Listing chemistry objects

Clone this repository.

Store the archive files (.zip) you want to list the chemistry objets from in the data folder. (For example this yareta record.)

If the program has been compiled for your system (see src/cpp src/cpp/README.md) a list of the chemistry objects will be generated and stored in the data/ folder with this bash script:

src/bash/generateChemistryObjects.bash

More details

The chemisty objects are generated in two steps.

1 Extraction of the relevant files from the archive file

The first step uses a shell script (src/bash/unzipRelevant.bash) extracting the list of files. It generates a lists of the relevant files in the “_listFiles.txt” file located in the data folder. In some cases the second step will need to read the content of some of the files (to test of presence of a keyword, for example). In this case the script will extract the file and store it in the unziped folder, otherwise it will just create an empty file.

Usage:

cd data
../src/bash/unzipRelevant.bash
cd ..

2 Analysis of the relevant files

The analysis uses the C++ program src/cpp/listChemObjects.cpp.

It includes tests to identify chemistry objects.

The criteria for the identification of chemistry objects are included in the program (see specifications). It generates Json, but other formats could be easily generated - Just submitting a ticket.

Analysis of the data

The compiled C++ program reads the relevant files and generates the list of chemisty objects as a json:

Examples of generation of .json output from a list of files:

src/cpp/listChemObjects.o data/62c9dc3b-6f44-4b3b-963d-1ab31c17f6c6.zip_listFiles.txt "" unziped/
src/cpp/listChemObjects.o data/prepareYaretaFolderNasca_phyto.zip_listFiles.txt "" unziped/

The output can be redirected into a file:

src/cpp/listChemObjects.o data/62c9dc3b-6f44-4b3b-963d-1ab31c17f6c6.zip_listFiles.txt "" unziped/ > examples/demo_archive_yareta.json

This will also create a xml file which can be used to make html (second line)

src/cpp/listChemObjects.o data/62c9dc3b-6f44-4b3b-963d-1ab31c17f6c6.zip_listFiles.txt "" unziped/ ./out.xml >out.json
xsltproc src/xmltStylesheet/stylesheet.xml out.xml > doc/index.html

Example of Json file

demo_archive_yareta.json on GihHub (crude data).

demo_archive_yareta.json (This file may be reformated by the browser).

After converting the json to xml and using the xml to generate xsd we get the following schema:

<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
  <xs:element name="root" type="rootType"/>
  <xs:complexType name="rowType">
    <xs:sequence>
      <xs:element type="xs:string" name="objTitle"/>
      <xs:element type="xs:string" name="basicCategory"/>
      <xs:element type="xs:string" name="type"/>
      <xs:element type="xs:string" name="subType"/>
      <xs:element type="xs:string" name="fileKey"/>
      <xs:element type="xs:byte" name="level"/>
      <xs:element type="xs:string" name="file"/>
    </xs:sequence>
  </xs:complexType>
  <xs:complexType name="rootType">
    <xs:sequence>
      <xs:element type="rowType" name="row" maxOccurs="unbounded" minOccurs="0"/>
    </xs:sequence>
  </xs:complexType>
</xs:schema>

Note that only some of these objects are worth being listed to a visitor of the repository.

show examples of output

get doi only:

xsltproc src/xmltStylesheet/stylesheetOnlydoi.xml /Volumes/san256/users_for_mac_system_macPro/jeannerat/mygit/djeanner/ResearchObjectFinder/unziped/data/62c9dc3b-6f44-4b3b-963d-1ab31c17f6c6/dlcm.xml

get doi and author information :

xsltproc src/xmltStylesheet/stylesheetheader.xml /Volumes/san256/users_for_mac_system_macPro/jeannerat/mygit/djeanner/ResearchObjectFinder/unziped/data/62c9dc3b-6f44-4b3b-963d-1ab31c17f6c6/dlcm.xml