From 0d6c9ab0b34199e94aaf262f7a7eb7f6e0f77b72 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 29 Apr 2019 11:12:48 -0500
Subject: Started API readme file

---
 api_readme.md | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 api_readme.md

diff --git a/api_readme.md b/api_readme.md
new file mode 100644
index 00000000..eef0b2d7
--- /dev/null
+++ b/api_readme.md
@@ -0,0 +1,62 @@
+# API Command Documentation #
+
+## Fetch Species List ##
+
+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
+[
+  {
+    "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
+``` 
+OR 
+```
+curl http://gn2-zach.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*
+
+## Fetch Groups/RISets ##
+
+This query can optionally filter by species:
+
+```
+curl http://gn2-zach.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)
+[ { "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 Datasets ##
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd
+```
+OR
+```
+curl http://gn2-zach.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)
+
+
+
+
-- 
cgit v1.2.3


From 7daf96560d0b1f945a0a5fd0aed4a9961b718635 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 29 Apr 2019 11:48:51 -0500
Subject: Added the rest of the currently existing commands

---
 api_readme.md | 72 ++++++++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 56 insertions(+), 16 deletions(-)

diff --git a/api_readme.md b/api_readme.md
index eef0b2d7..00ba25d7 100644
--- a/api_readme.md
+++ b/api_readme.md
@@ -1,25 +1,11 @@
-# API Command Documentation #
+# API Query Documentation #
 
 ## Fetch Species List ##
 
 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
-[
-  {
-    "FullName": "Mus musculus", 
-    "Id": 1, 
-    "Name": "mouse", 
-    "TaxonomyId": 10090
-  }, 
-  ...
-  {
-    "FullName": "Populus trichocarpa", 
-    "Id": 10, 
-    "Name": "poplar", 
-    "TaxonomyId": 3689
-  }
-]
+[ { "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:
@@ -57,6 +43,60 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd
 ```
 (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)
 
+## Fetch Individual Dataset Info ##
+### For mRNA Assay/"ProbeSet" ###
 
+```
+curl http://gn2-zach.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```
+{ "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)
 
+### 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
+{ "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 Single Trait ##
+```
+curl http://gn2-zach.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 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
+{ "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" }
+```
+
+### For "Phenotypes" ###
+For phenotypes this just gets the  max LRS, its location, and additive effect (as calculated by qtlreaper)
+
+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
+{ "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 }
+```
+
+## Calculate Correlation ##
+Currently only Pearson Sample and Tissue correlations are implemented
+
+This query currently takes the following parameters (though more will be added):
+* trait_id (*required*) - ID for trait used for correlation
+* db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets)
+* target_db (*required*) - Target DB name to be correlated against
+* type - Sample or Tissue (default = Sample)
+* return - Number of results to return (default = 500)
+
+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
+[ { "#_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 }, ... ]
+```
-- 
cgit v1.2.3


From c39a7ca68c2584c49a86fac2d05144a1b32ccd56 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 3 May 2019 11:06:47 -0500
Subject: Added examples for fetching sample data & genotypes

---
 api_readme.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/api_readme.md b/api_readme.md
index 00ba25d7..d0102d67 100644
--- a/api_readme.md
+++ b/api_readme.md
@@ -32,6 +32,12 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse gro
 [ { "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
+```
+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
@@ -43,6 +49,13 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd
 ```
 (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)
 
+## Fetch Sample Data for Dataset ##
+``` 
+curl http://gn2-zach.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 Individual Dataset Info ##
 ### For mRNA Assay/"ProbeSet" ###
 
-- 
cgit v1.2.3


From 7749cec3336f5ecd3233be7f91cf5750a270c37d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 21 May 2019 15:40:29 -0500
Subject: Added mapping and some other changes to readme

---
 api_readme.md | 46 +++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 43 insertions(+), 3 deletions(-)

diff --git a/api_readme.md b/api_readme.md
index d0102d67..96e8b246 100644
--- a/api_readme.md
+++ b/api_readme.md
@@ -1,5 +1,7 @@
 # API Query Documentation #
-
+---
+# Fetching Dataset/Trait info/data #
+---
 ## Fetch Species List ##
 
 To get a list of species with data available in GN (and their associated names and ids):
@@ -98,14 +100,52 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001
 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 }
 ```
 
+---
+
+# Analyses #
+---
+## Mapping ##
+Currently two mapping tools can be used - GEMMA and R/qtl. qtlreaper will be added later with Christian Fischer's RUST implementation - https://github.com/chfi/rust-qtlreaper
+
+Each method's query takes the following parameters respectively (more will be added):
+### GEMMA ###
+* trait_id (*required*) - ID for trait being mapped
+* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets)
+* use_loco - Whether to use LOCO (leave one chromosome out) method (default = false)
+* maf - minor allele frequency (default = 0.01)
+
+Example query:
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true
+```
+
+### R/qtl ###
+(See the R/qtl guide for information on some of these options - http://www.rqtl.org/manual/qtl-manual.pdf)
+* trait_id (*required*) - ID for trait being mapped
+* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets)
+* rqtl_method - hk (default) | ehk | em | imp | mr | mr-imp | mr-argmax ; Corresponds to the "method" option for the R/qtl scanone function.
+* rqtl_model - normal (default) | binary | 2-part | np ; corresponds to the "model" option for the R/qtl scanone function
+* num_perm - number of permutations; 0 by default
+* control_marker - Name of marker to use as control; this relies on the user knowing the name of the marker they want to use as a covariate
+* interval_mapping - Whether to use interval mapping; "false" by default
+* pair_scan - *NYI*
+
+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
+```
+
+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)
+
 ## Calculate Correlation ##
-Currently only Pearson Sample and Tissue correlations are implemented
+Currently only Sample and Tissue correlations are implemented
 
 This query currently takes the following parameters (though more will be added):
 * trait_id (*required*) - ID for trait used for correlation
 * db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets)
 * target_db (*required*) - Target DB name to be correlated against
-* type - Sample or Tissue (default = Sample)
+* type - sample (default) | tissue
+* method - pearson (default) | spearman
 * return - Number of results to return (default = 500)
 
 Example query:
-- 
cgit v1.2.3


From 7dd9a3f8d232f3f747167de082eff22c30657ea0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 21 Apr 2020 16:42:22 -0500
Subject: Testing

---
 wqflask/wqflask/templates/base.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ec55ebeb..90be6111 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -4,7 +4,7 @@
 
 <head>
     <meta charset="utf-8">
-    <title>{% block title %}{% endblock %} GeneNetwork</title>
+    <title>{% block title %}{% endblock %} GeneNetwork2</title>
     <meta name="description" content="">
     <meta name="author" content="">
     <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
-- 
cgit v1.2.3


From 1444f5618361a1c91bd792cfab8c8c53beb3421c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 21 Apr 2020 16:43:11 -0500
Subject: Testing 2

---
 wqflask/wqflask/templates/tutorials.html | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 wqflask/wqflask/templates/tutorials.html

diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html
new file mode 100644
index 00000000..44e6a2c4
--- /dev/null
+++ b/wqflask/wqflask/templates/tutorials.html
@@ -0,0 +1 @@
+Testing123
-- 
cgit v1.2.3