Initial steps by @biodavidjm

[biodavidjm]

@biodavidjm starts on 6 Mar 2014

• Read all the documentation about this project
• Review docs about similar related projects (ontology, bibliography, etc)
• Install all the required software, modules, packages

[biodavidjm]

Installing Test-Chado

I installed it using cpanm, as this:

cpanm git://github.com/dictyBase/Test-Chado

After a long installation, these are the last outputs:

...
Building and testing Test-Chado-v4.1.0 ... OK
Successfully installed Test-Chado-v4.1.0
63 distributions installed

I will suggest to @cybersiddhu to include the suggestion of using cpanm as a way to install Test-Chado in the README file of Test-Chad, in order to facilitate the installation to beginners.

[biodavidjm]

The test didn't work.

prove -lv t/dbtest.t
t/dbtest.t .. Undefined subroutine &main::chado_schema called at t/dbtest.t line 5.
Dubious, test returned 255 (wstat 65280, 0xff00)
No subtests run

Test Summary Report
-------------------
t/dbtest.t (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: No plan found in TAP output
Files=1, Tests=0,  0 wallclock secs ( 0.03 usr  0.00 sys +  0.12 cusr  0.01 csys =  0.16 CPU)
Result: FAIL

I checked if the Module was correctly installed and it does not seem to be the case:

perl -e 'while (<@INC>) { while (<$_/*.pm>) { print "$_\n"; } }' | grep Test
with no results

I am advised to not to install Test-Chado. Instead, I should install Modware-Loader

[cybersiddhu]

If you developing or working with Test::Chado then you need to install Test::Chado. However, if you are going to work with data migration you need to pull Modware::Loader which will pull Test::Chado.

[biodavidjm]

But at the same time, the installation of all this modules is different if one is planning to either develop or just use it. I need to go through Modern Perl and figure out the differences, as advised by Sidd. At the same time, the installation of modware::loader threw different errors that I need to go through (basically install libraries that I have not installed yet).

[cybersiddhu]

Check out the docs here, should give you some idea. Please make sure modify and add information as you go along. Later on those could be turned into bigger documents, should be really handy in the future.

[biodavidjm]

Testing Stock-Export

modware-dump dictystrain -c configuration_file.yaml worked mostly successfully. The only problem was to specify the folder in which the data is expected to be dumped (the option --output_dir did not work. As a consequence, everything was dumped to the current directory)

The resulting files (and the number of lines in each file) are:

   18243 strain_characteristics.tsv
    1498 strain_genes.tsv
    5820 strain_genotype.tsv
    2424 strain_inventory.tsv
   15173 strain_parent.tsv
    7061 strain_phenotype.tsv
    4487 strain_plasmid.tsv
   14515 strain_props.tsv
    5753 strain_publications.tsv
    1951 strain_publications_no_pubmed.tsv
    5820 strain_strain.tsv

modware-dump dictyplasmid -c ../davidtest.yaml also worked (with the same little problem), dumping the following files:

      50 plasmid_genbank.tsv
     531 plasmid_genes.tsv
     835 plasmid_inventory.tsv
     749 plasmid_plasmid.tsv
    3666 plasmid_props.tsv
     657 plasmid_publications.tsv
     456 plasmid_publications_no_pubmed.tsv