Samuel Lampa samuell

💻

Hacking away

Bioinformatician in clinical microbiology. Occasionally hacking on stuff like @flowbase, @scipipe & @rdfio

samuell / query_rdfio_via_swiprolog.pro

Last active August 17, 2017 18:12

	?- use_module(library(semweb/sparql_client)).
	true.

	?- sparql_query('CONSTRUCT { ?s ?p ?o } WHERE { ?s ?p ?o }',
	Row,
	[ host('localhost'),
	path('/w/index.php/Special:SPARQLEndpoint'),
	port(8080),
	search( [equivuri_q=1, equivuri_o=1] ) ]).

samuell / swi_prolog_sparql_construct_error.pro

Created August 17, 2017 17:17

	?- use_module(library(semweb/sparql_client)).
	true.

	?- sparql_query('CONSTRUCT { ?s ?p ?o } WHERE { ?s ?p ?o } LIMIT 1',
	Row,
	[ host('localhost'),
	path('/w/index.php/Special:SPARQLEndpoint'),
	port(8080) ]).
	ERROR: Domain error: `sparql_result_document' expected, found `'application/xml'' (<?xml version="1.0" encoding="UTF-8"?>
	<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">

samuell / rdfio_smw2.5_errors.log

Created August 9, 2017 17:02

	PHP Warning: mysqli_connect(): (HY000/1045): Access denied for user ''@'localhost' (using password: NO) in /vagrant/w/vendor/semsol/arc2/store/ARC2_Store.php on line 51
	PHP Stack trace:
	PHP 1. {main}() /vagrant/w/maintenance/importDump.php:0
	PHP 2. require_once() /vagrant/w/maintenance/importDump.php:327
	PHP 3. BackupReader->execute() /vagrant/w/maintenance/doMaintenance.php:111
	PHP 4. BackupReader->importFromFile() /vagrant/w/maintenance/importDump.php:106
	PHP 5. BackupReader->importFromHandle() /vagrant/w/maintenance/importDump.php:269
	PHP 6. WikiImporter->doImport() /vagrant/w/maintenance/importDump.php:322
	PHP 7. WikiImporter->handlePage() /vagrant/w/includes/import/WikiImporter.php:577
	PHP 8. WikiImporter->handleRevision() /vagrant/w/includes/import/WikiImporter.php:769

samuell / test.sh

Created June 1, 2017 14:01

         1         2         3         4         5         6         7         8         9         0         1         2         31234567890

samuell / caw_scipipe_yamlexperiment_generated.go

Last active June 14, 2018 15:25

SciPipe Go code that would be generated from this Yaml syntax: https://gist.github.com/samuell/7aca5a41bbace015f8a94856d78a70d7

	package main

	import (
	"flag"
	"strconv"

	sp "github.com/scipipe/scipipe"
	spcomp "github.com/scipipe/scipipe/components"
	)

samuell / caw_scipipe_yamlexperiment.yml

Last active June 14, 2018 15:11

This yaml-code would be fed into a tool that generates something like this Go code: https://gist.github.com/samuell/e89ccc2544c8d4def5eeef9d2f7e46bc

	# --------------------------------------------------------------------------------------------
	# Quick syntax intro
	# --------------------------------------------------------------------------------------------
	# Process definitions:
	# Processes can be defined as "file:" or "shell:" type.
	# - The "shell:" type takes a command pattern with the following special syntax:
	# - {i:portname} defines an in-port (for feeding inputs from upstream processes)
	# - {o:portname} defines an out-port (where outputs will be sent to connected downstream processes)
	# - {p:portname} defines a parameter port, where parameters can be fed as a stream of strings
	# Connections:

samuell / plot_file_sizes.py

Created May 17, 2017 11:49

	#!/usr/bin/env python
	from sys import stdin, stdout
	import csv

	rdr = csv.reader(stdin, delimiter='\t')
	wrt = csv.writer(stdout, delimiter='\t')

	vals = []
	rows = []
	for row in rdr:

samuell / rdfio_demo2_wikidata_query.sparql

Last active May 2, 2017 12:00

SPARQL query to obtain the data for Demonstrator II in the RDFIO paper. The link directly to the data is available in a comment below.

	CONSTRUCT {
	?wikidata <http://pharmb.io/onto/haspKa> ?pKa ;
	<http://pharmb.io/onto/hasDOI> ?doi ;
	rdfs:label ?compound . ?wikidata rdf:type <http://pharmb.io/onto/Compound> .
	<http://pharmb.io/onto/Compound> rdfs:label "Compound" .
	} WHERE {
	?wikidata p:P1117 ?foo ;
	rdfs:label ?compound ;
	p:P31 ?type .
	?foo a wikibase:BestRank ;

samuell / list_minikube_jobinfo.go

Created February 13, 2017 08:24

	package main

	import (
	"flag"
	"fmt"
	"k8s.io/client-go/kubernetes"
	"k8s.io/client-go/pkg/api/v1"
	"k8s.io/client-go/tools/clientcmd"
	)

samuell / k8s_jobs_api_test.go

Created February 11, 2017 08:43

	package main

	import (
	"flag"
	"k8s.io/client-go/kubernetes"
	"k8s.io/client-go/tools/clientcmd"
	)

	var (
	kubeconfig = flag.String("kubeconfig", "/home/samuel/.kube/config", "absolute path to the kubeconfig file")