diff options
| -rw-r--r-- | issues/create-rdf-traits-page.gmi | 12 | ||||
| -rw-r--r-- | issues/probeset-metadata-upload.gmi | 19 |
2 files changed, 27 insertions, 4 deletions
diff --git a/issues/create-rdf-traits-page.gmi b/issues/create-rdf-traits-page.gmi index 8fb6764..2cc2ab6 100644 --- a/issues/create-rdf-traits-page.gmi +++ b/issues/create-rdf-traits-page.gmi @@ -4,14 +4,18 @@ * assigned: bonfacem * type: feature -* status: in progress +* status: closed Create end-points that query RDF for the following: -* [ ] Phenotypes: (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") -* [ ] Genotypes: (prefix "phenotype:" "<http://genenetwork.org/genotype/>") -* [ ] Probesets: (prefix "phenotype:" "<http://genenetwork.org/probesets/>") +* [x] Phenotypes: (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") +* [x] Genotypes: (prefix "phenotype:" "<http://genenetwork.org/genotype/>") +* [x] Probesets: (prefix "phenotype:" "<http://genenetwork.org/probesets/>") In the process, also add examples here: => /topics/RDF/example-sparql-queries Querying SPARQL Examples + +I ran into a problem where I can't upload probeset metadata, despite chunking and reducing the size of the dump. This is issue is tracked here: + +=> /issues/probeset-metadata-upload Upload probeset metadata diff --git a/issues/probeset-metadata-upload.gmi b/issues/probeset-metadata-upload.gmi new file mode 100644 index 0000000..4020416 --- /dev/null +++ b/issues/probeset-metadata-upload.gmi @@ -0,0 +1,19 @@ +# Upload probeset metadata + +## Tags + +* assigned: bonfacem +* type: bug +* status: open + +Probeset metadata is the only significant metadata that remains to be uploaded. Uploading using SPARQL'S endpoint (either using CURL or the load-rdf script) doesn't work. As such, I'll have to work out a different way to upload this metadata. Here's the current size of the datasets I'm trying to upload: + +``` +bonfacem@tux02:/export3/local/home/bonfacem/dump-genenetwork-database$ ls -lah data/ +total 3.2G +drwxr-xr-x 2 bonfacem bonfacem 4.0K Jun 16 08:04 . +drwxr-xr-x 9 bonfacem bonfacem 4.0K Jun 15 07:04 .. +-rw-r--r-- 1 bonfacem bonfacem 1.2G Jun 16 07:48 dump-probeset-0.ttl +-rw-r--r-- 1 bonfacem bonfacem 1014M Jun 16 08:04 dump-probeset-1.ttl +-rw-r--r-- 1 bonfacem bonfacem 1009M Jun 16 08:18 dump-probeset-2.ttl +``` |