Skip to content

Latest commit

 

History

History
95 lines (57 loc) · 2.57 KB

README.md

File metadata and controls

95 lines (57 loc) · 2.57 KB

pISA -- ISA-Tab validation

pISA xml and ISA-Tab Investigation templates

pISA assay types

at https://github.com/NIB-SI/pISA-tree-assay-types/tree/main/Assay-types

external links

Code Beautify

https://github.com/ISA-tools/Configuration-Files/tree/master/isaconfig-default_v2015-07-02 source for investigation.xml

https://github.com/ISA-tools/isa-api/blob/master/isatools/examples/validateISAtab.py

https://github.com/ISA-tools/isa-api/blob/master/isatools/isatab.py

http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000911

... and more at Ontobee

generic notes

DO

tree/master/ to trunk/ - oneliner with subversion

svn export https://github.com/ISA-tools/Configuration-Files/trunk/isaconfig-default_v2015-07-02

DO NOT

wget https://github.com/ISA-tools/ISAvalidator-ISAconverter-BIImanager/releases/download/1.6.5/ISA-validator-1.6.5.zip

types

type="xs:decimal" not supported

add .xml templates

to isaconfig-default_v2015-07-02 subdir

and call for e.g. qPCR set

python3

>>> import os, json, isatools; from isatools import utils, isatab

>>> my_json_report = isatab.validate(open(os.path.join('directory_path', 'i__I_Test-extended.txt')), 'path-to/isaconfig-default_v2015-07-02')

>>> with open('report-i__I_Test-qPCR.txt', 'w') as report_file:
     report_file.write(utils.format_report_csv(my_json_report))

general note

in https://github.com/ISA-tools/isa-api/blob/master/isatools/isatab.py, besides hardcoded

Investigation Person Last Name
Investigation Person First Name
Investigation Person Mid Initials
Investigation Person Email
Investigation Person Phone
Investigation Person Fax
Investigation Person Address
Investigation Person Affiliation
Investigation Person Roles
Investigation Person Roles Term Accession Number
Investigation Person Roles Term Source REF

also 'Source Name', 'Sample Name', 'Extract Name', 'Labeled Extract Name' are hardcoded/reserved to grep positions (and ignore all after),

plus be aware of


field_headers = [i for i in table.columns if
                         i.lower().endswith(' name') or i.lower().endswith(
                             ' data file') or i.lower().endswith(
                             ' data matrix file')]
        protos = [i for i in table.columns if i.lower() == 'protocol ref']
        if len(protos) > 0:
            last_proto_indx = table.columns.get_loc(protos[len(protos) - 1])

and which colnames will be even considered

doesnt parse well strings containing {[]}