Merge branch 'dev-flasksmorest' into 'dev'

change default handling of missing value : the server and the command line...

See merge request !33

Dockerfile

@@ -2,8 +2,9 @@ FROM centos:7
 
 RUN yum install -y epel-release wget gcc https://repo.ius.io/ius-release-el7.rpm
 RUN yum update -y
-RUN yum install -y python35u python35u-libs python35u-devel python35u-pip openssl-devel  libffi-devel
-RUN pip3.5 install ansible
+RUN yum install -y python36u python36u-libs python36u-devel python36u-pip openssl-devel  libffi-devel
+RUN pip3.6 install --upgrade pip
+RUN pip3.6 install ansible
 RUN yum install -y python-pip
 RUN python -m pip install --upgrade pip
 COPY . /code

jass/__init__.py

@@ -17,4 +17,4 @@ Submodules
 """
 import os
 
-from jass.tasks import celery
\ No newline at end of file
+from jass.tasks import celery

jass/__main__.py

@@ -5,59 +5,66 @@ import os
 import sys
 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
 from jass.models.inittable import create_inittable_file, add_gene_annotation
 from jass.models.worktable import create_worktable_file
-from jass.models.plots import ( create_global_plot,
-                                create_quadrant_plot,
-                                create_local_plot,
-                                create_qq_plot)
+from jass.models.plots import (
+    create_global_plot,
+    create_quadrant_plot,
+    create_local_plot,
+    create_qq_plot,
+)
 
-def absolute_path_of_the_file(fileName, output_file = False):
+
+def absolute_path_of_the_file(fileName, output_file=False):
     """
     Builds the absolute path of the file : fileName
     This makes the execution of JASS functions more robust and flexible
     """
- 
+
     # Build an absolute path if possible
     absoluteFilePath = os.path.abspath(fileName)
 
     # Test if the file name is a pattern
-    is_a_pattern = (os.path.basename(fileName).find("*") > -1)
+    is_a_pattern = os.path.basename(fileName).find("*") > -1
 
-    if (is_a_pattern or output_file) :
+    if is_a_pattern or output_file:
         # Test if the directory path exist
         Directory_path_exist = os.path.exists(os.path.dirname(absoluteFilePath))
 
-        if (Directory_path_exist == False):
+        if Directory_path_exist == False:
             # Test the path using the Jass data directory
-            absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName))
+            absoluteFilePath = os.path.normpath(
+                os.path.join(config["DATA_DIR"], fileName)
+            )
 
             Directory_path_exist = os.path.exists(os.path.dirname(absoluteFilePath))
 
-        if (Directory_path_exist == False):
+        if Directory_path_exist == False:
             Message = "The directory of the file {} does not exist".format(fileName)
             raise NameError(Message)
     else:
         # Test if the file path exist
         File_path_exist = os.path.exists(absoluteFilePath)
 
-        if (File_path_exist == False):
+        if File_path_exist == False:
             # Test the path using the Jass data directory
-            absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName))
+            absoluteFilePath = os.path.normpath(
+                os.path.join(config["DATA_DIR"], fileName)
+            )
             File_path_exist = os.path.exists(absoluteFilePath)
 
-        if (File_path_exist == False):
+        if File_path_exist == False:
             Message = "The file {} does not exist".format(fileName)
             raise NameError(Message)
 
         # Test if it is realy a file
         Is_a_file = os.path.isfile(absoluteFilePath)
 
-        if (not Is_a_file) :
+        if not Is_a_file:
             Message = "{} is not a file".format(fileName)
             raise NameError(Message)
 
@@ -65,8 +72,7 @@ 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):
@@ -77,12 +83,12 @@ def w_list_phenotypes(args):
 def compute_worktable(args):
 
     csv_file_path = args.csv_file_path
-    if (csv_file_path is not None):
+    if csv_file_path is not None:
         csv_file_path = absolute_path_of_the_file(csv_file_path, True)
     init_table_path = absolute_path_of_the_file(args.init_table_path)
     worktable_path = absolute_path_of_the_file(args.worktable_path, True)
     selected_phenotypes = args.phenotypes
-    remove_nan = (args.remove_nans)
+    remove_nan = args.remove_nans
     significance_treshold = float(args.significance_treshold)
     post_filtering = bool(args.post_filtering)
     custom_loadings = args.custom_loadings
@@ -91,9 +97,9 @@ def compute_worktable(args):
     pos_End = args.end_position
 
     if args.omnibus:
-        strategy = 'jass.models.stats:omnibus_stat'
+        strategy = "jass.models.stats:omnibus_stat"
     elif args.sumz:
-        strategy = 'jass.models.stats:sumz_stat'
+        strategy = "jass.models.stats:sumz_stat"
     elif args.fisher_test:
         strategy = "jass.models.stats:fisher_test"
     elif args.meta_analysis:
@@ -102,21 +108,21 @@ def compute_worktable(args):
         strategy = args.strategy
 
     create_worktable_file(
-        phenotype_ids = selected_phenotypes,
-        init_file_path = init_table_path,
-        project_hdf_path = worktable_path,
-        remove_nan = remove_nan,
-        stat = strategy,
-        optim_na = True,
-        csv_file = csv_file_path,
-        chunk_size = int(args.chunk_size),
-        significance_treshold = significance_treshold,
-        post_filtering = post_filtering,
-        delayed_gen_csv_file = False,
-        chromosome = chromosome,
-        pos_Start = pos_Start,
-        pos_End = pos_End,
-        custom_loadings = custom_loadings
+        phenotype_ids=selected_phenotypes,
+        init_file_path=init_table_path,
+        project_hdf_path=worktable_path,
+        remove_nan=remove_nan,
+        stat=strategy,
+        optim_na=True,
+        csv_file=csv_file_path,
+        chunk_size=int(args.chunk_size),
+        significance_treshold=significance_treshold,
+        post_filtering=post_filtering,
+        delayed_gen_csv_file=False,
+        chromosome=chromosome,
+        pos_Start=pos_Start,
+        pos_End=pos_End,
+        custom_loadings=custom_loadings,
     )
 
 
@@ -126,28 +132,25 @@ def w_create_worktable(args):
 
 def w_create_project_data(args):
     compute_worktable(args)
-    
     worktable_path = absolute_path_of_the_file(args.worktable_path, True)
-    
     manhattan_plot_path = args.manhattan_plot_path
-    if (manhattan_plot_path is not None):
+    if manhattan_plot_path is not None:
         manhattan_plot_path = absolute_path_of_the_file(manhattan_plot_path, True)
         create_global_plot(worktable_path, manhattan_plot_path)
-    
     quadrant_plot_path = args.quadrant_plot_path
-    if (quadrant_plot_path is not None):
-        quadrant_plot_path = absolute_path_of_the_file(quadrant_plot_path, True)    
-        create_quadrant_plot(worktable_path, 
-                             quadrant_plot_path, 
-                             significance_treshold = float(args.significance_treshold))
-    
+    if quadrant_plot_path is not None:
+        quadrant_plot_path = absolute_path_of_the_file(quadrant_plot_path, True)
+        create_quadrant_plot(
+            worktable_path,
+            quadrant_plot_path,
+            significance_treshold=float(args.significance_treshold),
+        )
     zoom_plot_path = args.zoom_plot_path
-    if (zoom_plot_path is not None):
+    if zoom_plot_path is not None:
         zoom_plot_path = absolute_path_of_the_file(zoom_plot_path, True)
         create_local_plot(worktable_path, zoom_plot_path)
-    
     qq_plot_path = args.qq_plot_path
-    if (qq_plot_path is not None):
+    if qq_plot_path is not None:
         qq_plot_path = absolute_path_of_the_file(qq_plot_path, True)
         create_qq_plot(worktable_path, qq_plot_path)
 
@@ -155,7 +158,9 @@ def w_create_project_data(args):
 def w_create_inittable(args):
     input_data_path = absolute_path_of_the_file(args.input_data_path)
     init_covariance_path = absolute_path_of_the_file(args.init_covariance_path)
-    init_genetic_covariance_path = absolute_path_of_the_file(args.init_genetic_covariance_path)
+    init_genetic_covariance_path = absolute_path_of_the_file(
+        args.init_genetic_covariance_path
+    )
     regions_map_path = absolute_path_of_the_file(args.regions_map_path)
     description_file_path = absolute_path_of_the_file(args.description_file_path)
     init_table_path = absolute_path_of_the_file(args.init_table_path, True)
@@ -166,7 +171,7 @@ def w_create_inittable(args):
         description_file_path,
         init_table_path,
         init_covariance_path,
-        init_genetic_covariance_path
+        init_genetic_covariance_path,
     )
 
 
@@ -180,9 +185,9 @@ def w_plot_quadrant(args):
     worktable_path = absolute_path_of_the_file(args.worktable_path)
     plot_path = absolute_path_of_the_file(args.plot_path)
     significance_treshold = float(args.significance_treshold)
-    create_quadrant_plot(worktable_path,
-                         plot_path,
-                         significance_treshold=significance_treshold)
+    create_quadrant_plot(
+        worktable_path, plot_path, significance_treshold=significance_treshold
+    )
 
 
 def w_gene_annotation(args):
@@ -190,10 +195,9 @@ def w_gene_annotation(args):
     initTable_path = absolute_path_of_the_file(args.init_table_path, True)
     df_gene_csv_path = absolute_path_of_the_file(args.gene_csv_path, True)
     df_exon_csv_path = absolute_path_of_the_file(args.exon_csv_path, True)
-    add_gene_annotation(gene_data_path,
-                        initTable_path,
-                        df_gene_csv_path,
-                        df_exon_csv_path)
+    add_gene_annotation(
+        gene_data_path, initTable_path, df_gene_csv_path, df_exon_csv_path
+    )
 
 
 def get_parser():
@@ -256,7 +260,7 @@ def get_parser():
     )
     parser_create_pd.add_argument(
         "--significance-treshold",
-        default=5*10**-8,
+        default=5 * 10 ** -8,
         help="The treshold at which a p-value is considered significant",
     )
     parser_create_pd.add_argument(
@@ -279,27 +283,25 @@ def get_parser():
     )
 
     parser_create_pd.add_argument(
-        "--csv-file-path",
-        required=False,
-        help="path to the results file in csv format"
+        "--csv-file-path", required=False, help="path to the results file in csv format"
     )
 
     parser_create_pd.add_argument(
         "--chromosome-number",
         required=False,
-        help="option used only for local analysis: chromosome number studied"
+        help="option used only for local analysis: chromosome number studied",
     )
 
     parser_create_pd.add_argument(
         "--start-position",
         required=False,
-        help="option used only for local analysis: start position of the region studied"
+        help="option used only for local analysis: start position of the region studied",
     )
 
     parser_create_pd.add_argument(
         "--end-position",
         required=False,
-        help="option used only for local analysis: end position of the region studied"
+        help="option used only for local analysis: end position of the region studied",
     )
 
     strategies = parser_create_pd.add_mutually_exclusive_group()
@@ -344,7 +346,7 @@ def get_parser():
     parser_create_it.add_argument(
         "--init-genetic-covariance-path",
         default=None,
-        help = "path to the genetic covariance file to import",
+        help="path to the genetic covariance file to import",
     )
     parser_create_it.set_defaults(func=w_create_inittable)
     # ------- create-worktable -------
@@ -366,13 +368,13 @@ def get_parser():
     )
     parser_create_wt.add_argument(
         "--significance-treshold",
-        default=5*10**-8,
-        help="threshold at which a p-value is considered significant"
-        )
+        default=5 * 10 ** -8,
+        help="threshold at which a p-value is considered significant",
+    )
     parser_create_wt.add_argument(
         "--post-filtering",
         default=True,
-        help="If a filtering to remove outlier will be applied (in this case the result of SNPs considered aberant will not appear in the worktable)"
+        help="If a filtering to remove outlier will be applied (in this case the result of SNPs considered aberant will not appear in the worktable)",
     )
 
     parser_create_wt.add_argument(
@@ -382,9 +384,7 @@ def get_parser():
     )
 
     parser_create_wt.add_argument(
-        "--csv-file-path",
-        required=False,
-        help="path to the results file in csv format"
+        "--csv-file-path", required=False, help="path to the results file in csv format"
     )
 
     parser_create_wt.add_argument(
@@ -399,19 +399,19 @@ def get_parser():
     parser_create_wt.add_argument(
         "--chromosome-number",
         required=False,
-        help="option used only for local analysis: chromosome number studied"
+        help="option used only for local analysis: chromosome number studied",
     )
 
     parser_create_wt.add_argument(
         "--start-position",
         required=False,
-        help="option used only for local analysis: start position of the region studied"
+        help="option used only for local analysis: start position of the region studied",
     )
 
     parser_create_wt.add_argument(
         "--end-position",
         required=False,
-        help="option used only for local analysis: end position of the region studied"
+        help="option used only for local analysis: end position of the region studied",
     )
 
     strategies = parser_create_wt.add_mutually_exclusive_group()
@@ -435,9 +435,7 @@ def get_parser():
         help="path to the worktable file containing the data",
     )
     parser_create_mp.add_argument(
-        "--plot-path",
-        required=True,
-        help="path to the manhattan plot file to generate"
+        "--plot-path", required=True, help="path to the manhattan plot file to generate"
     )
     parser_create_mp.set_defaults(func=w_plot_manhattan)
 
@@ -452,21 +450,20 @@ def get_parser():
         help="path to the worktable file containing the data",
     )
     parser_create_mp.add_argument(
-        "--plot-path",
-        required=True,
-        help="path to the quadrant plot file to generate"
+        "--plot-path", required=True, help="path to the quadrant plot file to generate"
     )
     parser_create_mp.add_argument(
         "--significance-treshold",
-        default=5*10**-8,
-        help="threshold at which a p-value is considered significant"
+        default=5 * 10 ** -8,
+        help="threshold at which a p-value is considered significant",
     )
     parser_create_mp.set_defaults(func=w_plot_quadrant)
 
     # ------- add-gene-annotation -------
 
     parser_create_mp = subparsers.add_parser(
-        "add-gene-annotation", help="add information about genes ansd exons to the inittable"
+        "add-gene-annotation",
+        help="add information about genes ansd exons to the inittable",
     )
     parser_create_mp.add_argument(
         "--gene-data-path",
@@ -476,17 +473,13 @@ def get_parser():
     parser_create_mp.add_argument(
         "--init-table-path",
         required=True,
-        help="path to the initial table file to update"
+        help="path to the initial table file to update",
     )
     parser_create_mp.add_argument(
-        "--gene-csv-path",
-        required=False,
-        help="path to the file df_gene.csv"
+        "--gene-csv-path", required=False, help="path to the file df_gene.csv"
     )
     parser_create_mp.add_argument(
-        "--exon-csv-path",
-        required=False,
-        help="path to the file df_exon.csv"
+        "--exon-csv-path", required=False, help="path to the file df_exon.csv"
     )
     parser_create_mp.set_defaults(func=w_gene_annotation)
 
@@ -494,16 +487,16 @@ def get_parser():
 
 
 def main():
-    print("", file = sys.stderr)
-    print("        **     *******      *******   *******", file = sys.stderr)
-    print("        **    **     **    **        **", file = sys.stderr)
-    print("        **   **       **   **        **", file = sys.stderr)
-    print("        **   **       **    ******    ******", file = sys.stderr)
-    print("        **   ***********         **        **", file = sys.stderr)
-    print(" **     **   **       **         **        **", file = sys.stderr)
-    print("  *******    **       **   *******   *******", file = sys.stderr)
-    print("", file = sys.stderr)
-    print("", file = sys.stderr)
+    print("", file=sys.stderr)
+    print("        **     *******      *******   *******", file=sys.stderr)
+    print("        **    **     **    **        **", file=sys.stderr)
+    print("        **   **       **   **        **", file=sys.stderr)
+    print("        **   **       **    ******    ******", file=sys.stderr)
+    print("        **   ***********         **        **", file=sys.stderr)
+    print(" **     **   **       **         **        **", file=sys.stderr)
+    print("  *******    **       **   *******   *******", file=sys.stderr)
+    print("", file=sys.stderr)
+    print("", file=sys.stderr)
     parser = get_parser()
     args = parser.parse_args()
     args.func(args)

jass/celeryconfig.py

 import os
 
 ## Broker settings.
-broker_url = os.getenv('JASS_RABBITMQ_URL','amqp://guest:guest@localhost:5672//')
+broker_url = os.getenv("JASS_RABBITMQ_URL", "amqp://guest:guest@localhost:5672//")
 
 ## Broker settings.
-#result_backend = os.getenv('JASS_RABBITMQ_URL','amqp://guest2:guest@localhost:5672//')
-result_backend='rpc://'
+# result_backend = os.getenv('JASS_RABBITMQ_URL','amqp://guest2:guest@localhost:5672//')
+result_backend = "rpc://"
 # List of modules to import when the Celery worker starts.
-#imports = ('myapp.tasks',)
+# imports = ('myapp.tasks',)
 
 ## Using the database to store task state and results.
-#result_backend = 'db+sqlite:///results.db'
-
-#task_annotations = {'tasks.add': {'rate_limit': '10/s'}}
-
+# result_backend = 'db+sqlite:///results.db'
 
+# task_annotations = {'tasks.add': {'rate_limit': '10/s'}}

jass/controllers/__init__.py

-"""
-the list of controller functions called by the JASS REST web services
-
-Submodules
-==========
-
-.. autosummary::
-    :toctree: _autosummary
-
-    default_controller
-"""

jass/controllers/default_controller.py

-# -*- coding: utf-8 -*-
-
-"""
-default_controller ensures the connection between the web interface and the Python JASS-analysis module
-"""
-import os
-from typing import List, Dict
-
-import connexion
-from flask import send_file, abort
-from six import iteritems
-
-from jass.config import config
-from jass.models.project import Project
-from jass.models.phenotype import Phenotype, get_available_phenotypes
-from jass.tasks import create_project
-
-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 local_project_post(phenotypeID, chromosome, start, end):
-    """
-    local_project_post
-    Create a new local project from a chromosome number, start and end positions 
-    and a selection of phenotypes 
-    :param param: IDs of the phenotypes selected for the project
-    :type phenotypeID: List[str]
- 
-    :rtype: str
-    """    
-    return create_project(phenotypeID, PHENOTYPES, chromosome, start, end)
-
-
-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_zoom_plot_get(projectID):
-    """
-    projects_project_id_zoom_plot_get
-    Gets the zoom plot stored in the local Project folder to display it on the Web interface
-    """
-    try:
-        return send_file(
-            Project(id=projectID).get_zoom_plot_path(), mimetype="image/png"
-        )
-    except FileNotFoundError:
-        status = Project(id=projectID).status
-        if status == Project.DOES_NOT_EXIST:
-            abort(404)
-        elif status["zoom_plot"] == 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