diff --git a/jass/__main__.py b/jass/__main__.py
index 743b290525e685bba88ef410b2283158cebfc795..69d18b64501dc05ee6a6fd4c023f393b49d48813 100644
--- a/jass/__main__.py
+++ b/jass/__main__.py
@@ -4,7 +4,7 @@
import os
import argparse
-from jass.server import get_jass_app
+from jass.server import jass_app
from jass.config import config
from jass.models.phenotype import get_available_phenotypes
@@ -62,8 +62,7 @@ def absolute_path_of_the_file(fileName, output_file = False):
def serve(args):
- app = get_jass_app()
- app.run(host=config["HOST"], port=config["PORT"])
+ jass_app.flask_app.run(host=config["HOST"], port=config["PORT"])
def w_list_phenotypes(args):
diff --git a/jass/controllers/__init__.py b/jass/controllers/__init__.py
index 0e94abd262a9ad33a4968618f3ba933bf97c6740..38c03398ba0b04686bea26fed970650be5a16167 100644
--- a/jass/controllers/__init__.py
+++ b/jass/controllers/__init__.py
@@ -7,5 +7,4 @@ Submodules
.. autosummary::
:toctree: _autosummary
- default_controller
"""
diff --git a/jass/controllers/default_controller.py b/jass/controllers/default_controller.py
deleted file mode 100644
index f447e63262de6c024fabcc61ff85c18c1d35abae..0000000000000000000000000000000000000000
--- a/jass/controllers/default_controller.py
+++ /dev/null
@@ -1,172 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-default_controller ensures the connection between the web interface and the Python JASS-analysis module
-"""
-
-from jass.config import config
-from jass.models.project import Project, create_project
-from jass.models.phenotype import Phenotype, get_available_phenotypes
-import connexion
-from flask import send_file, abort
-from six import iteritems
-import os
-from typing import List, Dict
-
-PHENOTYPES = get_available_phenotypes(
- os.path.join(config["DATA_DIR"], "initTable.hdf5")
-) # FIXME part of the config
-
-
-def phenotypes_get():
- """
- phenotypes_get
- Gets the list of available phenotypes
-
- :rtype: List[Phenotype]
- """
- return PHENOTYPES
-
-
-def projects_post(phenotypeID):
- """
- projects_post
- Create a new project from a selection of phenotypes
- :param phenotypeID: IDs of the phenotypes selected for the project
- :type phenotypeID: List[str]
-
- :rtype: str
- """
- return create_project(phenotypeID, PHENOTYPES)
-
-
-def projects_project_id_csv_status_get(projectID):
- """
- projects_project_id_csv_status_get
- Retrieve the generation status of the genome full csv file
- :param projectID: project ID
- :type projectID: str
-
- :rtype: str
- """
- return Project(id=projectID).get_csv_file_generation()
-
-
-def projects_project_id_summary_statistics(projectID):
- """
- projects_project_id_summary_statistics
- Retrieve project summary statistics
- """
- return Project(id=projectID).get_project_summary_statistics()
-
-
-def projects_project_id_genome_get(projectID, threshold=None):
- """
- projects_project_id_genome_get
- Retrieve genome data for a given project
- :param projectID: project ID
- :type projectID: str
-
- :rtype: str
- """
- return Project(id=projectID).get_project_genomedata()
-
-
-def projects_project_id_global_manhattan_plot_get(projectID):
- """
- projects_project_id_global_manhattan_plot_get
- Gets the global Manhattan plot stored in the Project folder to display it on the Web interface
- """
- try:
- return send_file(
- Project(id=projectID).get_global_manhattan_plot_path(), mimetype="image/png"
- )
- except FileNotFoundError:
- status = Project(id=projectID).status
- if status == Project.DOES_NOT_EXIST:
- abort(404)
- elif status["global_manhattan"] == Project.CREATING:
- return (
- "Plot is not ready yet",
- 202,
- {"Content-Type": "text/plain; charset=utf-8"},
- )
- else:
- abort(500)
-
-
-def projects_project_id_quadrant_plot_get(projectID):
- """
- projects_project_id_quadrant_plot_get
- Gets the quadrant plot stored in the Project folder to display it on the Web interface
- """
- try:
- return send_file(
- Project(id=projectID).get_quadrant_plot_path(), mimetype="image/png"
- )
- except FileNotFoundError:
- status = Project(id=projectID).status
- if status == Project.DOES_NOT_EXIST:
- abort(404)
- elif status["quadrant_plot_status"] == Project.CREATING:
- return (
- "Plot is not ready yet",
- 202,
- {"Content-Type": "text/plain; charset=utf-8"},
- )
- else:
- abort(500)
-
-
-def projects_project_id_genome_full_get(projectID):
- """
- projects_project_id_genome_full_get
- Downloads the file genome_full.csv stored in the Project folder
- """
- try:
- return send_file(
- Project(id=projectID).get_csv_path(),
- mimetype="text/csv",
- as_attachment=True,
- attachment_filename="genome_full.csv"
- )
- except FileNotFoundError:
- status = Project(id=projectID).status
- if status == Project.DOES_NOT_EXIST:
- abort(404)
- elif status["worktable"] == Project.CREATING:
- return (
- "CSV is not ready yet",
- 202,
- {"Content-Type": "text/plain; charset=utf-8"},
- )
- else:
- abort(500)
-
-
-def projects_project_id_local_manhattan_data_get(projectID, chromosome, region):
- """
- projects_project_id_local_manhattan_data_get
- Return the SumStatTab dataframe of the Project for a given chromosome and region for the Manhattan plot
- """
- return Project(id=projectID).get_project_local_manhattan_data(chromosome, region)
-
-
-def projects_project_id_local_heatmap_data_get(projectID, chromosome, region):
- """
- projects_project_id_local_heatmap_data_get
- Return the SumStatTab dataframe of the Project for a given chromosome and region for the Heatmap plot
- """
- return Project(id=projectID).get_project_local_heatmap_data(chromosome, region)
-
-
-def projects_project_idget(projectID):
- """
- projects_project_idget
- Retrieve a project definition
- :param projectID: project ID
- :type projectID: str
-
- :rtype: Phenotype
- """
- return Project(id=projectID)
diff --git a/jass/encoder.py b/jass/encoder.py
deleted file mode 100644
index 175502a4df6e905113b701e38214b296e82af577..0000000000000000000000000000000000000000
--- a/jass/encoder.py
+++ /dev/null
@@ -1,25 +0,0 @@
-from connexion.apps.flask_app import FlaskJSONEncoder
-
-# from connexion.decorators import produces
-from six import iteritems
-from jass.models.base_model_ import Model
-from pandas import isnull
-
-
-class JSONEncoder(FlaskJSONEncoder):
- include_nulls = False
-
- def default(self, o):
- if isinstance(o, Model):
- dikt = {}
- for attr, _ in iteritems(o.swagger_types):
- value = getattr(o, attr)
- if not (isinstance(value, list)) and (value is None or isnull(value)):
- if not self.include_nulls:
- continue
- else:
- return None
- attr = o.attribute_map[attr]
- dikt[attr] = value
- return dikt
- return produces.JSONEncoder.default(self, o)
diff --git a/jass/models/project.py b/jass/models/project.py
index 86d84fd67007687a84e205385ae732fdc8a05f81..438c4d8f807d3ee442099bc93f9b70cea5f86b8b 100644
--- a/jass/models/project.py
+++ b/jass/models/project.py
@@ -1,404 +1,404 @@
-# -*- coding: utf-8 -*-
-"""
-compute joint statistics and generate plots for a given set of phenotypes
-"""
-from __future__ import absolute_import
-from typing import List, Dict
-import os, sys
-import shutil
-import hashlib
-import traceback
-
-from celery import Celery
-
-from jass.models.base_model_ import Model
-from jass.util import deserialize_model
-from jass.models.phenotype import Phenotype
-from jass.models.worktable import (
- create_worktable_file,
- get_worktable_summary,
- get_worktable_genomedata,
- get_worktable_local_manhattan_data,
- get_worktable_local_heatmap_data,
- create_genome_full_csv
-)
-from jass.models.plots import create_global_plot, create_quadrant_plot
-from jass.config import config
-
-app = Celery("tasks", broker="pyamqp://guest@localhost//")
-
-
-class Project(Model):
-
- DOES_NOT_EXIST = "DOES_NOT_EXIST"
-
- CREATING = "CREATING"
-
- READY = "READY"
-
- ERROR = "ERROR"
-
- def __init__(self, id: str = None, phenotypes: List[Phenotype] = None):
- """
- Project - a project (list of phenotypes)
-
- :param id: project ID.
- :type id: str
- """
- self.swagger_types = {"id": str,
- "status": str,
- "phenotypes": List[Phenotype],
- "progress": str}
-
- self.attribute_map = {
- "id": "id",
- "status": "status",
- "phenotypes": "phenotypes",
- "progress": "progress",
- }
-
- self._id = id
- self._phenotypes = phenotypes
- if self._id is None:
- self._id = self.get_id()
-
- @classmethod
- def from_dict(cls, dikt) -> "Project":
- """
- Returns the dict as a model
-
- :param dikt: A dict.
- :type: dict
- :return: The Project.
- :rtype: Project
- """
- return deserialize_model(dikt, cls)
-
- @property
- def id(self) -> str:
- """
- Gets the id of this Project.
-
- :return: The id of this Project.
- :rtype: str
- """
- return self._id
-
- @id.setter
- def id(self, id: str):
- """
- Lists the id of this Project.
-
- :param id: The id of this Project.
- :type id: str
- """
-
- self._id = id
-
- @property
- def phenotypes(self) -> List[Phenotype]:
- """
- Gets the phenotypes list for this project.
-
- :return: The phenotypes.
- :rtype: str
- """
- return self._phenotypes
-
- @phenotypes.setter
- def cohort(self, phenotypes: List[Phenotype]):
- """
- Lists the phenotypes list for this project.
-
- :param phenotypes: The phenotypes.
- :type phenotypes: str
- """
-
- self._phenotypes = phenotypes
-
- def get_folder_path(self):
- """
- get_folder_path
- Gets the path of the folder where the project data are stored
- """
- return os.path.join(config["DATA_DIR"], "project_{}".format(self.id))
-
- def get_worktable_path(self):
- """
- get_worktable_path
- Gets the path of the file workTable.hdf5
- """
- return os.path.join(self.get_folder_path(), "workTable.hdf5")
-
- def get_csv_path(self):
- """
- get_csv_path
- Gets the path of the file genome_full.csv
- """
- return os.path.join(self.get_folder_path(), "workTable.csv")
-
- def get_progress_path(self):
- """
- get_progress_path
- Gets the path of the file containing the current progress percentage of \
- the analysis performed within the project
- """
- return os.path.join(self.get_folder_path(), "JASS_progress.txt")
-
- def get_csv_lock_path(self):
- """
- get_csv_lock_path
- Gets the path of the lock set-on when the csv file is not available yet
- """
- return os.path.join(self.get_folder_path(), "the_lock.txt")
-
- def get_project_summary_statistics(self):
- return get_worktable_summary(self.get_worktable_path())
-
- def get_project_genomedata(self):
- return get_worktable_genomedata(self.get_worktable_path())
-
- def get_project_local_manhattan_data(self, chromosome: str, region: str):
- return get_worktable_local_manhattan_data(
- self.get_worktable_path(), chromosome, region
- )
-
- def get_project_local_heatmap_data(self, chromosome: str, region: str):
- return get_worktable_local_heatmap_data(
- self.get_worktable_path(), chromosome, region
- )
-
- def get_id(self):
- m = hashlib.md5()
- for phenotype_id in [phenotype.id for phenotype in self._phenotypes]:
- m.update(str(phenotype_id).encode("utf-8"))
- return m.hexdigest()
-
- def get_global_manhattan_plot_path(self):
- return os.path.join(self.get_folder_path(), "Manhattan_Plot_Omnibus.png")
-
- def get_quadrant_plot_path(self):
- return os.path.join(self.get_folder_path(), "Quadrant_Plot_Omnibus.png")
-
- @property
- def status(self):
- """
- status
- Gets the status of the project
- """
- if not os.path.exists(self.get_folder_path()):
- return Project.DOES_NOT_EXIST
- else:
- worktable_status = get_file_status(self.get_worktable_path())
- global_manhattan_status = get_file_status(
- self.get_global_manhattan_plot_path()
- )
- quadrant_plot_status = get_file_status(self.get_quadrant_plot_path())
- return {
- # WARNING: project status is hacked so that everything is ready
- # only once the final step has completed.
- # This avoids the apparent "corrupted hdf5" file situation
- # "worktable": worktable_status,
- # "global_manhattan": global_manhattan_status,
- "worktable": quadrant_plot_status,
- "global_manhattan": quadrant_plot_status,
- "quadrant_plot_status": quadrant_plot_status,
- }
-
- @property
- def progress(self):
- """
- progress
- Gets the percentage of completion of the phenotype analysis
- """
- JASS_progress = 0
- progress_path = self.get_progress_path()
- if os.path.exists(progress_path):
- file_progress = open(progress_path, "r")
- JASS_progress = file_progress.read()
- file_progress.close()
- return JASS_progress
-
- def get_csv_file_generation(self):
- """
- csv_file_generation
- Gets the status of the genome_full csv file generation
- """
- the_lock_path = self.get_csv_lock_path()
- csv_file = self.get_csv_path()
- csv_file_status = Project.CREATING
- if (not os.path.isfile(the_lock_path)):
- if(os.path.isfile(csv_file)):
- csv_file_status = Project.READY
- else :
- csv_file_status = Project.ERROR
- print("csv_file_generation:csv_file_status={}".format(csv_file_status))
- return csv_file_status
-
-def get_file_building_tb_path(file_path):
- return file_path + ".log"
-
-
-def get_file_status(file_path):
- if os.path.exists(file_path):
- return Project.READY
- elif os.path.exists(get_file_building_tb_path(file_path)):
- return Project.ERROR
- else:
- return Project.CREATING
-
-
-@app.task
-def create_project_global_plot(worktable_path, plot_path):
- try:
- create_global_plot(worktable_path, plot_path)
- except Exception as e:
- exc_type, exc_value, exc_traceback = sys.exc_info()
- log_path = get_file_building_tb_path(plot_path)
- log_fh = open(log_path, "w")
- traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
- log_fh.close()
-
-
-@app.task
-def create_project_quadrant_plot(worktable_path, plot_path):
- try:
- create_quadrant_plot(worktable_path, plot_path)
- except Exception as e:
- exc_type, exc_value, exc_traceback = sys.exc_info()
- log_path = get_file_building_tb_path(plot_path)
- log_fh = open(log_path, "w")
- traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
- log_fh.close()
-
-
-@app.task
-def create_project_csv_file(worktable_path, csv_file, Nchunk):
- try:
- create_genome_full_csv(worktable_path, csv_file, Nchunk=Nchunk)
- except Exception as e:
- exc_type, exc_value, exc_traceback = sys.exc_info()
- log_path = get_file_building_tb_path(plot_path)
- log_fh = open(log_path, "w")
- traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
- log_fh.close()
-
-
-@app.task
-def create_project_data(
- phenotype_ids,
- init_table_path,
- worktable_path,
- remove_nan = False,
- stat = "jass.models.stats:omnibus_stat",
- csv_file = None,
- chunk_size = 50,
- significance_treshold = 5*10**-8,
- post_filtering = True,
- delayed_gen_csv_file = False,
- chromosome = None,
- start = None,
- end = None,
- custom_loadings = None,
- global_plot_path = None,
- quadrant_plot_path = None
- ):
-
- try:
- Nchunk = create_worktable_file(
- phenotype_ids = phenotype_ids,
- init_file_path = init_table_path,
- project_hdf_path = worktable_path,
- remove_nan = remove_nan,
- stat = stat,
- optim_na = True,
- csv_file = csv_file,
- chunk_size = chunk_size,
- significance_treshold = significance_treshold,
- post_filtering = post_filtering,
- delayed_gen_csv_file = delayed_gen_csv_file,
- chromosome = chromosome,
- pos_Start = start,
- pos_End = end,
- custom_loadings = custom_loadings
- )
- except Exception as e:
- exc_type, exc_value, exc_traceback = sys.exc_info()
- log_path = get_file_building_tb_path(worktable_path)
- log_fh = open(log_path, "w")
- traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
- log_fh.close()
- return
-
- if (global_plot_path is not None):
- create_project_global_plot.delay(worktable_path, global_plot_path)
- if (quadrant_plot_path is not None):
- create_project_quadrant_plot.delay(worktable_path, quadrant_plot_path)
- if (delayed_gen_csv_file and (csv_file is not None)):
- create_project_csv_file.delay(worktable_path, csv_file, Nchunk=Nchunk)
-
-
-def create_project(phenotype_ids: List[str], available_phenotypes: List[Phenotype]):
- available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
- unavailable_requested_ids = set(phenotype_ids).difference(
- set(available_phenotype_ids)
- )
- if len(unavailable_requested_ids) > 0:
- raise Exception() # FIXME with a nice exception
- phenotypes = [
- phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
- ]
- project = Project(phenotypes=phenotypes)
- folder_path = project.get_folder_path()
- # if project does not exist
- if project.status == Project.DOES_NOT_EXIST:
- os.makedirs(folder_path)
- create_project_data.delay(
- phenotype_ids=phenotype_ids,
- init_table_path=os.path.join(config["DATA_DIR"], "initTable.hdf5"),
- worktable_path=project.get_worktable_path(),
- global_plot_path=project.get_global_manhattan_plot_path(),
- quadrant_plot_path=project.get_quadrant_plot_path(),
- csv_file=project.get_csv_path(),
- delayed_gen_csv_file=True
- )
- return project
-
-
-def create_project_local(
- phenotype_ids: List[str],
- available_phenotypes: List[Phenotype],
- ip: str,
- chromosome: str,
- start: str = None,
- end: str = None
- ):
- available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
- unavailable_requested_ids = set(phenotype_ids).difference(
- set(available_phenotype_ids)
- )
- if len(unavailable_requested_ids) > 0:
- raise Exception() # FIXME with a nice exception
- phenotypes = [
- phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
- ]
- ip = ip.replace('.', '_')
- id_project = "local_{}".format(ip)
- project = Project(phenotypes=phenotypes, id=id_project)
- folder_path = project.get_folder_path()
- # If the folder exists, it is deleted with the files it contains
- if os.path.exists(folder_path):
- shutil.rmtree(folder_path)
- # The folder is created
- os.makedirs(folder_path)
- create_project_data.delay(
- phenotype_ids=phenotype_ids,
- init_table_path=os.path.join(config["DATA_DIR"], "initTable.hdf5"),
- worktable_path=project.get_worktable_path(),
- csv_file=project.get_csv_path(),
- chromosome=chromosome,
- start=start,
- end=end
- )
- return project
-
\ No newline at end of file
+# -*- coding: utf-8 -*-
+"""
+compute joint statistics and generate plots for a given set of phenotypes
+"""
+from __future__ import absolute_import
+from typing import List, Dict
+import os, sys
+import shutil
+import hashlib
+import traceback
+
+from celery import Celery
+
+from jass.models.base_model_ import Model
+from jass.util import deserialize_model
+from jass.models.phenotype import Phenotype
+from jass.models.worktable import (
+ create_worktable_file,
+ get_worktable_summary,
+ get_worktable_genomedata,
+ get_worktable_local_manhattan_data,
+ get_worktable_local_heatmap_data,
+ create_genome_full_csv
+)
+from jass.models.plots import create_global_plot, create_quadrant_plot
+from jass.config import config
+
+app = Celery("tasks", broker="pyamqp://guest@localhost//")
+
+
+class Project(Model):
+
+ DOES_NOT_EXIST = "DOES_NOT_EXIST"
+
+ CREATING = "CREATING"
+
+ READY = "READY"
+
+ ERROR = "ERROR"
+
+ def __init__(self, id: str = None, phenotypes: List[Phenotype] = None):
+ """
+ Project - a project (list of phenotypes)
+
+ :param id: project ID.
+ :type id: str
+ """
+ self.swagger_types = {"id": str,
+ "status": str,
+ "phenotypes": List[Phenotype],
+ "progress": str}
+
+ self.attribute_map = {
+ "id": "id",
+ "status": "status",
+ "phenotypes": "phenotypes",
+ "progress": "progress",
+ }
+
+ self._id = id
+ self._phenotypes = phenotypes
+ if self._id is None:
+ self._id = self.get_id()
+
+ @classmethod
+ def from_dict(cls, dikt) -> "Project":
+ """
+ Returns the dict as a model
+
+ :param dikt: A dict.
+ :type: dict
+ :return: The Project.
+ :rtype: Project
+ """
+ return deserialize_model(dikt, cls)
+
+ @property
+ def id(self) -> str:
+ """
+ Gets the id of this Project.
+
+ :return: The id of this Project.
+ :rtype: str
+ """
+ return self._id
+
+ @id.setter
+ def id(self, id: str):
+ """
+ Lists the id of this Project.
+
+ :param id: The id of this Project.
+ :type id: str
+ """
+
+ self._id = id
+
+ @property
+ def phenotypes(self) -> List[Phenotype]:
+ """
+ Gets the phenotypes list for this project.
+
+ :return: The phenotypes.
+ :rtype: str
+ """
+ return self._phenotypes
+
+ @phenotypes.setter
+ def cohort(self, phenotypes: List[Phenotype]):
+ """
+ Lists the phenotypes list for this project.
+
+ :param phenotypes: The phenotypes.
+ :type phenotypes: str
+ """
+
+ self._phenotypes = phenotypes
+
+ def get_folder_path(self):
+ """
+ get_folder_path
+ Gets the path of the folder where the project data are stored
+ """
+ return os.path.join(config["DATA_DIR"], "project_{}".format(self.id))
+
+ def get_worktable_path(self):
+ """
+ get_worktable_path
+ Gets the path of the file workTable.hdf5
+ """
+ return os.path.join(self.get_folder_path(), "workTable.hdf5")
+
+ def get_csv_path(self):
+ """
+ get_csv_path
+ Gets the path of the file genome_full.csv
+ """
+ return os.path.join(self.get_folder_path(), "workTable.csv")
+
+ def get_progress_path(self):
+ """
+ get_progress_path
+ Gets the path of the file containing the current progress percentage of \
+ the analysis performed within the project
+ """
+ return os.path.join(self.get_folder_path(), "JASS_progress.txt")
+
+ def get_csv_lock_path(self):
+ """
+ get_csv_lock_path
+ Gets the path of the lock set-on when the csv file is not available yet
+ """
+ return os.path.join(self.get_folder_path(), "the_lock.txt")
+
+ def get_project_summary_statistics(self):
+ return get_worktable_summary(self.get_worktable_path())
+
+ def get_project_genomedata(self):
+ return get_worktable_genomedata(self.get_worktable_path())
+
+ def get_project_local_manhattan_data(self, chromosome: str, region: str):
+ return get_worktable_local_manhattan_data(
+ self.get_worktable_path(), chromosome, region
+ )
+
+ def get_project_local_heatmap_data(self, chromosome: str, region: str):
+ return get_worktable_local_heatmap_data(
+ self.get_worktable_path(), chromosome, region
+ )
+
+ def get_id(self):
+ m = hashlib.md5()
+ for phenotype_id in [phenotype.id for phenotype in self._phenotypes]:
+ m.update(str(phenotype_id).encode("utf-8"))
+ return m.hexdigest()
+
+ def get_global_manhattan_plot_path(self):
+ return os.path.join(self.get_folder_path(), "Manhattan_Plot_Omnibus.png")
+
+ def get_quadrant_plot_path(self):
+ return os.path.join(self.get_folder_path(), "Quadrant_Plot_Omnibus.png")
+
+ @property
+ def status(self):
+ """
+ status
+ Gets the status of the project
+ """
+ if not os.path.exists(self.get_folder_path()):
+ return Project.DOES_NOT_EXIST
+ else:
+ worktable_status = get_file_status(self.get_worktable_path())
+ global_manhattan_status = get_file_status(
+ self.get_global_manhattan_plot_path()
+ )
+ quadrant_plot_status = get_file_status(self.get_quadrant_plot_path())
+ return {
+ # WARNING: project status is hacked so that everything is ready
+ # only once the final step has completed.
+ # This avoids the apparent "corrupted hdf5" file situation
+ # "worktable": worktable_status,
+ # "global_manhattan": global_manhattan_status,
+ "worktable": quadrant_plot_status,
+ "global_manhattan": quadrant_plot_status,
+ "quadrant_plot_status": quadrant_plot_status,
+ }
+
+ @property
+ def progress(self):
+ """
+ progress
+ Gets the percentage of completion of the phenotype analysis
+ """
+ JASS_progress = 0
+ progress_path = self.get_progress_path()
+ if os.path.exists(progress_path):
+ file_progress = open(progress_path, "r")
+ JASS_progress = file_progress.read()
+ file_progress.close()
+ return JASS_progress
+
+ def get_csv_file_generation(self):
+ """
+ csv_file_generation
+ Gets the status of the genome_full csv file generation
+ """
+ the_lock_path = self.get_csv_lock_path()
+ csv_file = self.get_csv_path()
+ csv_file_status = Project.CREATING
+ if (not os.path.isfile(the_lock_path)):
+ if(os.path.isfile(csv_file)):
+ csv_file_status = Project.READY
+ else :
+ csv_file_status = Project.ERROR
+ print("csv_file_generation:csv_file_status={}".format(csv_file_status))
+ return csv_file_status
+
+def get_file_building_tb_path(file_path):
+ return file_path + ".log"
+
+
+def get_file_status(file_path):
+ if os.path.exists(file_path):
+ return Project.READY
+ elif os.path.exists(get_file_building_tb_path(file_path)):
+ return Project.ERROR
+ else:
+ return Project.CREATING
+
+
+@app.task
+def create_project_global_plot(worktable_path, plot_path):
+ try:
+ create_global_plot(worktable_path, plot_path)
+ except Exception as e:
+ exc_type, exc_value, exc_traceback = sys.exc_info()
+ log_path = get_file_building_tb_path(plot_path)
+ log_fh = open(log_path, "w")
+ traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
+ log_fh.close()
+
+
+@app.task
+def create_project_quadrant_plot(worktable_path, plot_path):
+ try:
+ create_quadrant_plot(worktable_path, plot_path)
+ except Exception as e:
+ exc_type, exc_value, exc_traceback = sys.exc_info()
+ log_path = get_file_building_tb_path(plot_path)
+ log_fh = open(log_path, "w")
+ traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
+ log_fh.close()
+
+
+@app.task
+def create_project_csv_file(worktable_path, csv_file, Nchunk):
+ try:
+ create_genome_full_csv(worktable_path, csv_file, Nchunk=Nchunk)
+ except Exception as e:
+ exc_type, exc_value, exc_traceback = sys.exc_info()
+ log_path = get_file_building_tb_path(plot_path)
+ log_fh = open(log_path, "w")
+ traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
+ log_fh.close()
+
+
+@app.task
+def create_project_data(
+ phenotype_ids,
+ init_table_path,
+ worktable_path,
+ remove_nan = False,
+ stat = "jass.models.stats:omnibus_stat",
+ csv_file = None,
+ chunk_size = 50,
+ significance_treshold = 5*10**-8,
+ post_filtering = True,
+ delayed_gen_csv_file = False,
+ chromosome = None,
+ start = None,
+ end = None,
+ custom_loadings = None,
+ global_plot_path = None,
+ quadrant_plot_path = None
+ ):
+
+ try:
+ Nchunk = create_worktable_file(
+ phenotype_ids = phenotype_ids,
+ init_file_path = init_table_path,
+ project_hdf_path = worktable_path,
+ remove_nan = remove_nan,
+ stat = stat,
+ optim_na = True,
+ csv_file = csv_file,
+ chunk_size = chunk_size,
+ significance_treshold = significance_treshold,
+ post_filtering = post_filtering,
+ delayed_gen_csv_file = delayed_gen_csv_file,
+ chromosome = chromosome,
+ pos_Start = start,
+ pos_End = end,
+ custom_loadings = custom_loadings
+ )
+ except Exception as e:
+ exc_type, exc_value, exc_traceback = sys.exc_info()
+ log_path = get_file_building_tb_path(worktable_path)
+ log_fh = open(log_path, "w")
+ traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
+ log_fh.close()
+ return
+
+ if (global_plot_path is not None):
+ create_project_global_plot.delay(worktable_path, global_plot_path)
+ if (quadrant_plot_path is not None):
+ create_project_quadrant_plot.delay(worktable_path, quadrant_plot_path)
+ if (delayed_gen_csv_file and (csv_file is not None)):
+ create_project_csv_file.delay(worktable_path, csv_file, Nchunk=Nchunk)
+
+
+def create_project(phenotype_ids: List[str], available_phenotypes: List[Phenotype]):
+ available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
+ unavailable_requested_ids = set(phenotype_ids).difference(
+ set(available_phenotype_ids)
+ )
+ if len(unavailable_requested_ids) > 0:
+ raise Exception() # FIXME with a nice exception
+ phenotypes = [
+ phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
+ ]
+ project = Project(phenotypes=phenotypes)
+ folder_path = project.get_folder_path()
+ # if project does not exist
+ if project.status == Project.DOES_NOT_EXIST:
+ os.makedirs(folder_path)
+ create_project_data.delay(
+ phenotype_ids=phenotype_ids,
+ init_table_path=os.path.join(config["DATA_DIR"], "initTable.hdf5"),
+ worktable_path=project.get_worktable_path(),
+ global_plot_path=project.get_global_manhattan_plot_path(),
+ quadrant_plot_path=project.get_quadrant_plot_path(),
+ csv_file=project.get_csv_path(),
+ delayed_gen_csv_file=True
+ )
+ return project
+
+
+def create_project_local(
+ phenotype_ids: List[str],
+ available_phenotypes: List[Phenotype],
+ ip: str,
+ chromosome: str,
+ start: str = None,
+ end: str = None
+ ):
+ available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
+ unavailable_requested_ids = set(phenotype_ids).difference(
+ set(available_phenotype_ids)
+ )
+ if len(unavailable_requested_ids) > 0:
+ raise Exception() # FIXME with a nice exception
+ phenotypes = [
+ phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
+ ]
+ ip = ip.replace('.', '_')
+ id_project = "local_{}".format(ip)
+ project = Project(phenotypes=phenotypes, id=id_project)
+ folder_path = project.get_folder_path()
+ # If the folder exists, it is deleted with the files it contains
+ if os.path.exists(folder_path):
+ shutil.rmtree(folder_path)
+ # The folder is created
+ os.makedirs(folder_path)
+ create_project_data.delay(
+ phenotype_ids=phenotype_ids,
+ init_table_path=os.path.join(config["DATA_DIR"], "initTable.hdf5"),
+ worktable_path=project.get_worktable_path(),
+ csv_file=project.get_csv_path(),
+ chromosome=chromosome,
+ start=start,
+ end=end
+ )
+ return project
+
diff --git a/jass/server.py b/jass/server.py
index a6900afbf9c4b68ca8d5413578ebb403a5d5031b..9fd5eff2a383770af390d6569f3aa27331d79ea5 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -1,30 +1,307 @@
#!/usr/bin/env python3
-"""
-Module that creates the flask app used to run JASS as a web server
-"""
-import connexion
-import flask
+import os
-from .encoder import JSONEncoder
-from .config import config
+from flask import Flask, redirect, send_file
+from flask.views import MethodView
+import marshmallow as ma
+from flask_smorest import Api, Blueprint, abort
+from webargs.flaskparser import FlaskParser
+from jass.config import config
+from jass.models.phenotype import get_available_phenotypes
+from jass.models.project import create_project, Project
-class JassFlaskApp(connexion.FlaskApp):
+
+class PhenotypeSchema(ma.Schema):
+ id = ma.fields.String()
+ consortium = ma.fields.String()
+ outcome = ma.fields.String()
+ full_name = ma.fields.String()
+ typ = ma.fields.String()
+ ref = ma.fields.String()
+ ref_link = ma.fields.String()
+ data_link = ma.fields.String()
+ data_path = ma.fields.String()
+
+
+class PhenotypeIdsListSchema(ma.Schema):
+ class Meta:
+ unknown = ma.EXCLUDE
+
+ phenotypeID = ma.fields.List(ma.fields.String())
+
+
+class ProjectStatusSchema(ma.Schema):
+ STATUS_VALUES = ["DOES_NOT_EXIST", "CREATING", "READY", "ERROR"]
+ global_manhattan = ma.fields.String(validate=ma.validate.OneOf(STATUS_VALUES))
+ quadrant_plot_status = ma.fields.String(validate=ma.validate.OneOf(STATUS_VALUES))
+ worktable = ma.fields.String(validate=ma.validate.OneOf(STATUS_VALUES))
+
+
+class ProjectSchema(ma.Schema):
+ id = ma.fields.String()
+ status = ma.fields.Nested(ProjectStatusSchema)
+ phenotypes = ma.fields.List(ma.fields.String())
+ progress = ma.fields.String()
+
+
+blp_phenotypes = Blueprint(
+ "phenotypes",
+ "phenotypes",
+ url_prefix="/phenotypes",
+ description="Operations on phenotypes",
+)
+
+blp_projects = Blueprint(
+ "projects", "projects", url_prefix="/projects", description="Operations on projects"
+)
+
+def get_phenotypes():
+ return get_available_phenotypes(
+ os.path.join(config["DATA_DIR"], "initTable.hdf5")
+ )
+
+
+@blp_phenotypes.route("/")
+class PhenotypesMethodView(MethodView):
+ @blp_phenotypes.response(200, PhenotypeSchema(many=True))
+ def get(self):
+ """List phenotypes"""
+ return get_phenotypes()
+
+
+@blp_projects.route("/")
+class ProjectCreateMethodView(MethodView):
+ @blp_projects.arguments(PhenotypeIdsListSchema(), location="form")
+ @blp_projects.response(200, ProjectSchema())
+ def post(self, phenotype_ids):
+ """List projects"""
+ phenotype_ids = [
+ phenotype_id
+ for ids_with_commas in phenotype_ids["phenotypeID"]
+ for phenotype_id in ids_with_commas.split(",")
+ ]
+ phenotypes = list(filter(lambda d: d.id in phenotype_ids, get_phenotypes()))
+ return create_project([p.id for p in phenotypes], get_phenotypes())
+
+
+@blp_projects.route("/<project_id>")
+class ProjectDetailMethodView(MethodView):
+ @blp_projects.response(200, ProjectSchema())
+ def get(self, project_id):
+ return Project(id=project_id)
+
+
+@blp_projects.route("/<project_id>/csv_status")
+class ProjectCSVStatusMethodView(MethodView):
+
+ def get(self, project_id):
+ return Project(id=project_id).get_csv_file_generation()
+
+
+@blp_projects.route("/<project_id>/summary")
+class ProjectSummaryMethodView(MethodView):
+ @blp_projects.response(200, ProjectSchema())
+ def get(self, project_id):
+ return Project(id=project_id).get_project_summary_statistics()
+
+
+@blp_projects.route("/<project_id>/genome")
+class ProjectGenomeMethodView(MethodView):
+
+ # @blp_projects.response(200, headers={"Content-Type": "text/csv"})
+ def get(self, project_id):
+ try:
+ return (
+ Project(id=project_id).get_project_genomedata(),
+ 200,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ except FileNotFoundError:
+ status = Project(id=project_id).status
+ if status == Project.DOES_NOT_EXIST:
+ return (
+ f"project {project_id} does not exist",
+ 404,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ abort(404)
+ elif status["worktable"] == Project.CREATING:
+ return (
+ "data not ready yet",
+ 202,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ else:
+ abort(500)
+
+
+@blp_projects.route("/<project_id>/genome_full")
+class ProjectGenomeFullMethodView(MethodView):
+
+ def get(self, project_id):
+ try:
+ return send_file(
+ Project(id=project_id).get_csv_path(),
+ mimetype="text/csv",
+ as_attachment=True,
+ attachment_filename="genome_full.csv",
+ )
+ except FileNotFoundError:
+ status = Project(id=project_id).status
+ if status == Project.DOES_NOT_EXIST:
+ return (
+ f"project {project_id} does not exist",
+ 404,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ elif status["worktable"] == Project.CREATING:
+ return (
+ "data not ready yet",
+ 202,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ else:
+ abort(500)
+
+
+@blp_projects.route("/<project_id>/globalmanhattan")
+class ProjectGlobalManhattanMethodView(MethodView):
+
+ def get(self, project_id):
+ try:
+ return send_file(
+ Project(id=project_id).get_global_manhattan_plot_path(),
+ mimetype="image/png",
+ )
+ except FileNotFoundError:
+ status = Project(id=project_id).status
+ if status == Project.DOES_NOT_EXIST:
+ return (
+ f"project {project_id} does not exist",
+ 404,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ elif status["global_manhattan"] == Project.CREATING:
+ return (
+ "data not ready yet",
+ 202,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ else:
+ abort(500)
+
+
+@blp_projects.route("/<project_id>/quadrant")
+class ProjectQuadrantMethodView(MethodView):
+
+ def get(self, project_id):
+ try:
+ return send_file(
+ Project(id=project_id).get_quadrant_plot_path(),
+ mimetype="image/png",
+ )
+ except FileNotFoundError:
+ status = Project(id=project_id).status
+ if status == Project.DOES_NOT_EXIST:
+ return (
+ f"project {project_id} does not exist",
+ 404,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ elif status["quadrant_plot_status"] == Project.CREATING:
+ return (
+ "data not ready yet",
+ 202,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ else:
+ abort(500)
+
+
+@blp_projects.route("/<project_id>/manhattan/<chromosome>/<region>")
+class ProjectLocalManhattanMethodView(MethodView):
+
+ def get(self, project_id, chromosome, region):
+ try:
+ return (
+ Project(id=project_id).get_project_local_manhattan_data(
+ chromosome, region
+ ),
+ 200,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ except FileNotFoundError:
+ status = Project(id=project_id).status
+ if status == Project.DOES_NOT_EXIST:
+ return (
+ f"project {project_id} does not exist",
+ 404,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ elif status["worktable"] == Project.CREATING:
+ return (
+ "data not ready yet",
+ 202,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ else:
+ abort(500)
+
+
+@blp_projects.route("/<project_id>/heatmap/<chromosome>/<region>")
+class ProjectLocalHeatMapMethodView(MethodView):
+
+ def get(self, project_id, chromosome, region):
+ try:
+ return (
+ Project(id=project_id).get_project_local_heatmap_data(
+ chromosome, region
+ ),
+ 200,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ except FileNotFoundError:
+ status = Project(id=project_id).status
+ if status == Project.DOES_NOT_EXIST:
+ return (
+ f"project {project_id} does not exist",
+ 404,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ elif status["worktable"] == Project.CREATING:
+ return (
+ "data not ready yet",
+ 202,
+ {"Content-Type": "text/plain; charset=utf-8"},
+ )
+ else:
+ abort(500)
+
+
+class JassApp(Flask):
"""
- JassFlaskApp subclasses connexion's FlaskApp only to customize the static url path
+ JassApp builds the JASS Flask application
"""
+ def __init__(self):
+ self.flask_app = Flask(__name__, static_url_path="", static_folder="static")
+ self.flask_app.config["API_TITLE"] = "JASS API"
+ self.flask_app.config["API_VERSION"] = "v2.0"
+ self.flask_app.config["OPENAPI_VERSION"] = "3.0.2"
+ self.flask_app.route("/")(self.redirect_to_index)
+ self.api = Api(self.flask_app)
+
def create_app(self):
- app = flask.Flask(self.import_name, static_url_path="", static_folder="static")
- app.json_encoder = JSONEncoder
- app.route("/")(self.redirect_to_index)
- return app
+ return self.flask_app
def redirect_to_index(self):
- return flask.redirect("index.html")
+ return redirect("index.html")
+
+ def register_api_blueprint(self, blp):
+ self.api.register_blueprint(blp, url_prefix=f"/api/{blp.url_prefix}")
-def get_jass_app():
- app = JassFlaskApp(__name__, specification_dir="./swagger/")
- app.add_api("swagger.yaml", arguments={"title": "JASS"}, base_path="/api")
- return app
+jass_app = JassApp()
+jass_app.register_api_blueprint(blp_phenotypes)
+jass_app.register_api_blueprint(blp_projects)
diff --git a/jass/swagger/swagger.yaml b/jass/swagger/swagger.yaml
index c47461d30df983b6ba9c213ded0e1ab49e17d23a..cf0b67d7e705109209ed409afbedbb53b81b6885 100644
--- a/jass/swagger/swagger.yaml
+++ b/jass/swagger/swagger.yaml
@@ -35,7 +35,6 @@ paths:
"ref": "Okada et al. 2014"
"ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/24390342"
"type": "Immunity"
- x-openapi-router-controller: jass.controllers.default_controller
/projects:
post:
description: |
@@ -117,7 +116,6 @@ paths:
"worktable": "READY"
progress":
"progress": "100"
- x-openapi-router-controller: jass.controllers.default_controller
"/projects/{projectID}":
get:
description: |
@@ -146,7 +144,6 @@ paths:
"worktable": "READY"
progress":
"progress": "100"
- x-openapi-router-controller: jass.controllers.default_controller
"/projects/{projectID}/summary":
get:
description: Retrieve summary statistics for a given project
@@ -174,8 +171,6 @@ paths:
"NoJOSTSignif":
"NoPhenoSignif": 1470
"PhenoSignif": 14
- x-openapi-router-controller: jass.controllers.default_controller
-
"/projects/{projectID}/csv_status":
get:
description: |
@@ -200,8 +195,6 @@ paths:
title: csv_file_generation
example: |
READY
- x-openapi-router-controller: jass.controllers.default_controller
-
"/projects/{projectID}/genome":
get:
description: |
@@ -234,8 +227,6 @@ paths:
Region5,6580614.0,rs2986741,chr1,6548774,G,A,0.0013472918321710914,0.0011119999999999993,None,-3.260540717377886,2.726551316504396
Region6,8306267.0,rs79412885,chr1,9241839,A,G,2.0889091093474285e-13,8.106999999999937e-14,Both,7.46857160133221,-1.2003588580308502
Region7,10086091.5,rs113829298,chr1,10061038,T,C,4.3158209846991565e-05,6.135999999999996e-06,None,-4.5216481219798474,0.5100734569685951
- x-openapi-router-controller: jass.controllers.default_controller
-
"/projects/{projectID}/genome_full":
get:
description: |
@@ -275,7 +266,6 @@ paths:
4841,1,1,rs10907190,1773772,A,G,951595.0,0.12979175667585227,0.07999999999999982,0.15999999999999964,,-0.938281041511616,1.7506860712521708
4842,1,1,rs10907193,1805391,A,G,951595.0,0.09562672355608258,0.06299999999999988,0.12599999999999975,,-1.0405165049626888,1.8591914944718688
4843,1,1,rs10907194,1712230,T,C,951595.0,0.2669995168398967,0.16000000000000425,0.3200000000000085,,-0.7600913211933399,1.4050715603096189
- x-openapi-router-controller: jass.controllers.default_controller
"/projects/{projectID}/globalmanhattan":
get:
description: |
@@ -300,7 +290,6 @@ paths:
title: Global manhattan plot
example:
externalValue: 'globalmanhattan_example.png'
- x-openapi-router-controller: jass.controllers.default_controller
"/projects/{projectID}/quadrant":
get:
description: |
@@ -325,7 +314,6 @@ paths:
title: Quadrant plot
example:
externalValue: 'quadrant_example.png'
- x-openapi-router-controller: jass.controllers.default_controller
"/projects/{projectID}/manhattan/{chromosome}/{region}":
get:
description: Retrieve local manhattan data
@@ -380,7 +368,6 @@ paths:
Region1,chr1,725196,rs377099097,0.594983644175122
Region1,chr1,725389,rs375619475,0.7032290172253173
Region1,chr1,727841,rs116587930,0.9078685880041112
- x-openapi-router-controller: jass.controllers.default_controller
"/projects/{projectID}/heatmap/{chromosome}/{region}":
get:
description: Retrieve local heatmap data
@@ -420,7 +407,6 @@ paths:
ID,rs545945172,rs371628865,rs61769339,rs539032812,rs12238997,rs189800799
z_IHEC_MONOP,-0.3623372836601329,-0.429856541533544,-0.8457360635272954,-0.9809852811227732,-0.6936527568935886,0.4382385293216385
z_RA_RA,,,,,,
- x-openapi-router-controller: jass.controllers.default_controller
components:
schemas:
Phenotype:
diff --git a/jass/test/__init__.py b/jass/test/__init__.py
index 86f967d82f02120c4f61393f690934c58972ad34..cbe532b806217bf04a1fbaba907cf68c5a85fef4 100644
--- a/jass/test/__init__.py
+++ b/jass/test/__init__.py
@@ -1,12 +1,19 @@
import unittest
-from ..encoder import JSONEncoder
import logging
import os, shutil, tempfile
import unittest
-import connexion
import flask_testing
+
+# replace delay() method with a mock
+# which freezes calls in unit tests
+from celery.app.task import Task
+from unittest.mock import MagicMock
+Task.delay = MagicMock()
+
+
+from jass.server import jass_app
from jass.models.inittable import create_inittable_file
@@ -20,16 +27,16 @@ class JassTestCase(unittest.TestCase):
class JassFlaskTestCase(JassTestCase, flask_testing.TestCase):
def create_app(self):
- logging.getLogger("connexion.operation").setLevel("ERROR")
from jass.config import config
-
self.test_dir = tempfile.mkdtemp()
config["DATA_DIR"] = self.test_dir
shutil.copy(self.get_file_path_fn("initTable.hdf5"), self.test_dir)
- app = connexion.App(__name__, specification_dir="../swagger/")
- app.app.json_encoder = JSONEncoder
- app.add_api("swagger.yaml")
- return app.app
+
+ self.jass_app = jass_app
+ application = self.jass_app.create_app()
+ application.config["TESTING"] = True
+ self.testing_client = application.test_client()
+ return application
def tearDown(self):
shutil.rmtree(self.test_dir)
diff --git a/jass/test/test_default_controller.py b/jass/test/test_server.py
similarity index 52%
rename from jass/test/test_default_controller.py
rename to jass/test/test_server.py
index 839f48375abe67b5f4acc4fd5e9623ca0790f032..da1b77160fc8e09a8bc18f1eaddcb5976c2624bf 100644
--- a/jass/test/test_default_controller.py
+++ b/jass/test/test_server.py
@@ -4,7 +4,7 @@ from __future__ import absolute_import
import os, shutil, tempfile
from six import BytesIO
-from flask import json
+from flask import json, url_for
from jass.config import config
from . import JassFlaskTestCase
@@ -17,11 +17,16 @@ class TestDefaultController(JassFlaskTestCase):
def test_phenotypes_get(self):
"""
- Test case for phenotypes_get
+ Test case retrieving available phenotypes
+ """
+ response = self.testing_client.open("/api/phenotypes/", method="GET")
+ self.assert200(response, "Response body is : " + response.data.decode("utf-8"))
-
+ def test_create_project(self):
+ """
+ Test case for creating a project
"""
- response = self.client.open("/phenotypes", method="GET")
+ response = self.testing_client.open("/api/projects/", method="POST",data={"phenotypeID":"z_IHEC_MONOP,z_RA_RA"})
self.assert200(response, "Response body is : " + response.data.decode("utf-8"))
diff --git a/requirements.txt b/requirements.txt
index 25400d93c0388519cea98149d04e2cacbade82a3..f6fc215883a802969f2cf7bcf01d9f501d150a46 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-git+https://github.com/hmenager/connexion.git@master#egg=connexion[swagger-ui]
+flask-smorest
aiohttp
python_dateutil
setuptools
diff --git a/setup.py b/setup.py
index 19675e52aa5d51210c488a360066df4de0043581..67e274e329c3082dabf0228d1e82f7e5dd93eea1 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,7 @@ README = os.path.join(SETUP_DIR, 'README.md')
readme = open(README).read()
REQUIRES = [
- "connexion[swagger-ui] @ git+https://github.com/hmenager/connexion.git@master#egg=connexion[swagger-ui]",
+ "flask-smorest",
"aiohttp",
"python_dateutil",
"setuptools",