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All of Bob's modifications since September #1

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All of Bob's modifications since September #1

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@bobular bobular commented Dec 5, 2019

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.

@bobular
started work on providing better tracing of 'bad' ontology terms. Cur…
76ce434 
…rently only works for investigation sheet.
@bobular
renamed to getDebugContext, improved usage and stopped null terms bei…
f99bf8f 
…ng processed
@bobular
proper checking of empty ontology terms
a857f06
@bobular
skipping empty lines to avoid '_'=>undef in data structures
904f4df
@bobular
added new DataEntity class so that Assays can have characteristics an…
e9f6081 
…d descriptions too
@bobular
groundwork laid for loading p_phenotype and g_genotype files
a5a0ac3
@bobular
now reads in ISA-like popbio Phenotype data from p_*.txt data files
2cdf1bd
@bobular
added new classes to handle VB popbio genotype sheets
00e0367
@bobular
added debugContext for ontology terms created from study-assay files
5e52b3e
@bobular
Implemented the parsing of ontology source IDs from Characteristics h…
3f1b3e1 
…eadings
@bobular
added handling for custom STUDY TAGS section
9b4edb1
@bobular
characteristics qualifier syntax to allow OBI:OBI_0012345 or SO:SO:01…
5962b04 
…23456
@bobular
renamed Value attribute to PhenotypeValue to avoid method name clash …
c0db4d6 
…for getValue(). ISA-Tab-like phenotype files remain the same.
@bobular
Comment headings can now have optional white space between 'comment' …
c50d312 
…and left brace
@bobular
disabled the debug-context code
2fc8659
@bobular
fixed #38395 to allow zero values to be loaded from ISA-Tab
d794c2d
@bobular
was missing parent child relationship between Phenotype, Genotype and…
1d87295 
… Characteristics
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@bobular