From be09d207ee4e2705e358102f8bdbcd1da7f70ca2 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 24 Apr 2020 16:06:36 -0500 Subject: Replaced hard-coded instances of GN2 urls with ones pulled from settings file --- doc/API_readme.md | 42 +++++++++++----------- wqflask/base/data_set.py | 4 +-- wqflask/base/trait.py | 7 ++-- wqflask/utility/tools.py | 2 ++ wqflask/wqflask/ctl/ctl_analysis.py | 4 ++- wqflask/wqflask/do_search.py | 3 +- wqflask/wqflask/network_graph/network_graph.py | 2 ++ wqflask/wqflask/search_results.py | 3 +- wqflask/wqflask/static/new/javascript/ctl_graph.js | 8 +---- .../new/javascript/dataset_select_menu_orig.js | 1 - .../wqflask/static/new/javascript/network_graph.js | 4 +-- wqflask/wqflask/templates/ctl_results.html | 1 + wqflask/wqflask/templates/index_page.html | 4 +-- wqflask/wqflask/templates/index_page_orig.html | 4 +-- wqflask/wqflask/templates/network_graph.html | 1 + 15 files changed, 47 insertions(+), 43 deletions(-) diff --git a/doc/API_readme.md b/doc/API_readme.md index 652376a0..be6668dc 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.genenetwork.org/api/v_pre1/species +curl http://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.genenetwork.org/api/v_pre1/species/mouse +curl http://genenetwork.org/api/v_pre1/species/mouse ``` OR ``` -curl http://gn2.genenetwork.org/api/v_pre1/species/mouse.json +curl http://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* @@ -26,33 +26,33 @@ curl http://gn2.genenetwork.org/api/v_pre1/species/mouse.json This query can optionally filter by species: ``` -curl http://gn2.genenetwork.org/api/v_pre1/groups (for all species) +curl http://genenetwork.org/api/v_pre1/groups (for all species) ``` OR ``` -curl http://gn2.genenetwork.org/api/v_pre1/groups/mouse (for just mouse groups/RISets) +curl http://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.genenetwork.org/api/v_pre1/genotypes/bimbam/BXD -curl http://gn2.genenetwork.org/api/v_pre1/genotypes/BXD.bimbam +curl http://genenetwork.org/api/v_pre1/genotypes/bimbam/BXD +curl http://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 +curl http://genenetwork.org/api/v_pre1/genotypes/rqtl2/BXD/HC_M2_0606_P.zip ``` ## Fetch Datasets ## ``` -curl http://gn2.genenetwork.org/api/v_pre1/datasets/bxd +curl http://genenetwork.org/api/v_pre1/datasets/bxd ``` OR ``` -curl http://gn2.genenetwork.org/api/v_pre1/datasets/mouse/bxd +curl http://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) @@ -61,11 +61,11 @@ curl http://gn2.genenetwork.org/api/v_pre1/datasets/mouse/bxd ### For mRNA Assay/"ProbeSet" ### ``` -curl http://gn2.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P +curl http://genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P ``` OR ``` -curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` +curl http://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) @@ -73,26 +73,26 @@ curl http://gn2.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.genenetwork.org/api/v_pre1/dataset/bxd/10001 +curl http://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.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv +curl http://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.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at +curl http://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.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json +curl http://genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json [ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ] ``` @@ -101,7 +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.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at +curl http://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" } ``` @@ -110,7 +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.genenetwork.org/api/v_pre1/trait/BXD/10001 +curl http://genenetwork.org/api/v_pre1/trait/BXD/10001 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } ``` @@ -130,7 +130,7 @@ Each method's query takes the following parameters respectively (more will be ad Example query: ``` -curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true +curl http://genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true ``` ### R/qtl ### @@ -146,7 +146,7 @@ curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish& Example query: ``` -curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 +curl http://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) @@ -164,6 +164,6 @@ This query currently takes the following parameters (though more will be added): Example query: ``` -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 +curl http://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 }, ... ] ``` diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index fae62875..8652e6b7 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -56,7 +56,7 @@ from pprint import pformat as pf from db.gn_server import menu_main from db.call import fetchall,fetchone,fetch1 -from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists +from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL from utility.logger import getLogger logger = getLogger(__name__ ) @@ -94,7 +94,7 @@ Publish or ProbeSet. E.g. """ self.datasets = {} if rebuild: #ZS: May make this the only option - data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content) + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) #data = gen_menu.gen_dropdown_json() else: file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 5525472e..e454c593 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -14,6 +14,7 @@ from base.data_set import create_dataset from db import webqtlDatabaseFunction from utility import webqtlUtil from utility import hmac +from utility.tools import GN2_BASE_URL from wqflask import app @@ -135,9 +136,9 @@ class GeneralTrait(object): alias = 'Not available' if self.symbol: - human_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.upper()) - mouse_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.capitalize()) - other_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.lower()) + human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper()) + mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize()) + other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower()) if human_response and mouse_response and other_response: alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 0fbedccb..9354ece6 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -234,6 +234,8 @@ def show_settings(): GN_VERSION = get_setting('GN_VERSION') HOME = get_setting('HOME') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') +GN2_BASE_URL = get_setting('GN2_BASE_URL') +GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') GN_SERVER_URL = get_setting('GN_SERVER_URL') SERVER_PORT = get_setting_int('SERVER_PORT') SQL_URI = get_setting('SQL_URI') diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 6fda02fd..4415b86a 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -20,7 +20,7 @@ from base import data_set from base import trait as TRAIT from utility import helper_functions -from utility.tools import locate +from utility.tools import locate, GN2_BRANCH_URL from rpy2.robjects.packages import importr @@ -56,6 +56,8 @@ class CTL(object): self.edges_list = [] logger.info("Obtained pointers to CTL functions") + self.gn2_url = GN2_BRANCH_URL + def addNode(self, gt): node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name), 'sid' : str(gt.name), diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 05caa100..b0ca5ced 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -13,6 +13,7 @@ import sys # sys.path.append("..") Never in a running webserver from db import webqtlDatabaseFunction +from utility.tools import GN2_BASE_URL import logging from utility.logger import getLogger @@ -919,7 +920,7 @@ def get_aliases(symbol, species): return [] filtered_aliases = [] - response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + symbol_string) + response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string) if response: alias_list = json.loads(response.content) diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index a332db46..152e4168 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -47,6 +47,7 @@ from utility.TDCell import TDCell from base.trait import GeneralTrait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers +from utility.tools import GN2_BRANCH_URL from db import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions @@ -195,6 +196,7 @@ class NetworkGraph(object): self.nodes_list.append(node_dict) self.elements = json.dumps(self.nodes_list + self.edges_list) + self.gn2_url = GN2_BRANCH_URL groups = [] for sample in self.all_sample_list: diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 698389ab..8f702d58 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -28,6 +28,7 @@ from flask import render_template, Flask, g from utility import formatting from utility import hmac +from utility.tools import GN2_BASE_URL from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string from utility.logger import getLogger @@ -295,7 +296,7 @@ def get_aliases(symbol_list, species): symbols_string = ",".join(updated_symbols) filtered_aliases = [] - response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases2/" + symbols_string) + response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string) if response: alias_lists = json.loads(response.content) seen = set() diff --git a/wqflask/wqflask/static/new/javascript/ctl_graph.js b/wqflask/wqflask/static/new/javascript/ctl_graph.js index 94bd7e9d..bd950592 100644 --- a/wqflask/wqflask/static/new/javascript/ctl_graph.js +++ b/wqflask/wqflask/static/new/javascript/ctl_graph.js @@ -82,18 +82,12 @@ window.onload=function() { function create_qtips(cy){ cy.nodes().qtip({ content: function(){ - gn_link = ''+''+this.data().id +''+'
' + gn_link = ''+''+this.data().id +''+'
' ncbi_link = 'NCBI'+'
' omim_link = 'OMIM'+'
' qtip_content = gn_link + ncbi_link + omim_link return qtip_content - //return ''+''+this.data().id +''+'' }, - // content: { - // title: ''+''+this.target() +''+'', - // text: this.target, - // button: true - // }, position: { my: 'top center', at: 'bottom center' diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js index fad600d2..794804f4 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -74,7 +74,6 @@ redo_dropdown = function(dropdown, items) { this_opt_group = null for (_i = 0, _len = group_family_list.length; _i < _len; _i++) { item = group_family_list[_i]; - console.log("THE ITEM:", item) if (item[2] != "None" && current_family == ""){ current_family = item[2] this_opt_group = $("") diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js index 4d507a18..02c3b817 100644 --- a/wqflask/wqflask/static/new/javascript/network_graph.js +++ b/wqflask/wqflask/static/new/javascript/network_graph.js @@ -85,7 +85,7 @@ window.onload=function() { cy.nodes().qtip({ content: function(){ qtip_content = '' - gn_link = ''+''+this.data().id +''+'
' + gn_link = ''+''+this.data().id +''+'
' qtip_content += gn_link if (typeof(this.data().geneid) !== 'undefined'){ ncbi_link = 'NCBI'+'
' @@ -115,7 +115,7 @@ window.onload=function() { correlation_line = 'Sample r: ' + this.data().correlation + '
' p_value_line = 'Sample p(r): ' + this.data().p_value + '
' overlap_line = 'Overlap: ' + this.data().overlap + '
' - scatter_plot = 'View Scatterplot' + scatter_plot = 'View Scatterplot' return correlation_line + p_value_line + overlap_line + scatter_plot }, position: { diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html index d85075a9..0108d93a 100644 --- a/wqflask/wqflask/templates/ctl_results.html +++ b/wqflask/wqflask/templates/ctl_results.html @@ -61,6 +61,7 @@ diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 0116245d..f8720d39 100644 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -219,9 +219,9 @@

GN1 Mirror and development sites

diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 963531cb..06b71f53 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -254,8 +254,8 @@

GeneNetwork v2:

GeneNetwork v1: