diff options
| -rw-r--r-- | wqflask/utility/pillow_utils.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/__init__.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/api/__init__.py | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/api/router.py | 107 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 79 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/top_level_routes.py | 3 |
7 files changed, 110 insertions, 100 deletions
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py index e302df18..eca45244 100644 --- a/wqflask/utility/pillow_utils.py +++ b/wqflask/utility/pillow_utils.py @@ -1,6 +1,7 @@ +from flask import current_app as app from PIL import Image, ImageColor, ImageDraw, ImageFont -from utility.tools import TEMPDIR +from utility.configuration import get_setting BLACK = ImageColor.getrgb("black") WHITE = ImageColor.getrgb("white") @@ -15,7 +16,7 @@ def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90): draw_text = ImageDraw.Draw(tmp_img) draw_text.text(text=text, xy=(0, 0), font=font, fill=fill) tmp_img2 = tmp_img.rotate(angle, expand=1) - tmp_img2.save("/{0}/{1}.png".format(TEMPDIR, text), format="png") + tmp_img2.save("/{0}/{1}.png".format(get_setting(app, "TEMPDIR"), text), format="png") canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy])) # def draw_open_polygon(canvas: Image, xy: tuple, fill: ImageColor=WHITE, outline: ImageColor=BLACK): diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index fe66d1b7..45b5a14b 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -130,7 +130,6 @@ def include_data_role_class(): return {'DataRole': DataRole} -from wqflask.api import router from wqflask import group_manager from wqflask import resource_manager from wqflask import search_results diff --git a/wqflask/wqflask/api/__init__.py b/wqflask/wqflask/api/__init__.py index e69de29b..abeb6e56 100644 --- a/wqflask/wqflask/api/__init__.py +++ b/wqflask/wqflask/api/__init__.py @@ -0,0 +1,9 @@ +""" +Set up the package's top-level objects. +""" +from flask import Blueprint + +from . import router as router + +api_bp = Blueprint("api", __name__) +api_bp.register_blueprint(router.pre1_router) diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index d7eeac34..afa150dc 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -11,30 +11,27 @@ from zipfile import ZipFile, ZIP_DEFLATED import flask -from flask import current_app -from wqflask.database import database_connection from flask import request -from flask import make_response +from flask import Blueprint from flask import send_file +from flask import make_response +from flask import current_app as app -from wqflask import app - -from wqflask.api import correlation, mapping, gen_menu - -from utility.tools import flat_files +from utility.configuration import flat_files from wqflask.database import database_connection +from wqflask.api import correlation, mapping, gen_menu version = "pre1" +pre1_router = Blueprint("pre1_router", __name__) - -@app.route("/api/v_{}/".format(version)) +@pre1_router.route("/v_{}/".format(version)) def hello_world(): return flask.jsonify({"hello": "world"}) -@app.route("/api/v_{}/species".format(version)) +@pre1_router.route("/v_{}/species".format(version)) def get_species_list(): species_list = [] with database_connection() as conn, conn.cursor() as cursor: @@ -52,8 +49,8 @@ def get_species_list(): return flask.jsonify(species_list) -@app.route("/api/v_{}/species/<path:species_name>".format(version)) -@app.route("/api/v_{}/species/<path:species_name>.<path:file_format>".format(version)) +@pre1_router.route("/v_{}/species/<path:species_name>".format(version)) +@pre1_router.route("/v_{}/species/<path:species_name>.<path:file_format>".format(version)) def get_species_info(species_name, file_format="json"): with database_connection() as conn, conn.cursor() as cursor: cursor.execute( @@ -71,8 +68,8 @@ def get_species_info(species_name, file_format="json"): return flask.jsonify(species_dict) -@app.route("/api/v_{}/groups".format(version)) -@app.route("/api/v_{}/groups/<path:species_name>".format(version)) +@pre1_router.route("/v_{}/groups".format(version)) +@pre1_router.route("/v_{}/groups/<path:species_name>".format(version)) def get_groups_list(species_name=None): _groups = () with database_connection() as conn, conn.cursor() as cursor: @@ -117,10 +114,10 @@ def get_groups_list(species_name=None): return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/group/<path:group_name>".format(version)) -@app.route("/api/v_{}/group/<path:group_name>.<path:file_format>".format(version)) -@app.route("/api/v_{}/group/<path:species_name>/<path:group_name>".format(version)) -@app.route("/api/v_{}/group/<path:species_name>/<path:group_name>.<path:file_format>".format(version)) +@pre1_router.route("/v_{}/group/<path:group_name>".format(version)) +@pre1_router.route("/v_{}/group/<path:group_name>.<path:file_format>".format(version)) +@pre1_router.route("/v_{}/group/<path:species_name>/<path:group_name>".format(version)) +@pre1_router.route("/v_{}/group/<path:species_name>/<path:group_name>.<path:file_format>".format(version)) def get_group_info(group_name, species_name=None, file_format="json"): group = () with database_connection() as conn, conn.cursor() as cursor: @@ -172,8 +169,8 @@ def get_group_info(group_name, species_name=None, file_format="json"): return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/datasets/<path:group_name>".format(version)) -@app.route("/api/v_{}/datasets/<path:species_name>/<path:group_name>".format(version)) +@pre1_router.route("/v_{}/datasets/<path:group_name>".format(version)) +@pre1_router.route("/v_{}/datasets/<path:species_name>/<path:group_name>".format(version)) def get_datasets_for_group(group_name, species_name=None): _datasets = () with database_connection() as conn, conn.cursor() as cursor: @@ -237,10 +234,10 @@ def get_datasets_for_group(group_name, species_name=None): return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/dataset/<path:dataset_name>".format(version)) -@app.route("/api/v_{}/dataset/<path:dataset_name>.<path:file_format>".format(version)) -@app.route("/api/v_{}/dataset/<path:group_name>/<path:dataset_name>".format(version)) -@app.route("/api/v_{}/dataset/<path:group_name>/<path:dataset_name>.<path:file_format>".format(version)) +@pre1_router.route("/v_{}/dataset/<path:dataset_name>".format(version)) +@pre1_router.route("/v_{}/dataset/<path:dataset_name>.<path:file_format>".format(version)) +@pre1_router.route("/v_{}/dataset/<path:group_name>/<path:dataset_name>".format(version)) +@pre1_router.route("/v_{}/dataset/<path:group_name>/<path:dataset_name>.<path:file_format>".format(version)) def get_dataset_info(dataset_name, group_name=None, file_format="json"): # ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets @@ -343,8 +340,8 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"): return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=("GET",)) -@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=("GET",)) +@pre1_router.route("/v_{}/traits/<path:dataset_name>".format(version), methods=("GET",)) +@pre1_router.route("/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=("GET",)) def fetch_traits(dataset_name, file_format="json"): trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids( dataset_name, request.args) @@ -492,8 +489,8 @@ def fetch_traits(dataset_name, file_format="json"): details="") -@app.route("/api/v_{}/sample_data/<path:dataset_name>".format(version)) -@app.route("/api/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version)) +@pre1_router.route("/v_{}/sample_data/<path:dataset_name>".format(version)) +@pre1_router.route("/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version)) def all_sample_data(dataset_name, file_format="csv"): trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids( dataset_name, request.args) @@ -601,8 +598,8 @@ def all_sample_data(dataset_name, file_format="csv"): return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/sample_data/<path:dataset_name>/<path:trait_name>".format(version)) -@app.route("/api/v_{}/sample_data/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version)) +@pre1_router.route("/v_{}/sample_data/<path:dataset_name>/<path:trait_name>".format(version)) +@pre1_router.route("/v_{}/sample_data/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version)) def trait_sample_data(dataset_name, trait_name, file_format="json"): with database_connection() as conn, conn.cursor() as cursor: cursor.execute( @@ -688,10 +685,10 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"): return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/trait/<path:dataset_name>/<path:trait_name>".format(version)) -@app.route("/api/v_{}/trait/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version)) -@app.route("/api/v_{}/trait_info/<path:dataset_name>/<path:trait_name>".format(version)) -@app.route("/api/v_{}/trait_info/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version)) +@pre1_router.route("/v_{}/trait/<path:dataset_name>/<path:trait_name>".format(version)) +@pre1_router.route("/v_{}/trait/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version)) +@pre1_router.route("/v_{}/trait_info/<path:dataset_name>/<path:trait_name>".format(version)) +@pre1_router.route("/v_{}/trait_info/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version)) def get_trait_info(dataset_name, trait_name, file_format="json"): with database_connection() as conn, conn.cursor() as cursor: cursor.execute( @@ -753,7 +750,7 @@ def get_trait_info(dataset_name, trait_name, file_format="json"): return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/correlation".format(version), methods=("GET",)) +@pre1_router.route("/v_{}/correlation".format(version), methods=("GET",)) def get_corr_results(): results = correlation.do_correlation(request.args) @@ -764,7 +761,7 @@ def get_corr_results(): return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/mapping".format(version), methods=("GET",)) +@pre1_router.route("/v_{}/mapping".format(version), methods=("GET",)) def get_mapping_results(): results, format = mapping.do_mapping_for_api(request.args) @@ -788,18 +785,18 @@ def get_mapping_results(): return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/genotypes/view/<string:group_name>".format(version)) +@pre1_router.route("/v_{}/genotypes/view/<string:group_name>".format(version)) def view_genotype_files(group_name): - if os.path.isfile("{0}/{1}.json".format(flat_files("genotype"), group_name)): - with open("{0}/{1}.json".format(flat_files("genotype"), group_name)) as geno_json: + if os.path.isfile("{0}/{1}.json".format(flat_files(app, "genotype"), group_name)): + with open("{0}/{1}.json".format(flat_files(app, "genotype"), group_name)) as geno_json: return flask.jsonify(json.load(geno_json)) -@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>.zip".format(version)) -@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>".format(version)) -@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>.zip".format(version)) -@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>".format(version)) -@app.route("/api/v_{}/genotypes/<string:group_name>.<string:file_format>".format(version)) +@pre1_router.route("/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>.zip".format(version)) +@pre1_router.route("/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>".format(version)) +@pre1_router.route("/v_{}/genotypes/<string:file_format>/<string:group_name>.zip".format(version)) +@pre1_router.route("/v_{}/genotypes/<string:file_format>/<string:group_name>".format(version)) +@pre1_router.route("/v_{}/genotypes/<string:group_name>.<string:file_format>".format(version)) def get_genotypes(group_name, file_format="csv", dataset_name=None): limit_num = None if 'limit_to' in request.args: @@ -810,9 +807,9 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): if file_format == "csv" or file_format == "geno": filename = group_name + ".geno" - if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)): + if os.path.isfile("{0}/{1}.geno".format(flat_files(app, "genotype"), group_name)): output_lines = [] - with open("{0}/{1}.geno".format(flat_files("genotype"), group_name)) as genofile: + with open("{0}/{1}.geno".format(flat_files(app, "genotype"), group_name)) as genofile: i = 0 for line in genofile: if line[0] == "#" or line[0] == "@": @@ -834,18 +831,18 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): else: filename = group_name - if os.path.isfile("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name)): + if os.path.isfile("{0}/{1}_geno.csv".format(flat_files(app, "genotype/rqtl2"), group_name)): yaml_file = json.load( - open("{0}/{1}.json".format(flat_files("genotype/rqtl2"), group_name))) + open("{0}/{1}.json".format(flat_files(app, "genotype/rqtl2"), group_name))) yaml_file["geno"] = filename + "_geno.csv" yaml_file["gmap"] = filename + "_gmap.csv" yaml_file["pheno"] = filename + "_pheno.csv" config_file = [filename + ".json", json.dumps(yaml_file)] - #config_file = [filename + ".yaml", open("{0}/{1}.yaml".format(flat_files("genotype/rqtl2"), group_name))] + #config_file = [filename + ".yaml", open("{0}/{1}.yaml".format(flat_files(app, "genotype/rqtl2"), group_name))] geno_file = [filename + "_geno.csv", - open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))] + open("{0}/{1}_geno.csv".format(flat_files(app, "genotype/rqtl2"), group_name))] gmap_file = [filename + "_gmap.csv", - open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))] + open("{0}/{1}_gmap.csv".format(flat_files(app, "genotype/rqtl2"), group_name))] if dataset_name: phenotypes = requests.get( "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name) @@ -867,9 +864,9 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): else: filename = group_name + ".bimbam" - if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)): + if os.path.isfile("{0}/{1}.geno".format(flat_files(app, "genotype"), group_name)): output_lines = [] - with open("{0}/{1}_geno.txt".format(flat_files("genotype/bimbam"), group_name)) as genofile: + with open("{0}/{1}_geno.txt".format(flat_files(app, "genotype/bimbam"), group_name)) as genofile: i = 0 for line in genofile: if limit_num and i >= limit_num: @@ -890,7 +887,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): return output -@app.route("/api/v_{}/gen_dropdown".format(version), methods=("GET",)) +@pre1_router.route("/v_{}/gen_dropdown".format(version), methods=("GET",)) def gen_dropdown_menu(): with database_connection() as conn: results = gen_menu.gen_dropdown_json(conn) diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 4420796c..d6e75b86 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -4,22 +4,23 @@ import string import random import json +from flask import current_app as app + +from gn3.computations.gemma import generate_hash_of_string + from base import webqtlConfig from base.trait import create_trait from base.data_set import create_dataset from utility.redis_tools import get_redis_conn -from utility.tools import flat_files, assert_file -from utility.tools import GEMMA_WRAPPER_COMMAND -from utility.tools import TEMPDIR -from utility.tools import WEBSERVER_MODE +from utility.configuration import flat_files, assert_file, get_setting from wqflask.database import database_connection -from gn3.computations.gemma import generate_hash_of_string - -GEMMAOPTS = "-debug" -if WEBSERVER_MODE == 'PROD': - GEMMAOPTS = "-no-check" +def gemma_options(): + GEMMAOPTS = "-debug" + if get_setting(app, "WEBSERVER_MODE") == 'PROD': + GEMMAOPTS = "-no-check" + return GEMMAOPTS def generate_random_n_string(n): return ''.join(random.choice(string.ascii_uppercase + string.digits) @@ -59,66 +60,66 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, if covariates != "": covar_filename = gen_covariates_file(this_dataset, covariates, samples) if str(use_loco).lower() == "true": - bimbam_dir = flat_files('genotype/bimbam') + bimbam_dir = flat_files(app, 'genotype/bimbam') geno_filepath = assert_file( f"{bimbam_dir}/{genofile_name}_geno.txt") - pheno_filepath = f"{TEMPDIR}/gn2/{pheno_filename}.txt" + pheno_filepath = f"{get_setting(app, 'TEMPDIR')}/gn2/{pheno_filename}.txt" snps_filepath = assert_file( f"{bimbam_dir}/{genofile_name}_snps.txt") - k_json_output_filepath = f"{TEMPDIR}/gn2/{k_output_filename}.json" - generate_k_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco " - f"{chr_list_string} -- {GEMMAOPTS} " + k_json_output_filepath = f"{get_setting(app, 'TEMPDIR')}/gn2/{k_output_filename}.json" + generate_k_command = (f"{get_setting(app, 'GEMMA_WRAPPER_COMMAND')} --json --loco " + f"{chr_list_string} -- {gemma_options()} " f"-g {geno_filepath} -p " f"{pheno_filepath} -a " f"{snps_filepath} -gk > " f"{k_json_output_filepath}") os.system(generate_k_command) - gemma_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco " + gemma_command = (f"{get_setting(app, 'GEMMA_WRAPPER_COMMAND')} --json --loco " f"--input {k_json_output_filepath} " - f"-- {GEMMAOPTS} " + f"-- {gemma_options()} " f"-g {geno_filepath} " f"-p {pheno_filepath} ") if covariates != "": - gemma_command += (f"-c {flat_files('mapping')}/" + gemma_command += (f"-c {flat_files(app, 'mapping')}/" f"{covar_filename}.txt " - f"-a {flat_files('genotype/bimbam')}/" + f"-a {flat_files(app, 'genotype/bimbam')}/" f"{genofile_name}_snps.txt " - f"-lmm 9 -maf {maf} > {TEMPDIR}/gn2/" + f"-lmm 9 -maf {maf} > {get_setting(app, 'TEMPDIR')}/gn2/" f"{gwa_output_filename}.json") else: - gemma_command += (f"-a {flat_files('genotype/bimbam')}/" + gemma_command += (f"-a {flat_files(app, 'genotype/bimbam')}/" f"{genofile_name}_snps.txt -lmm 9 -maf " f"{maf} > " - f"{TEMPDIR}/gn2/{gwa_output_filename}.json") + f"{get_setting(app, 'TEMPDIR')}/gn2/{gwa_output_filename}.json") else: - generate_k_command = (f"{GEMMA_WRAPPER_COMMAND} --json -- " - f"{GEMMAOPTS} " - f" -g {flat_files('genotype/bimbam')}/" + generate_k_command = (f"{get_setting(app, 'GEMMA_WRAPPER_COMMAND')} --json -- " + f"{gemma_options()} " + f" -g {flat_files(app, 'genotype/bimbam')}/" f"{genofile_name}_geno.txt -p " - f"{TEMPDIR}/gn2/{pheno_filename}.txt -a " - f"{flat_files('genotype/bimbam')}/" + f"{get_setting(app, 'TEMPDIR')}/gn2/{pheno_filename}.txt -a " + f"{flat_files(app, 'genotype/bimbam')}/" f"{genofile_name}_snps.txt -gk > " - f"{TEMPDIR}/gn2/{k_output_filename}.json") + f"{get_setting(app, 'TEMPDIR')}/gn2/{k_output_filename}.json") os.system(generate_k_command) - gemma_command = (f"{GEMMA_WRAPPER_COMMAND} --json --input " - f"{TEMPDIR}/gn2/{k_output_filename}.json -- " - f"{GEMMAOPTS} " - f"-a {flat_files('genotype/bimbam')}/" + gemma_command = (f"{get_setting(app, 'GEMMA_WRAPPER_COMMAND')} --json --input " + f"{get_setting(app, 'TEMPDIR')}/gn2/{k_output_filename}.json -- " + f"{gemma_options()} " + f"-a {flat_files(app, 'genotype/bimbam')}/" f"{genofile_name}_snps.txt " - f"-lmm 9 -g {flat_files('genotype/bimbam')}/" + f"-lmm 9 -g {flat_files(app, 'genotype/bimbam')}/" f"{genofile_name}_geno.txt -p " - f"{TEMPDIR}/gn2/{pheno_filename}.txt ") + f"{get_setting(app, 'TEMPDIR')}/gn2/{pheno_filename}.txt ") if covariates != "": - gemma_command += (f" -c {flat_files('mapping')}/" + gemma_command += (f" -c {flat_files(app, 'mapping')}/" f"{covar_filename}.txt > " - f"{TEMPDIR}/gn2/{gwa_output_filename}.json") + f"{get_setting(app, 'TEMPDIR')}/gn2/{gwa_output_filename}.json") else: - gemma_command += f" > {TEMPDIR}/gn2/{gwa_output_filename}.json" + gemma_command += f" > {get_setting(app, 'TEMPDIR')}/gn2/{gwa_output_filename}.json" os.system(gemma_command) else: @@ -138,7 +139,7 @@ def gen_pheno_txt_file(this_dataset, genofile_name, vals): filename = "PHENO_" + generate_hash_of_string(this_dataset.name + str(vals)).replace("/", "_") - with open(f"{TEMPDIR}/gn2/{filename}.txt", "w") as outfile: + with open(f"{get_setting(app, 'TEMPDIR')}/gn2/{filename}.txt", "w") as outfile: for value in vals: if value == "x": outfile.write("NA\n") @@ -178,7 +179,7 @@ def gen_covariates_file(this_dataset, covariates, samples): filename = "COVAR_" + generate_hash_of_string(this_dataset.name + str(covariate_data_object)).replace("/", "_") - with open((f"{flat_files('mapping')}/" + with open((f"{flat_files(app, 'mapping')}/" f"{filename}.txt"), "w") as outfile: for i in range(len(covariate_data_object[0])): @@ -191,7 +192,7 @@ def gen_covariates_file(this_dataset, covariates, samples): def parse_loco_output(this_dataset, gwa_output_filename, loco="True"): - output_filename = f"{TEMPDIR}/gn2/{gwa_output_filename}.json" + output_filename = f"{get_setting(app, 'TEMPDIR')}/gn2/{gwa_output_filename}.json" if os.stat(output_filename).st_size == 0: return {} diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index ae5e1ebb..3ae7d1b9 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -10,6 +10,7 @@ from collections import OrderedDict import numpy as np import scipy.stats as ss +from flask import current_app as app from wqflask.database import database_connection @@ -18,8 +19,7 @@ from wqflask.show_trait.SampleList import SampleList from base.trait import create_trait from base import data_set from utility import helper_functions -from utility.tools import locate_ignore_error -from utility.tools import GN_PROXY_URL +from utility.configuration import locate_ignore_error from utility.redis_tools import get_redis_conn, get_resource_id from gn3.authentication import get_highest_user_access_role @@ -753,7 +753,7 @@ def get_genotype_scales(genofiles): def get_scales_from_genofile(file_location): - geno_path = locate_ignore_error(file_location, 'genotype') + geno_path = locate_ignore_error(app, file_location, 'genotype') # ZS: This is just to allow the code to run when if not geno_path: return [["physic", "Mb"]] diff --git a/wqflask/wqflask/top_level_routes.py b/wqflask/wqflask/top_level_routes.py index 73a91dfc..680736ec 100644 --- a/wqflask/wqflask/top_level_routes.py +++ b/wqflask/wqflask/top_level_routes.py @@ -1,6 +1,7 @@ """Top-Level routes.""" from flask import Blueprint +from .api import api_bp # from .views import main_views from base.trait import trait_bp from .collect import collections_bp @@ -14,3 +15,5 @@ toplevel.register_blueprint(trait_bp) toplevel.register_blueprint(pcorrs_bp) # toplevel.register_blueprint(main_views) toplevel.register_blueprint(collections_bp) + +toplevel.register_blueprint(api_bp, url_prefix="/api") |