nelsonlab frank changes

Added columns 'is_cv' and 'alias' to manifest_table, these should make the life of the developer a little easier by cutting down on the number of characters that need to be typed to uniquely identify ...

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Added columns 'is_cv' and 'alias' to manifest_table, these should make the life of the developer a little easier by cutting down on the number of characters that need to be typed to uniquely identify a table. eg. experiment_sample_expected_basecall -> es_eb. Added a new table 'experiment_sample_run' which will make it possible to enter runs into the database without having provide details about the content of the run such as what samples and barcodes should be expected. Moved 'sector' column from 'run_file' to 'experiment_sample_run' table. Effectively modified 'run_file_experiment_sample' to become 'run_file_experiment_sample_run' to associate data files with samples.
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Modified schema diagram to be in agreement with schema.m4

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Modified schema diagram to be in agreement with schema.m4
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Added shell completions for study_type. Added &list_nospace() so that bash shell completion wouldn't append an extra single quote

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Added shell completions for study_type. Added &list_nospace() so that bash shell completion wouldn't append an extra single quote
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Reworked all the DBI code that relied on $sth->rows, because it's not supported in sqlite

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Reworked all the DBI code that relied on $sth->rows, because it's not supported in sqlite
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Changed the configuration file parsing semantics to use Config::General(ParseConfig)

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Changed the configuration file parsing semantics to use Config::General(ParseConfig)
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Updated documentation and default controlled vocabulary values to conform with SRA 1.4

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Updated documentation and default controlled vocabulary values to conform with SRA 1.4
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Processed the SRA 1.5 specification. There did not appear to be any substantial changes to the XML schema, and I did not make any changes to the application.

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Processed the SRA 1.5 specification. There did not appear to be any substantial changes to the XML schema, and I did not make any changes to the application.
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Slight modification to the bulk database interaction code because sqlite does not seem to have the ability to do a COPY

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Slight modification to the bulk database interaction code because sqlite does not seem to have the ability to do a COPY
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Just checking in some old stuff so at least it's in version control

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Just checking in some old stuff so at least it's in version control
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Fixed up some comments in the schema

Bret Harry — Thu, 19 Jun 2014 04:34:50 -0000

Fixed up some comments in the schema
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