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gaurav / Shell output
Last active May 12, 2021
linkml-classes-bug
View Shell output
$ pipenv install linkml==0.0.7
Creating a Pipfile for this project...
Installing linkml==0.0.7...
Adding linkml to Pipfile's [packages]...
✔ Installation Succeeded
Pipfile.lock not found, creating...
Locking [dev-packages] dependencies...
Locking [packages] dependencies...
Building requirements...
Resolving dependencies...
View PFB dd_100.avro metadata.json
{
"nodes": [
{
"name": "root",
"ontology_reference": "",
"values": {},
"links": [],
"properties": []
},
{
@gaurav
gaurav / CGEX_CtxAll010-shex-validation.json
Created Jan 14, 2020
ShEx validation of example validation for CGEX_CtxAll010
View CGEX_CtxAll010-shex-validation.json
{
"type": "Failure",
"node": "http://dataexchange.clinicalgenome.org/CGEX_CtxAll010",
"shape": "http://dataexchange.clinicalgenome.org/interpretation/shacl/shapes/ContextualAllele",
"errors": [
{
"type": "TypeMismatch",
"triple": {
"type": "TestedTriple",
"subject": "http://dataexchange.clinicalgenome.org/CGEX_CtxAll010",
@gaurav
gaurav / field_summaries.2019-nov-4
Created Nov 4, 2019
List of fields used in PubMed Annual Baseline 2019
View field_summaries.2019-nov-4
# '.' indicates XML nodes
# '/' indicates XML attributes
# '#' are XML values, but only for some fields
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText,34722040)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.mn,2)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.mrow.mi,7)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.mrow.mo,6)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.mrow.msub.mi,4)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.msup.mi,1)
(PubmedArticleSet.PubmedArticle.MedlineCitation.Article.Abstract.AbstractText.DispFormula.math.mfrac.msup.mrow.mi,1)
View batman bares bear arms
Jon Jon Wendt gives Gene Valgene his hooded cloak.
Gene Valgene: ...
Gene Valgene: [Batman voice] I'm the Batman now.
Jon Jon Wendt: Batman!
Gene Valgene: Batman.
Jon Jon Wendt: Batman! Batman! Batman!
Gene Valgene: BAAAAAAAAAT
Gene Valgene: MAAAAAAAAAAN
Jon Jon Wendt: That's the spirit!
Gene Valgene: [Batman voice] Hmm.
@gaurav
gaurav / gist:1475883
Created Dec 14, 2011
LaTeX to HTML on a Mac
View gist:1475883
1. Find your texbin directory. This is usually /usr/texbin, which is symlinked to wherever the actual directory is.
2. Add it to your PATH (i.e. `# export PATH=/usr/texbin:$PATH`)
3. Run the 'htlatex' command. This will convert your LaTeX file into an HTML document. Note that this really just a script around normal LaTeX, so you'll have to do the usual things (htlatex -> bibtex -> htlatex for citations, htlatex -> htlatex for references). I think: I had my LaTeX all PDF-LaTeXed and ready to go, so all the .bib/.toc/etc. files had already been created.
3.1. You might want to run 'htlatex file.tex "xhtml,fn-in"' if you have footnotes. Without that option, footnotes will be put into their own HTML file.
4. At this point, you have an HTML file. Check it and make sure it's good enough.
5. Open the HTML file in TextEdit. Oddly enough, Pages can't open HTML files, but TextEdit can. Go figure.
6. TextEdit can now save your file as an RTF or Doc file.
7. Success!
View .vimrc
" Activate pathogen.
call pathogen#infect()
call pathogen#helptags()
" These are a few of my favourite settings.
syntax on
set background=dark
set hlsearch
set incsearch
set smartindent
View paper-from-clade-ontology.owl
This file has been truncated, but you can view the full file.
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
xmlns:ns1="http://www.w3.org/2002/07/owl#"
xmlns:ns2="http://www.essepuntato.it/2012/04/tvc/"
xmlns:ns3="http://rs.tdwg.org/dwc/terms/"
xmlns:ns4="http://vocab.phyloref.org/phyloref/testcase.owl#"
xmlns:ns5="http://purl.org/opentree/nexson#"
xmlns:ns6="http://purl.obolibrary.org/obo/"
xmlns:ns7="http://ontology.phyloref.org/phyloref.owl#"
View fails.jsonld
[{
"@context": "https://www.phyloref.org/curation-tool/json/phyx.json",
"@type": "owl:Ontology",
"citation": "Example"
}]
@gaurav
gaurav / test.json
Last active Dec 13, 2017
Converting a blank node from JSON-LD (test.json) -> XML/RDF (test.xml) -> JSON-LD (test_back.json) and Turtle (test_back.ttl)
View test.json
{
"@context": {
"obo": "http://purl.obolibrary.org/obo/",
"denotes": {
"@id": "obo:IAO_0000219",
"@type": "@id"
}
},