## 6 Microsoft PowerPoint               dhaarsma  Calvin College
##   Content-Length    Content-Type        Creation-Date
## 1        5082624            <NA>                 <NA>
## 2          30720            <NA>                 <NA>
## 3        8350720            <NA>                 <NA>
## 4         160175 application/pdf 2001-07-20T19:21:49Z
## 5        1538048            <NA>                 <NA>
## 6        9430528            <NA>                 <NA>

Issue with R CMD check

When I run goodpractice:gp() on the current development version, I get this note about the new tikajar dependency:

fix this R CMD check NOTE: Namespace in Imports field not imported from: ‘tikajar’ 
All declared Imports should be used.

I have not built a package that uses a .jar file in this way so I do not know how to address this TBH.

Code style

I have some suggestions around code style to place this package more squarely within R community norms as expressed, for example, in Google's R Style Guide or the tidyverse style guide. I don't know how annoying you will find this 😳 but the value here is that other contributors will be able to read and understand your code more easily. Here are some big picture thoughts:

  • Commas at the end of a line, not the beginning; spaces after commas
  • No curly braces around pipes
  • Spaces around equal signs, use -> for assignment

This is especially important in the README and vignette where the code is exposed to more people. I am about to submit a PR with changes to parts of the package but I wasn't able to go thoroughly through all the code today. This is worth it to make this a welcoming R community package.

Thoughts on the vignette

The vignette currently focuses on text mining of the text that we can get out of this package. Almost the entire vignette focuses on text mining (using base R and some data.table) exploratory data analysis, which is not what this package is about; only the very first code chunk uses functions from rtika at all. The text mining community in R is active and healthy (I am part of it!) and there are lots of opportunities to learn about how to do text mining once you have text; I would suggest that a vignette for a package like rtika is not really the right spot for this kind of analysis. When I am learning how to use a new package, what I want from the vignette is how to use the functions in that package. I would love to see, instead, a more detailed exercise of how to use the actual rtika functions and what they can do. There is nothing in the vignette about handling metadata from multiple sources, for example. The current material that is in the vignette would be more appropriate for a blog post, or perhaps a secondary, supportive vignette.

I'd also like to address the tone of the vignette a little. I know it is so hard to write for audiences that you aren't quite sure where they are! 😃 I am 100% in favor of writing accessibly without jargon so that people can get started, but I want to make sure this vignette doesn't come off as condescending. For example, if a user has managed to install the correct version of Java and is attempting to walk through a vignette, they probably know what regular expressions are.

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commented Feb 25, 2018

Thanks for your thoughtful review, @juliasilge! I especially concur with your comments on the vignette.

Regarding the NOTE: I think the correct field for a package providing .jar files is Depends:. Perhaps @davidgohel can confirm.

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commented Feb 25, 2018

That's because tikajar is not imported in NAMESPACE (but is in Imports in DESCRIPTION)

Adding #' @import tikajar somewhere in R/ should solve the problem.

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commented Feb 25, 2018

@juliasilge Thank you for your helpful comments about making the package feel more welcoming. Based on the feedback here, we need a new vignette. It should demonstrate how to use the actual rtika functions and to show what they can do. It is also an opportunity to show the breadth of uses.

I'll merge your pull request, and go through each point in a coming response.

This morning, in the meantime, I'm brainstorming the vignette. If people know a good vignette to study, let me know please!

I'm thinking of a survey of uses and data. It will have more than five examples, each brief, each focused on a distinct case, each using a cool data set, and each following the 'tidy tools manifesto' principles of using pipes and common formats.

The more diverse the examples, the better. I'm thinking :

  • handling metadata from multiple sources using tika_json (Julia's example).
  • tokenizing and removing stop words with tika_text (similar to Julia's example)
  • handling sub-document metadata from the recursive tika_json
  • piping XHTML to rvest to get tabular data with tika_html
  • maybe an NLP example using tika_text? Something like: https://stanfordnlp.github.io/CoreNLP/
  • ? your idea here.

As for data, my data sources feel too similar to one another and am open to suggestions, especially anything from the Internet Archive (https://archive.org/ ). My initial ideas:

More diverse data examples feels more welcoming, especially documents appealing to the humanities and arts.

Thank you.

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commented Feb 25, 2018

Around five example data sets would be plenty for a vignette, I think! Even three small case studies would be good. I would be thoughtful in what tooling you choose to use in the vignettes. For example, if you wanted to use the Stanford CoreNLP in the vignette, then that package would need to be in Suggests, and that package is a BEAR 👿 to get to install on Travis. I know this from experience. I'd try to stay quite lean and simple in what you use in example analysis in the vignettes and keep complex dependencies for demonstration blog posts.

Two examples packages that I think are good to look to for how to handle vignettes in this case are gutenbergr (downloads public domain texts from Project Gutenberg) and fulltext (searches and downloads full text for journal articles).

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commented Mar 3, 2018

@juliasilge, I've implemented changes to address your helpful comments.

Issue with R CMD check

To avoid this issue, and make things simpler until CRAN complains, I've put the .jar file back into the 'rtika' package for now. So, the issues with importing 'tikajar' is gone on my end.

@davidgohel said: "About the size of the jar file, I did not read anything that says it's an
issue (it will be if often updated) "

The size might not be an issue unless the package is updated frequently, and I hope to update it infrequently.

Code style

The 'styler' package came in handy. I've tried to make the README and vignette use a standard style throughout.

Thoughts on the vignette

I've written an introductory vignette, and removed the last one. This one focuses on how to use the package functions and process the metadata.

It is on the Github Pages site:
https://predict-r.github.io/rtika/articles/rtika_introduction.html

I tried to keep it light and easy to read, and hope it meets your approval for a package vignette. The site was built with pkgdown::build_site().

By the way, I noticed that the review badge was not loading here, so had to remove it.

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commented Mar 3, 2018

Thanks for your response, @predict-r! @juliasilge, let us know if these changes have addressed your comments and check that box off if so, let us know what else remains if not. I see @davidgohel already has checked off his box.

FYI, we had a temporary snafu on the service serving badges. It should be back now.

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commented Mar 4, 2018

Thank you.

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commented Mar 6, 2018

Ah, I love the new vignette!!! 💕 It is full of so much useful, detailed information. This is going to be a great resource for users. I also am happy to see the other issues in the review addressed; I reviewed the package once more, did R CMD check and goodpractice::gp() again, and I have checked off the box in my review.

The only thing significant remaining in the checks is the NOTE about the size of the package.

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commented Mar 6, 2018

I do want this package to be a useful resource, and am so glad you liked the vignette!

The only thing significant remaining in the checks is the NOTE about the size of the package.

I will keep trying, but CRAN never got back to me at all.

Has anybody seen a package that downloads the required resources after package installation? There are Apache mirrors for Tika, such as http://mirrors.ocf.berkeley.edu/apache/tika/tika-app-1.17.jar .

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commented Mar 6, 2018

Thanks all for great reviews and follow-up, @juliasilge @davidgohel and @predict-r. We can accept the package as-is from our perspective, the size/CRAN issue isn't a precondition on our front, but it makes sense to work out the approach first. I'll be happy to do a full editors' check if you make major changes on this front.

Courtesy of great friend of rOpenSci Bob Rudis, here's the distribution of .jar file sizes on CRAN. the Tika .jar would be larger than any of them, but isn't a different order of magnitude. So you could go ahead and submit tikajar to CRAN and see the what the response is, then submit rtika if it goes in.

uzwxmpjq 1

If not, I believe having a package automatically install resources on installation is a violation of CRAN policies in most cases. The few exceptions I know of relate to license issues or platform-specific installs of compiled binaries. But plenty of packages have functions to install system dependencies that users run after install, such as keras::install_keras(). So having a tika::install_tika() function that downloads the .jar file (probably using rappdirs::user_data_dir() to select the install path) is a reasonable alternative strategy. In this case you will want to mark all examples as \dontrun{} and use skip_on_cran() for your tests so the package test properly on CRAN. You can still run install_tika() and run the tests on Travis.

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commented Mar 6, 2018

We can accept the package as-is from our perspective, the size/CRAN issue isn't a precondition on our front

I've slept on it, and am ready to give up on CRAN for now. The response from Uwe Ligges at CRAN is:

In principle a CRAN package should not exceed 5MB, 50 seems to be too much.

Since the Tika .jar is over 55.7MB (49.5MB compressed), there is no way to distribute the .jar on CRAN without violating that principle.

So, once accepted this package would be on both github and ropensci! I'm happy with that.

@noamross Thank you for showing a good way, and offering to do a full editor's check. Uwe from CRAN had a similar suggestion:

I wonder if you cannot host that software externally and provide some infrastructure that allows to install the jar files later on if a user requests it from an external source?

The way you suggested, using rappdirs::user_data_dir() to get a writable directory, sounds fine. However, I still want to move forward and keep the package simple to install and uninstall.

Perhaps we can return to this issue and I could requests an editorial review in the future? Maybe there could be two versions of the package--one without the .jar?

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commented Mar 7, 2018

I advise against two packages. It will be confusing for users and make more effort for maintenance. I think an install_tika() function makes for a fairly simple experience - you can print a package startup message if the .jar if missing, and a similar informative error for any Tika-calling function. Plus you can update the Tika version by one line of code - the download URL - in the package. CRAN publication will maximize your user base, as this package will of a great use to many people.

I'm OK with marking this as "accepted" now, but I would prefer that if the plan is to change the user experience in this way soon, we do so before we move forward with blog posts and such.

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commented Mar 7, 2018

Alright, I’ll make the install script. :)

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commented Mar 9, 2018

I've implemented install_tika().

However, along the way, I ran into a big Apache Tika bug! It was in the batch processor. The good news is that I reported the bug, and it was immediately patched! See [1].

The bug, combined with install_tika(), breaks rtika on OS X.

A potential issue is the next major release of Tika with the patch, Tika version 1.18, will be released soon, but I'm not sure exactly when...I've asked.

In the meantime, what about having install_tika() get the patched development version directly from Apache? See [2]. This would come with warnings that it is a development version.

If people have thoughts on installing a development version of Tika, I'd like to hear them.

[1] https://issues.apache.org/jira/browse/TIKA-2604?page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel&focusedCommentId=16393363#comment-16393363
[2] https://builds.apache.org/job/tika-branch-1x/10/org.apache.tika$tika-app/

P.S. I'm kinda proud of finding the bug!

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commented Mar 10, 2018

👏 Good work finding that @predict-r! I had problems with another program crashing recently because of spaces in file paths, so I'm glad this bug is squashed.

We'll see what the response is from the developer, but based on this email thread it seems that 1.18 is only a week or two off. If it were months away I would suggest an jumping ahead. I would say it's fine to the patched version on GitHub now, (esp. given that user_data_dir() is likely to have spaces on many machines), but wait until 1.18 before CRAN submission. GitHub packages are generally perceived to be "development" versions. You can put a note about the patched version in the README.

I will take a careful look at the remaining changes to wrap this up later this weekend.

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commented Mar 10, 2018

Thanks ! The install_tika() is temporarily set to download the development version. The package is passing Travis.

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commented Mar 12, 2018

Approved! Great work, and thanks a lot @juliasilge and @davidgohel for your reviews! The install_tika() functions and docs are looking good, and I commend your good use of assertions and failsafes.

To-dos:

  • Transfer the repo to the rOpenSci organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You'll be made admin once you do.

  • Update badges, CI and coverage links, and URLs to point to the new repo address.

  • If you would like to, and if your reviewers agree, you may choose to credit their reviews in the DESCRIPTION file by adding them as 'rev'-type contributors (example)

Welcome aboard! I for one am quite excited about rtika. We'd also love a blog post about your package, either a short-form intro to it (https://ropensci.org/tech-notes/) or long-form post with more narrative about its development. ((https://ropensci.org/blog/). If you are interested in writing one, let us know and, @stefaniebutland will be in touch about content and timing.

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commented Mar 12, 2018

Writing a long form post sounds good. It's an opportunity for me to introduce the package and reflect some on the process. Please express my interest and thanks for the opportunity to @stefaniebutland .

Okay, regarding the logistics of the transfer, it's now at:

https://github.com/ropensci/rtika

That was super easy. The README links are also changed, yet I don't know how to change the github repository title blurb at the very top to:

R Interface to Apache Tika https://ropensci.github.io/rtika/

I guess I no longer control repository level settings, which is okay, but that link should be changed.

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commented Mar 12, 2018

I made that change. You should have repo settings control now. All set! I'm going to close this issue, but @stefaniebutland will respond here about blog timing. Here are our editorial and technical guidelines for posts: https://github.com/ropensci/roweb2#contributing-a-blog-posts, and some other posts in the onboarding series https://ropensci.org/tags/review/

@noamross noamross closed this Mar 12, 2018

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commented Mar 12, 2018

👍

@noamross noamross referenced this issue Mar 14, 2018
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@stefaniebutland

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commented Mar 14, 2018

Hi @predict-r. Great to hear that you are interested in contributing a blog post and thanks to Noam for providing that link to recommendations. Would you be able to submit a draft via pull request by March 27? That will give us an opportunity to review it, give you feedback and set a date for publication.

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commented Mar 14, 2018

Greetings @stefaniebutland. That is reasonable. I'll submit the draft by the 27th. Based on https://github.com/ropensci/roweb2#contributing-a-blog-posts, I know what to try. If there are any examples of the blog you particularly liked or want to recommend, let me know and I'll take a closer look. Thanks.

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commented Mar 15, 2018

@predict-r This will give you a range of examples https://ropensci.org/tags/review/. Browsing them will give you an idea of the length you prefer, and different angles on the narrative.

I'm happy to give feedback on an early version or outline if that helps you.

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commented Mar 27, 2018

@stefaniebutland, I posted a draft here:

goodmansasha/roweb2#1

It's a pull request on a fork...hope I did that correctly.

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commented Mar 28, 2018

Thank you for doing this @predict-r.

hope I did that correctly
It looks like you made a pull request to your own fork of our repo.

From https://github.com/predict-r/roweb2 you should create a pull request with branch predict-r-patch-1 in your fork to master on the ropensci repo. It will look like the image here

screen shot 2018-03-27 at 3 09 51 pm

I have a few other blog posts to review first so I will get you some feedback likely early next week.

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