Merge pull request #2 from genenetwork/testing

Pulling changes from main branch

1 files changed, 26 insertions, 20 deletions

diff --git a/doc/API_readme.md b/doc/API_readme.md
index 6c88d413..652376a0 100644
--- a/doc/API_readme.md
+++ b/doc/API_readme.md
@@ -6,17 +6,17 @@
 
 To get a list of species with data available in GN (and their associated names and ids):
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/species
+curl http://gn2.genenetwork.org/api/v_pre1/species
 [ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ]
 ```
 
 Or to get a single species info:
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse
+curl http://gn2.genenetwork.org/api/v_pre1/species/mouse
 ``` 
 OR 
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json
+curl http://gn2.genenetwork.org/api/v_pre1/species/mouse.json
 ```
 
 *For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later*
@@ -26,27 +26,33 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json
 This query can optionally filter by species:
 
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/groups (for all species)
+curl http://gn2.genenetwork.org/api/v_pre1/groups (for all species)
 ```
 OR
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse groups/RISets)
+curl http://gn2.genenetwork.org/api/v_pre1/groups/mouse (for just mouse groups/RISets)
 [ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ]
 ```
 
 ## Fetch Genotypes for Group/RISet ##
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/genotypes/BXD
+curl http://gn2.genenetwork.org/api/v_pre1/genotypes/bimbam/BXD
+curl http://gn2.genenetwork.org/api/v_pre1/genotypes/BXD.bimbam
+```
+Returns a group's genotypes in one of several formats - bimbam, rqtl2, or geno (a format used by qtlreaper which is just a CSV file consisting of marker positions and genotypes)
+
+Rqtl2 genotype queries can also include the dataset name and will return a zip of the genotypes, phenotypes, and gene map (marker names/positions). For example:
+```
+curl http://gn2.genenetwork.org/api/v_pre1/genotypes/rqtl2/BXD/HC_M2_0606_P.zip
 ```
-Returns a CSV file with metadata in the first few rows, sample/strain names as columns, and markers as rows. Currently only works for genotypes we have stored in .geno files; I'll add the option to download BIMBAM files soon.
 
 ## Fetch Datasets ##
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd
+curl http://gn2.genenetwork.org/api/v_pre1/datasets/bxd
 ```
 OR
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd
+curl http://gn2.genenetwork.org/api/v_pre1/datasets/mouse/bxd
 [ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ]
 ```
 (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary)
@@ -55,11 +61,11 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd
 ### For mRNA Assay/"ProbeSet" ###
 
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P
+curl http://gn2.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P
 ```
 OR
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P```
+curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P```
 { "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 }
 ```
 (This also has the option to specify group/riset)
@@ -67,26 +73,26 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P```
 ### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ###
 For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example:
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/10001
+curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/10001
 { "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" }
 ```
 
 ## Fetch Sample Data for Dataset ##
 ``` 
-curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv
+curl http://gn2.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv
 ```
 
 Returns a CSV file with sample/strain names as the columns and trait IDs as rows
 
 ## Fetch Sample Data for Single Trait ##
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at
+curl http://gn2.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at
 [ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ]
 ```
 
 ## Fetch Trait List for Dataset ##
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json
+curl http://gn2.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json
 [ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ]
 ```
 
@@ -95,7 +101,7 @@ Both JSON and CSV formats can be specified, with JSON as default. There is also
 ## Fetch Trait Info (Name, Description, Location, etc) ##
 ### For mRNA Expression/"ProbeSet" ###
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at
+curl http://gn2.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at
 { "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" }
 ```
 
@@ -104,7 +110,7 @@ For phenotypes this just gets the  max LRS, its location, and additive effect (a
 
 Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001
+curl http://gn2.genenetwork.org/api/v_pre1/trait/BXD/10001
 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 }
 ```
 
@@ -124,7 +130,7 @@ Each method's query takes the following parameters respectively (more will be ad
 
 Example query:
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true
+curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true
 ```
 
 ### R/qtl ###
@@ -140,7 +146,7 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPub
 
 Example query:
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100
+curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100
 ```
 
 Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case)
@@ -158,6 +164,6 @@ This query currently takes the following parameters (though more will be added):
 
 Example query:
 ```
-curl http://gn2-zach.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100
+curl http://gn2.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100
 [ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ]
 ```