2015-08-05.md

JATS4R validator

Better Schematron results presentation

• Issue #5
• Work in ~/Projects/libxml2
• I am trying to see if I can use libxml to get the line and column numbers of XPath expressions that come from the Schematron validator.

Building libxml2 on my Mac

I first tried to clone from https://git.gnome.org/browse/libxml2, and then run the steps described here, starting with ./configure, but that failed. I guess that in the dev repo, there are preliminary steps required to make the configure script.

So I downloaded the compressed binary bundle libxml2-git-snapshot.tar.gz, and unzipped it to ~/Projects/libxml2/libxml2-2.9.2. Then, I was able to build with:

./configure --prefix=/Users/maloneyc/Projects/libxml2/install
make
make install

After that, the install directory had bin, include, lib, and share.

I added the bin directory to the front of my PATH:

export PATH=/Users/maloneyc/Projects/libxml2/install/bin:$PATH

Then, I was able to build the test program reader1.c with:

gcc `xml2-config --cflags --libs` -o reader1 reader1.c

My xpath locator utility

See saxparse.c.

Installing emscripten on ncbimac1131

• Downloaded https://s3.amazonaws.com/mozilla-games/emscripten/releases/emsdk-portable.tar.gz to ~/bin

• Testing which tools are already installed:

  • python --version: 2.7.10

  • node -v: v0.10.32

  • git --version: 2.4.4

  • java -version: 1.8.0_45

  • gcc --version:

    Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
    Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
    Target: x86_64-apple-darwin13.4.0
    Thread model: posix
    

  • cmake: exists

• Setup python2: Entering python2 --version gave me "2.7.10".

  • Anyway, I did this (not sure if it will help or not)

    cd ~/homebrew/bin
    ln ../Cellar/python/2.7.10/bin/python2.7 python22.7
    

• Extracting the SDK into ~/bin/emsdk-portable

  cd ~/bin
  tar xvfz emsdk-portable.tar.gz
  cd emsdk_portable
  

• Then:

  ./emsdk update
  ./emsdk install latest
  ./emsdk activate latest
  source ./emsdk_env.sh
  

• Added source /Users/maloneyc/bin/emsdk_portable/emsdk_env.sh to .bash_profile.

Verified the installation per [the tutorial](source ./emsdk_env.sh)

emcc -v

returns

INFO     root: (Emscripten: Running sanity checks)
emcc (Emscripten gcc/clang-like replacement + linker emulating GNU ld) 1.34.4
clang version 3.7.0
Target: x86_64-apple-darwin13.4.0
Thread model: posix
INFO     root: (Emscripten: Running sanity checks)

Wrote this to hello.c:

#include<stdio.h>

int main() {
  printf("hello, world!\n");
  return 0;
}

And compiled it with

emcc hello.c
node a.out.js

Works!

[archive] Investigating how to build a custom C program based on libxml2

I started out by reverse-engineering the Makefile. I abandoned this effort after realizing I could install a local copy of the library, and use xml2-config (see above).

This works to build xmllint:

/bin/sh ./libtool --silent --tag=CC --mode=link gcc -D_REENTRANT -I/Users/maloneyc/homebrew/Cellar/xz/5.2.1/include -g -O2 -pedantic -W -Wformat -Wunused -Wimplicit -Wreturn-type -Wswitch -Wcomment -Wtrigraphs -Wformat -Wchar-subscripts -Wuninitialized -Wparentheses -Wshadow -Wpointer-arith -Wcast-align -Wwrite-strings -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wnested-externs -Winline -Wredundant-decls -Wno-long-long -o xmllint xmllint.o ./libxml2.la -lpthread -lz -L/Users/maloneyc/homebrew/Cellar/xz/5.2.1/lib -llzma -liconv -lm

Works! To link a test program reader1.o -> reader1.c:

/bin/sh ./libtool --silent --tag=CC --mode=link gcc -D_REENTRANT -I/Users/maloneyc/homebrew/Cellar/xz/5.2.1/include -g -O2 -pedantic -W -Wformat -Wunused -Wimplicit -Wreturn-type -Wswitch -Wcomment -Wtrigraphs -Wformat -Wchar-subscripts -Wuninitialized -Wparentheses -Wshadow -Wpointer-arith -Wcast-align -Wwrite-strings -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wnested-externs -Winline -Wredundant-decls -Wno-long-long -o reader1 reader1.o ./libxml2.la -lpthread -lz -L/Users/maloneyc/homebrew/Cellar/xz/5.2.1/lib -llzma -liconv -lm

Try compiling reader1.c -> reader1.o:

gcc -DHAVE_CONFIG_H -I.  -I./include -I./include  -D_REENTRANT  -I/Users/maloneyc/homebrew/Cellar/xz/5.2.1/include  -g -O2 -pedantic -W -Wformat -Wunused -Wimplicit -Wreturn-type -Wswitch -Wcomment -Wtrigraphs -Wformat -Wchar-subscripts -Wuninitialized -Wparentheses -Wshadow -Wpointer-arith -Wcast-align -Wwrite-strings -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wnested-externs -Winline -Wredundant-decls -Wno-long-long

Building xml.js on ncbimac1131

I cloned it from scratch:

git clone https://github.com/hubgit/xml.js.git
cd xml.js
git checkout dtd-validation
git submodule init   # Failed with "arch: Can't find perl5.18 in PATH"

To try to fix the problem I tried to install and switch to perl 5.18 with perlbrew:

perlbrew install 5.18.4
perlbrew switch 5.18.4
cd /Users/maloneyc/perl5/perlbrew/perls/perl-5.18.4/bin
ln perl perl5.18

This failed:

While that's working, let's try a later version of git:

$ which git
/sw/bin/git
$ git --version
git version 2.4.4
$ brew update
$ brew install git    # Tried to install 2.5.0, but failed

Then, I was able to continue with

git submodule init
git submodule update   # failed to connect to git.gnome.org

I changed the git clone URL for libxml2 from git://git.gnome.org/libxml2 to https://git.gnome.org/browse/libxml2, and it worked.

Then,

npm install
npm install -g gulp
gulp clean
gulp libxml2
gulp compile
gulp test

Loaded http://localhost:8080/git/hubgit/xml.js/test/test.html, and it works!!