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| -rw-r--r-- | api/upload.md | 47 |
1 files changed, 42 insertions, 5 deletions
diff --git a/api/upload.md b/api/upload.md index 62b828c..dff9bc5 100644 --- a/api/upload.md +++ b/api/upload.md @@ -1,8 +1,8 @@ # GeneNetwork upload API -## API +## Upload API -The REST API will accept gzipped tar ball which contains multiple +The REST API will accept a gzipped tar ball which contains multiple files: 1. A metadata file (JSON) @@ -44,7 +44,17 @@ On error the result should include the error output } ``` -### Metadata +## Metadata + +For metadata we will follow the R/qtl2 input +[format]https://kbroman.org/qtl2/assets/vignettes/input_files.html). +See the examples at https://kbroman.org/qtl2/pages/sampledata.html. +One example is +[here](https://github.com/kbroman/qtl2/blob/gh-pages/assets/sampledata/iron/iron.yaml). We +will not be using YAML though! Use JSON instead. + + +The files that are uploaded are listed in the metadata. The metadata file is a simple JSON file containing @@ -56,11 +66,27 @@ The metadata file is a simple JSON file containing "authors": [ "R.W. Williams" ], - "cross": "BXD" + "crosstype": "BXD", + "geno": "iron_geno.csv", + "pheno": "iron_pheno.csv", } ``` -### Phenotype file +## File lookup (resolving) + +Files can be in three places: + +1. On the internet (URL) - fixme later +2. Uploaded in the local dir (file, but no path) +3. In the database (identifier) - fixme later + +For Genotype files a file name is passed in. We will first look in the +upload dir. If it is not there we will look in the genotype_files +directory of GeneNetwork. + +For phenotype files we currently only look in the upload directory. + +## Phenotype file The phenotype file is a tab delimited 'spreadsheet' where the columns contain phenotypes and the rows contain individuals. Example @@ -90,3 +116,14 @@ BXD20 309.500 ``` Missing data are 'NA'. Multiple pheno columns are possible. + +## Running GEMMA + +Using the hash received earlier we can run GEMMA against the uploaded +data. Example: `/api/gemma/lmm2/e524ee7ea9b1f452c58abe560960a60f` +should do the trick and result a status or error. The resulting output +files should be fetchable with something like: + +`/api/gemma/lmm2/loco/e524ee7ea9b1f452c58abe560960a60f/results.log.txt` +and +`/api/gemma/lmm2/loco/e524ee7ea9b1f452c58abe560960a60f/results.assoc.txt` |