All of Bob's modifications since September #1

bobular · 2019-12-05T22:13:06Z

Main changes are:

Assay nodes can have descriptions and characteristics (not strictly in ISA-Tab definition)
Genotype and Phenotype entities now handled in CBIL.
STUDY TAGS section.
Ontology term accessions parsed out of Characteristics column headings
Fixed the zero values issue

Added some debugging tracing but later disabled it.

…rently only works for investigation sheet.

…ng processed

…d descriptions too

…eadings

…23456

…for getValue(). ISA-Tab-like phenotype files remain the same.

…and left brace

… Characteristics

bobular added 17 commits September 25, 2019 19:32

started work on providing better tracing of 'bad' ontology terms. Cur…

76ce434

…rently only works for investigation sheet.

renamed to getDebugContext, improved usage and stopped null terms bei…

f99bf8f

…ng processed

proper checking of empty ontology terms

a857f06

skipping empty lines to avoid '_'=>undef in data structures

904f4df

added new DataEntity class so that Assays can have characteristics an…

e9f6081

…d descriptions too

groundwork laid for loading p_phenotype and g_genotype files

a5a0ac3

now reads in ISA-like popbio Phenotype data from p_*.txt data files

2cdf1bd

added new classes to handle VB popbio genotype sheets

00e0367

added debugContext for ontology terms created from study-assay files

5e52b3e

Implemented the parsing of ontology source IDs from Characteristics h…

3f1b3e1

…eadings

added handling for custom STUDY TAGS section

9b4edb1

characteristics qualifier syntax to allow OBI:OBI_0012345 or SO:SO:01…

5962b04

…23456

renamed Value attribute to PhenotypeValue to avoid method name clash …

c0db4d6

…for getValue(). ISA-Tab-like phenotype files remain the same.

Comment headings can now have optional white space between 'comment' …

c50d312

…and left brace

disabled the debug-context code

2fc8659

fixed #38395 to allow zero values to be loaded from ISA-Tab

d794c2d

was missing parent child relationship between Phenotype, Genotype and…

1d87295

… Characteristics

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