diff options
-rw-r--r-- | README.org | 2 | ||||
-rw-r--r-- | scripts/insert_data.py | 4 | ||||
-rw-r--r-- | scripts/insert_samples.py | 8 | ||||
-rw-r--r-- | scripts/process_rqtl2_bundle.py | 6 | ||||
-rw-r--r-- | scripts/qc.py | 2 | ||||
-rw-r--r-- | scripts/qc_on_rqtl2_bundle.py | 6 | ||||
-rw-r--r-- | scripts/qcapp_wsgi.py | 4 | ||||
-rw-r--r-- | scripts/rqtl2/entry.py | 6 | ||||
-rw-r--r-- | scripts/validate_file.py | 4 | ||||
-rw-r--r-- | scripts/worker.py | 4 | ||||
-rw-r--r-- | tests/conftest.py | 4 | ||||
-rw-r--r-- | tests/qc_app/test_parse.py | 4 | ||||
-rw-r--r-- | uploader/__init__.py (renamed from qc_app/__init__.py) | 0 | ||||
-rw-r--r-- | uploader/base_routes.py (renamed from qc_app/base_routes.py) | 0 | ||||
-rw-r--r-- | uploader/check_connections.py (renamed from qc_app/check_connections.py) | 2 | ||||
-rw-r--r-- | uploader/db/__init__.py (renamed from qc_app/db/__init__.py) | 0 | ||||
-rw-r--r-- | uploader/db/averaging.py (renamed from qc_app/db/averaging.py) | 0 | ||||
-rw-r--r-- | uploader/db/datasets.py (renamed from qc_app/db/datasets.py) | 0 | ||||
-rw-r--r-- | uploader/db/platforms.py (renamed from qc_app/db/platforms.py) | 0 | ||||
-rw-r--r-- | uploader/db/populations.py (renamed from qc_app/db/populations.py) | 0 | ||||
-rw-r--r-- | uploader/db/species.py (renamed from qc_app/db/species.py) | 0 | ||||
-rw-r--r-- | uploader/db/tissues.py (renamed from qc_app/db/tissues.py) | 0 | ||||
-rw-r--r-- | uploader/db_utils.py (renamed from qc_app/db_utils.py) | 0 | ||||
-rw-r--r-- | uploader/dbinsert.py (renamed from qc_app/dbinsert.py) | 4 | ||||
-rw-r--r-- | uploader/default_settings.py | 14 | ||||
-rw-r--r-- | uploader/entry.py (renamed from qc_app/entry.py) | 4 | ||||
-rw-r--r-- | uploader/errors.py (renamed from qc_app/errors.py) | 0 | ||||
-rw-r--r-- | uploader/files.py (renamed from qc_app/files.py) | 0 | ||||
-rw-r--r-- | uploader/input_validation.py (renamed from qc_app/input_validation.py) | 0 | ||||
-rw-r--r-- | uploader/jobs.py (renamed from qc_app/jobs.py) | 0 | ||||
-rw-r--r-- | uploader/parse.py (renamed from qc_app/parse.py) | 6 | ||||
-rw-r--r-- | uploader/samples.py (renamed from qc_app/samples.py) | 10 | ||||
-rw-r--r-- | uploader/static/css/custom-bootstrap.css (renamed from qc_app/static/css/custom-bootstrap.css) | 0 | ||||
-rw-r--r-- | uploader/static/css/styles.css (renamed from qc_app/static/css/styles.css) | 0 | ||||
-rw-r--r-- | uploader/static/css/two-column-with-separator.css (renamed from qc_app/static/css/two-column-with-separator.css) | 0 | ||||
-rw-r--r-- | uploader/static/images/CITGLogo.png (renamed from qc_app/static/images/CITGLogo.png) | bin | 11962 -> 11962 bytes | |||
-rw-r--r-- | uploader/static/js/select_platform.js (renamed from qc_app/static/js/select_platform.js) | 0 | ||||
-rw-r--r-- | uploader/static/js/upload_progress.js (renamed from qc_app/static/js/upload_progress.js) | 0 | ||||
-rw-r--r-- | uploader/static/js/upload_samples.js (renamed from qc_app/static/js/upload_samples.js) | 0 | ||||
-rw-r--r-- | uploader/static/js/utils.js (renamed from qc_app/static/js/utils.js) | 0 | ||||
-rw-r--r-- | uploader/templates/base.html (renamed from qc_app/templates/base.html) | 0 | ||||
-rw-r--r-- | uploader/templates/cli-output.html (renamed from qc_app/templates/cli-output.html) | 0 | ||||
-rw-r--r-- | uploader/templates/continue_from_create_dataset.html (renamed from qc_app/templates/continue_from_create_dataset.html) | 0 | ||||
-rw-r--r-- | uploader/templates/continue_from_create_study.html (renamed from qc_app/templates/continue_from_create_study.html) | 0 | ||||
-rw-r--r-- | uploader/templates/data_review.html (renamed from qc_app/templates/data_review.html) | 0 | ||||
-rw-r--r-- | uploader/templates/dbupdate_error.html (renamed from qc_app/templates/dbupdate_error.html) | 0 | ||||
-rw-r--r-- | uploader/templates/dbupdate_hidden_fields.html (renamed from qc_app/templates/dbupdate_hidden_fields.html) | 0 | ||||
-rw-r--r-- | uploader/templates/errors_display.html (renamed from qc_app/templates/errors_display.html) | 0 | ||||
-rw-r--r-- | uploader/templates/final_confirmation.html (renamed from qc_app/templates/final_confirmation.html) | 0 | ||||
-rw-r--r-- | uploader/templates/flash_messages.html (renamed from qc_app/templates/flash_messages.html) | 0 | ||||
-rw-r--r-- | uploader/templates/http-error.html (renamed from qc_app/templates/http-error.html) | 0 | ||||
-rw-r--r-- | uploader/templates/index.html (renamed from qc_app/templates/index.html) | 0 | ||||
-rw-r--r-- | uploader/templates/insert_error.html (renamed from qc_app/templates/insert_error.html) | 0 | ||||
-rw-r--r-- | uploader/templates/insert_progress.html (renamed from qc_app/templates/insert_progress.html) | 0 | ||||
-rw-r--r-- | uploader/templates/insert_success.html (renamed from qc_app/templates/insert_success.html) | 0 | ||||
-rw-r--r-- | uploader/templates/job_progress.html (renamed from qc_app/templates/job_progress.html) | 0 | ||||
-rw-r--r-- | uploader/templates/no_such_job.html (renamed from qc_app/templates/no_such_job.html) | 0 | ||||
-rw-r--r-- | uploader/templates/parse_failure.html (renamed from qc_app/templates/parse_failure.html) | 0 | ||||
-rw-r--r-- | uploader/templates/parse_results.html (renamed from qc_app/templates/parse_results.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/create-geno-dataset-success.html (renamed from qc_app/templates/rqtl2/create-geno-dataset-success.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/create-probe-dataset-success.html (renamed from qc_app/templates/rqtl2/create-probe-dataset-success.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/create-probe-study-success.html (renamed from qc_app/templates/rqtl2/create-probe-study-success.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/create-tissue-success.html (renamed from qc_app/templates/rqtl2/create-tissue-success.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/index.html (renamed from qc_app/templates/rqtl2/index.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/no-such-job.html (renamed from qc_app/templates/rqtl2/no-such-job.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/rqtl2-job-error.html (renamed from qc_app/templates/rqtl2/rqtl2-job-error.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/rqtl2-job-results.html (renamed from qc_app/templates/rqtl2/rqtl2-job-results.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/rqtl2-job-status.html (renamed from qc_app/templates/rqtl2/rqtl2-job-status.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/rqtl2-qc-job-error.html (renamed from qc_app/templates/rqtl2/rqtl2-qc-job-error.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/rqtl2-qc-job-results.html (renamed from qc_app/templates/rqtl2/rqtl2-qc-job-results.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/rqtl2-qc-job-status.html (renamed from qc_app/templates/rqtl2/rqtl2-qc-job-status.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/rqtl2-qc-job-success.html (renamed from qc_app/templates/rqtl2/rqtl2-qc-job-success.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/select-geno-dataset.html (renamed from qc_app/templates/rqtl2/select-geno-dataset.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/select-population.html (renamed from qc_app/templates/rqtl2/select-population.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/select-probeset-dataset.html (renamed from qc_app/templates/rqtl2/select-probeset-dataset.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/select-probeset-study-id.html (renamed from qc_app/templates/rqtl2/select-probeset-study-id.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/select-tissue.html (renamed from qc_app/templates/rqtl2/select-tissue.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/summary-info.html (renamed from qc_app/templates/rqtl2/summary-info.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html (renamed from qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html) | 0 | ||||
-rw-r--r-- | uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html (renamed from qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html) | 0 | ||||
-rw-r--r-- | uploader/templates/samples/select-population.html (renamed from qc_app/templates/samples/select-population.html) | 0 | ||||
-rw-r--r-- | uploader/templates/samples/select-species.html (renamed from qc_app/templates/samples/select-species.html) | 0 | ||||
-rw-r--r-- | uploader/templates/samples/upload-failure.html (renamed from qc_app/templates/samples/upload-failure.html) | 0 | ||||
-rw-r--r-- | uploader/templates/samples/upload-progress.html (renamed from qc_app/templates/samples/upload-progress.html) | 0 | ||||
-rw-r--r-- | uploader/templates/samples/upload-samples.html (renamed from qc_app/templates/samples/upload-samples.html) | 0 | ||||
-rw-r--r-- | uploader/templates/samples/upload-success.html (renamed from qc_app/templates/samples/upload-success.html) | 0 | ||||
-rw-r--r-- | uploader/templates/select_dataset.html (renamed from qc_app/templates/select_dataset.html) | 0 | ||||
-rw-r--r-- | uploader/templates/select_platform.html (renamed from qc_app/templates/select_platform.html) | 0 | ||||
-rw-r--r-- | uploader/templates/select_species.html (renamed from qc_app/templates/select_species.html) | 0 | ||||
-rw-r--r-- | uploader/templates/select_study.html (renamed from qc_app/templates/select_study.html) | 0 | ||||
-rw-r--r-- | uploader/templates/stdout_output.html (renamed from qc_app/templates/stdout_output.html) | 0 | ||||
-rw-r--r-- | uploader/templates/unhandled_exception.html (renamed from qc_app/templates/unhandled_exception.html) | 0 | ||||
-rw-r--r-- | uploader/templates/upload_progress_indicator.html (renamed from qc_app/templates/upload_progress_indicator.html) | 0 | ||||
-rw-r--r-- | uploader/templates/worker_failure.html (renamed from qc_app/templates/worker_failure.html) | 0 | ||||
-rw-r--r-- | uploader/upload/__init__.py (renamed from qc_app/upload/__init__.py) | 0 | ||||
-rw-r--r-- | uploader/upload/rqtl2.py (renamed from qc_app/upload/rqtl2.py) | 20 |
96 files changed, 64 insertions, 50 deletions
@@ -208,7 +208,7 @@ flask run To run the linter over the code base, run: #+BEGIN_SRC shell - pylint setup.py tests quality_control qc_app r_qtl scripts + pylint setup.py tests quality_control uploader r_qtl scripts #+END_SRC To check for correct type usage in the application, run: diff --git a/scripts/insert_data.py b/scripts/insert_data.py index 1465348..4b2e5f3 100644 --- a/scripts/insert_data.py +++ b/scripts/insert_data.py @@ -14,8 +14,8 @@ from MySQLdb.cursors import DictCursor from functional_tools import take from quality_control.file_utils import open_file -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis +from uploader.db_utils import database_connection +from uploader.check_connections import check_db, check_redis # Set up logging stderr_handler = logging.StreamHandler(stream=sys.stderr) diff --git a/scripts/insert_samples.py b/scripts/insert_samples.py index 8431462..87f29dc 100644 --- a/scripts/insert_samples.py +++ b/scripts/insert_samples.py @@ -7,10 +7,10 @@ import argparse import MySQLdb as mdb from redis import Redis -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis -from qc_app.db import species_by_id, population_by_id -from qc_app.samples import ( +from uploader.db_utils import database_connection +from uploader.check_connections import check_db, check_redis +from uploader.db import species_by_id, population_by_id +from uploader.samples import ( save_samples_data, read_samples_file, cross_reference_samples) diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py index 4da3936..a7e169d 100644 --- a/scripts/process_rqtl2_bundle.py +++ b/scripts/process_rqtl2_bundle.py @@ -17,9 +17,9 @@ import r_qtl.errors as rqe import r_qtl.r_qtl2 as rqtl2 import r_qtl.r_qtl2_qc as rqc -from qc_app import jobs -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis +from uploader import jobs +from uploader.db_utils import database_connection +from uploader.check_connections import check_db, check_redis from scripts.cli_parser import init_cli_parser from scripts.redis_logger import setup_redis_logger diff --git a/scripts/qc.py b/scripts/qc.py index e8573a9..6de051f 100644 --- a/scripts/qc.py +++ b/scripts/qc.py @@ -11,7 +11,7 @@ from quality_control.utils import make_progress_calculator from quality_control.errors import InvalidValue, DuplicateHeading from quality_control.parsing import FileType, strain_names, collect_errors -from qc_app.db_utils import database_connection +from uploader.db_utils import database_connection from .cli_parser import init_cli_parser diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py index 40809b7..150fbce 100644 --- a/scripts/qc_on_rqtl2_bundle.py +++ b/scripts/qc_on_rqtl2_bundle.py @@ -16,9 +16,9 @@ from redis import Redis from quality_control.errors import InvalidValue from quality_control.checks import decimal_points_error -from qc_app import jobs -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis +from uploader import jobs +from uploader.db_utils import database_connection +from uploader.check_connections import check_db, check_redis from r_qtl import errors as rqe from r_qtl import r_qtl2 as rqtl2 diff --git a/scripts/qcapp_wsgi.py b/scripts/qcapp_wsgi.py index 349c006..fe77031 100644 --- a/scripts/qcapp_wsgi.py +++ b/scripts/qcapp_wsgi.py @@ -5,8 +5,8 @@ from logging import getLogger, StreamHandler from flask import Flask -from qc_app import create_app -from qc_app.check_connections import check_db, check_redis +from uploader import create_app +from uploader.check_connections import check_db, check_redis def setup_logging(appl: Flask) -> Flask: """Setup appropriate logging paradigm depending on environment.""" diff --git a/scripts/rqtl2/entry.py b/scripts/rqtl2/entry.py index 93fc130..b7fb68e 100644 --- a/scripts/rqtl2/entry.py +++ b/scripts/rqtl2/entry.py @@ -6,9 +6,9 @@ from argparse import Namespace from redis import Redis from MySQLdb import Connection -from qc_app import jobs -from qc_app.db_utils import database_connection -from qc_app.check_connections import check_db, check_redis +from uploader import jobs +from uploader.db_utils import database_connection +from uploader.check_connections import check_db, check_redis from scripts.redis_logger import setup_redis_logger diff --git a/scripts/validate_file.py b/scripts/validate_file.py index 0028795..a40d7e7 100644 --- a/scripts/validate_file.py +++ b/scripts/validate_file.py @@ -12,8 +12,8 @@ from redis.exceptions import ConnectionError # pylint: disable=[redefined-builti from quality_control.utils import make_progress_calculator from quality_control.parsing import FileType, strain_names, collect_errors -from qc_app import jobs -from qc_app.db_utils import database_connection +from uploader import jobs +from uploader.db_utils import database_connection from .cli_parser import init_cli_parser from .qc import add_file_validation_arguments diff --git a/scripts/worker.py b/scripts/worker.py index 0eb9ea5..91b0332 100644 --- a/scripts/worker.py +++ b/scripts/worker.py @@ -11,8 +11,8 @@ from tempfile import TemporaryDirectory from redis import Redis -from qc_app import jobs -from qc_app.check_connections import check_redis +from uploader import jobs +from uploader.check_connections import check_redis def parse_args(): "Parse the command-line arguments" diff --git a/tests/conftest.py b/tests/conftest.py index a39acf0..9012221 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -11,8 +11,8 @@ from redis import Redis from functional_tools import take -from qc_app import jobs, create_app -from qc_app.jobs import JOBS_PREFIX +from uploader import jobs, create_app +from uploader.jobs import JOBS_PREFIX from quality_control.errors import InvalidValue, DuplicateHeading diff --git a/tests/qc_app/test_parse.py b/tests/qc_app/test_parse.py index 3915a4d..076c47c 100644 --- a/tests/qc_app/test_parse.py +++ b/tests/qc_app/test_parse.py @@ -4,7 +4,7 @@ import sys import redis import pytest -from qc_app.jobs import job, jobsnamespace +from uploader.jobs import job, jobsnamespace from tests.conftest import uploadable_file_object @@ -24,7 +24,7 @@ def test_parse_with_existing_uploaded_file(#pylint: disable=[too-many-arguments] 1. the system redirects to the job/parse status page 2. the job is placed on redis for processing """ - monkeypatch.setattr("qc_app.jobs.uuid4", lambda : job_id) + monkeypatch.setattr("uploader.jobs.uuid4", lambda : job_id) # Upload a file speciesid = 1 filename = "no_data_errors.tsv" diff --git a/qc_app/__init__.py b/uploader/__init__.py index 3ee8aa0..3ee8aa0 100644 --- a/qc_app/__init__.py +++ b/uploader/__init__.py diff --git a/qc_app/base_routes.py b/uploader/base_routes.py index 9daf439..9daf439 100644 --- a/qc_app/base_routes.py +++ b/uploader/base_routes.py diff --git a/qc_app/check_connections.py b/uploader/check_connections.py index ceccc32..2561e55 100644 --- a/qc_app/check_connections.py +++ b/uploader/check_connections.py @@ -5,7 +5,7 @@ import traceback import redis import MySQLdb -from qc_app.db_utils import database_connection +from uploader.db_utils import database_connection def check_redis(uri: str): "Check the redis connection" diff --git a/qc_app/db/__init__.py b/uploader/db/__init__.py index 36e93e8..36e93e8 100644 --- a/qc_app/db/__init__.py +++ b/uploader/db/__init__.py diff --git a/qc_app/db/averaging.py b/uploader/db/averaging.py index 62bbe67..62bbe67 100644 --- a/qc_app/db/averaging.py +++ b/uploader/db/averaging.py diff --git a/qc_app/db/datasets.py b/uploader/db/datasets.py index 767ec41..767ec41 100644 --- a/qc_app/db/datasets.py +++ b/uploader/db/datasets.py diff --git a/qc_app/db/platforms.py b/uploader/db/platforms.py index cb527a7..cb527a7 100644 --- a/qc_app/db/platforms.py +++ b/uploader/db/platforms.py diff --git a/qc_app/db/populations.py b/uploader/db/populations.py index 4485e52..4485e52 100644 --- a/qc_app/db/populations.py +++ b/uploader/db/populations.py diff --git a/qc_app/db/species.py b/uploader/db/species.py index 653e59b..653e59b 100644 --- a/qc_app/db/species.py +++ b/uploader/db/species.py diff --git a/qc_app/db/tissues.py b/uploader/db/tissues.py index 9fe7bab..9fe7bab 100644 --- a/qc_app/db/tissues.py +++ b/uploader/db/tissues.py diff --git a/qc_app/db_utils.py b/uploader/db_utils.py index ef26398..ef26398 100644 --- a/qc_app/db_utils.py +++ b/uploader/db_utils.py diff --git a/qc_app/dbinsert.py b/uploader/dbinsert.py index ef08423..88d16ef 100644 --- a/qc_app/dbinsert.py +++ b/uploader/dbinsert.py @@ -11,8 +11,8 @@ from flask import ( flash, request, url_for, Blueprint, redirect, render_template, current_app as app) -from qc_app.db_utils import with_db_connection, database_connection -from qc_app.db import species, species_by_id, populations_by_species +from uploader.db_utils import with_db_connection, database_connection +from uploader.db import species, species_by_id, populations_by_species from . import jobs diff --git a/uploader/default_settings.py b/uploader/default_settings.py new file mode 100644 index 0000000..7a9da0f --- /dev/null +++ b/uploader/default_settings.py @@ -0,0 +1,14 @@ +""" +The default configuration file. The values here should be overridden in the +actual configuration file used for the production and staging systems. +""" + +import os + +LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING") +SECRET_KEY = b"<Please! Please! Please! Change This!>" +UPLOAD_FOLDER = "/tmp/qc_app_files" +REDIS_URL = "redis://" +JOBS_TTL_SECONDS = 1209600 # 14 days +GNQC_REDIS_PREFIX="GNQC" +SQL_URI = "" diff --git a/qc_app/entry.py b/uploader/entry.py index f2db878..4a02f1e 100644 --- a/qc_app/entry.py +++ b/uploader/entry.py @@ -15,8 +15,8 @@ from flask import ( current_app as app, send_from_directory) -from qc_app.db import species -from qc_app.db_utils import with_db_connection +from uploader.db import species +from uploader.db_utils import with_db_connection entrybp = Blueprint("entry", __name__) diff --git a/qc_app/errors.py b/uploader/errors.py index 3e7c893..3e7c893 100644 --- a/qc_app/errors.py +++ b/uploader/errors.py diff --git a/qc_app/files.py b/uploader/files.py index b163612..b163612 100644 --- a/qc_app/files.py +++ b/uploader/files.py diff --git a/qc_app/input_validation.py b/uploader/input_validation.py index 9abe742..9abe742 100644 --- a/qc_app/input_validation.py +++ b/uploader/input_validation.py diff --git a/qc_app/jobs.py b/uploader/jobs.py index 21889da..21889da 100644 --- a/qc_app/jobs.py +++ b/uploader/jobs.py diff --git a/qc_app/parse.py b/uploader/parse.py index d20f6f0..865dae2 100644 --- a/qc_app/parse.py +++ b/uploader/parse.py @@ -8,9 +8,9 @@ from flask import current_app as app from quality_control.errors import InvalidValue, DuplicateHeading -from qc_app import jobs -from qc_app.dbinsert import species_by_id -from qc_app.db_utils import with_db_connection +from uploader import jobs +from uploader.dbinsert import species_by_id +from uploader.db_utils import with_db_connection parsebp = Blueprint("parse", __name__) diff --git a/qc_app/samples.py b/uploader/samples.py index 804f262..9c95770 100644 --- a/qc_app/samples.py +++ b/uploader/samples.py @@ -20,14 +20,14 @@ from flask import ( from functional_tools import take -from qc_app import jobs -from qc_app.files import save_file -from qc_app.input_validation import is_integer_input -from qc_app.db_utils import ( +from uploader import jobs +from uploader.files import save_file +from uploader.input_validation import is_integer_input +from uploader.db_utils import ( with_db_connection, database_connection, with_redis_connection) -from qc_app.db import ( +from uploader.db import ( species_by_id, save_population, population_by_id, diff --git a/qc_app/static/css/custom-bootstrap.css b/uploader/static/css/custom-bootstrap.css index 67f1199..67f1199 100644 --- a/qc_app/static/css/custom-bootstrap.css +++ b/uploader/static/css/custom-bootstrap.css diff --git a/qc_app/static/css/styles.css b/uploader/static/css/styles.css index a88c229..a88c229 100644 --- a/qc_app/static/css/styles.css +++ b/uploader/static/css/styles.css diff --git a/qc_app/static/css/two-column-with-separator.css b/uploader/static/css/two-column-with-separator.css index b6efd46..b6efd46 100644 --- a/qc_app/static/css/two-column-with-separator.css +++ b/uploader/static/css/two-column-with-separator.css diff --git a/qc_app/static/images/CITGLogo.png b/uploader/static/images/CITGLogo.png Binary files differindex ae99fed..ae99fed 100644 --- a/qc_app/static/images/CITGLogo.png +++ b/uploader/static/images/CITGLogo.png diff --git a/qc_app/static/js/select_platform.js b/uploader/static/js/select_platform.js index 4fdd865..4fdd865 100644 --- a/qc_app/static/js/select_platform.js +++ b/uploader/static/js/select_platform.js diff --git a/qc_app/static/js/upload_progress.js b/uploader/static/js/upload_progress.js index 9638b36..9638b36 100644 --- a/qc_app/static/js/upload_progress.js +++ b/uploader/static/js/upload_progress.js diff --git a/qc_app/static/js/upload_samples.js b/uploader/static/js/upload_samples.js index aed536f..aed536f 100644 --- a/qc_app/static/js/upload_samples.js +++ b/uploader/static/js/upload_samples.js diff --git a/qc_app/static/js/utils.js b/uploader/static/js/utils.js index 045dd47..045dd47 100644 --- a/qc_app/static/js/utils.js +++ b/uploader/static/js/utils.js diff --git a/qc_app/templates/base.html b/uploader/templates/base.html index eb5e6b7..eb5e6b7 100644 --- a/qc_app/templates/base.html +++ b/uploader/templates/base.html diff --git a/qc_app/templates/cli-output.html b/uploader/templates/cli-output.html index 33fb73b..33fb73b 100644 --- a/qc_app/templates/cli-output.html +++ b/uploader/templates/cli-output.html diff --git a/qc_app/templates/continue_from_create_dataset.html b/uploader/templates/continue_from_create_dataset.html index 03bb49c..03bb49c 100644 --- a/qc_app/templates/continue_from_create_dataset.html +++ b/uploader/templates/continue_from_create_dataset.html diff --git a/qc_app/templates/continue_from_create_study.html b/uploader/templates/continue_from_create_study.html index 34e6e5e..34e6e5e 100644 --- a/qc_app/templates/continue_from_create_study.html +++ b/uploader/templates/continue_from_create_study.html diff --git a/qc_app/templates/data_review.html b/uploader/templates/data_review.html index b7528fd..b7528fd 100644 --- a/qc_app/templates/data_review.html +++ b/uploader/templates/data_review.html diff --git a/qc_app/templates/dbupdate_error.html b/uploader/templates/dbupdate_error.html index e1359d2..e1359d2 100644 --- a/qc_app/templates/dbupdate_error.html +++ b/uploader/templates/dbupdate_error.html diff --git a/qc_app/templates/dbupdate_hidden_fields.html b/uploader/templates/dbupdate_hidden_fields.html index ccbc299..ccbc299 100644 --- a/qc_app/templates/dbupdate_hidden_fields.html +++ b/uploader/templates/dbupdate_hidden_fields.html diff --git a/qc_app/templates/errors_display.html b/uploader/templates/errors_display.html index 715cfcf..715cfcf 100644 --- a/qc_app/templates/errors_display.html +++ b/uploader/templates/errors_display.html diff --git a/qc_app/templates/final_confirmation.html b/uploader/templates/final_confirmation.html index 0727fc8..0727fc8 100644 --- a/qc_app/templates/final_confirmation.html +++ b/uploader/templates/final_confirmation.html diff --git a/qc_app/templates/flash_messages.html b/uploader/templates/flash_messages.html index b7af178..b7af178 100644 --- a/qc_app/templates/flash_messages.html +++ b/uploader/templates/flash_messages.html diff --git a/qc_app/templates/http-error.html b/uploader/templates/http-error.html index 374fb86..374fb86 100644 --- a/qc_app/templates/http-error.html +++ b/uploader/templates/http-error.html diff --git a/qc_app/templates/index.html b/uploader/templates/index.html index 89d2ae9..89d2ae9 100644 --- a/qc_app/templates/index.html +++ b/uploader/templates/index.html diff --git a/qc_app/templates/insert_error.html b/uploader/templates/insert_error.html index 5301288..5301288 100644 --- a/qc_app/templates/insert_error.html +++ b/uploader/templates/insert_error.html diff --git a/qc_app/templates/insert_progress.html b/uploader/templates/insert_progress.html index 52177d6..52177d6 100644 --- a/qc_app/templates/insert_progress.html +++ b/uploader/templates/insert_progress.html diff --git a/qc_app/templates/insert_success.html b/uploader/templates/insert_success.html index 7e1fa8d..7e1fa8d 100644 --- a/qc_app/templates/insert_success.html +++ b/uploader/templates/insert_success.html diff --git a/qc_app/templates/job_progress.html b/uploader/templates/job_progress.html index 1af0763..1af0763 100644 --- a/qc_app/templates/job_progress.html +++ b/uploader/templates/job_progress.html diff --git a/qc_app/templates/no_such_job.html b/uploader/templates/no_such_job.html index 42a2d48..42a2d48 100644 --- a/qc_app/templates/no_such_job.html +++ b/uploader/templates/no_such_job.html diff --git a/qc_app/templates/parse_failure.html b/uploader/templates/parse_failure.html index 31f6be8..31f6be8 100644 --- a/qc_app/templates/parse_failure.html +++ b/uploader/templates/parse_failure.html diff --git a/qc_app/templates/parse_results.html b/uploader/templates/parse_results.html index e2bf7f0..e2bf7f0 100644 --- a/qc_app/templates/parse_results.html +++ b/uploader/templates/parse_results.html diff --git a/qc_app/templates/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html index 1b50221..1b50221 100644 --- a/qc_app/templates/rqtl2/create-geno-dataset-success.html +++ b/uploader/templates/rqtl2/create-geno-dataset-success.html diff --git a/qc_app/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html index 790d174..790d174 100644 --- a/qc_app/templates/rqtl2/create-probe-dataset-success.html +++ b/uploader/templates/rqtl2/create-probe-dataset-success.html diff --git a/qc_app/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html index d0ee508..d0ee508 100644 --- a/qc_app/templates/rqtl2/create-probe-study-success.html +++ b/uploader/templates/rqtl2/create-probe-study-success.html diff --git a/qc_app/templates/rqtl2/create-tissue-success.html b/uploader/templates/rqtl2/create-tissue-success.html index 5f2c5a0..5f2c5a0 100644 --- a/qc_app/templates/rqtl2/create-tissue-success.html +++ b/uploader/templates/rqtl2/create-tissue-success.html diff --git a/qc_app/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html index f3329c2..f3329c2 100644 --- a/qc_app/templates/rqtl2/index.html +++ b/uploader/templates/rqtl2/index.html diff --git a/qc_app/templates/rqtl2/no-such-job.html b/uploader/templates/rqtl2/no-such-job.html index b17004f..b17004f 100644 --- a/qc_app/templates/rqtl2/no-such-job.html +++ b/uploader/templates/rqtl2/no-such-job.html diff --git a/qc_app/templates/rqtl2/rqtl2-job-error.html b/uploader/templates/rqtl2/rqtl2-job-error.html index 9817518..9817518 100644 --- a/qc_app/templates/rqtl2/rqtl2-job-error.html +++ b/uploader/templates/rqtl2/rqtl2-job-error.html diff --git a/qc_app/templates/rqtl2/rqtl2-job-results.html b/uploader/templates/rqtl2/rqtl2-job-results.html index 4ecd415..4ecd415 100644 --- a/qc_app/templates/rqtl2/rqtl2-job-results.html +++ b/uploader/templates/rqtl2/rqtl2-job-results.html diff --git a/qc_app/templates/rqtl2/rqtl2-job-status.html b/uploader/templates/rqtl2/rqtl2-job-status.html index e896f88..e896f88 100644 --- a/qc_app/templates/rqtl2/rqtl2-job-status.html +++ b/uploader/templates/rqtl2/rqtl2-job-status.html diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/rqtl2/rqtl2-qc-job-error.html index 90e8887..90e8887 100644 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html +++ b/uploader/templates/rqtl2/rqtl2-qc-job-error.html diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/rqtl2/rqtl2-qc-job-results.html index 59bc8cd..59bc8cd 100644 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html +++ b/uploader/templates/rqtl2/rqtl2-qc-job-results.html diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/rqtl2/rqtl2-qc-job-status.html index f4a6266..f4a6266 100644 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-status.html +++ b/uploader/templates/rqtl2/rqtl2-qc-job-status.html diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/rqtl2/rqtl2-qc-job-success.html index 2861a04..2861a04 100644 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html +++ b/uploader/templates/rqtl2/rqtl2-qc-job-success.html diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html index 873f9c3..873f9c3 100644 --- a/qc_app/templates/rqtl2/select-geno-dataset.html +++ b/uploader/templates/rqtl2/select-geno-dataset.html diff --git a/qc_app/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html index 37731f0..37731f0 100644 --- a/qc_app/templates/rqtl2/select-population.html +++ b/uploader/templates/rqtl2/select-population.html diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/rqtl2/select-probeset-dataset.html index 26f52ed..26f52ed 100644 --- a/qc_app/templates/rqtl2/select-probeset-dataset.html +++ b/uploader/templates/rqtl2/select-probeset-dataset.html diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/rqtl2/select-probeset-study-id.html index b9bf52e..b9bf52e 100644 --- a/qc_app/templates/rqtl2/select-probeset-study-id.html +++ b/uploader/templates/rqtl2/select-probeset-study-id.html diff --git a/qc_app/templates/rqtl2/select-tissue.html b/uploader/templates/rqtl2/select-tissue.html index 34e1758..34e1758 100644 --- a/qc_app/templates/rqtl2/select-tissue.html +++ b/uploader/templates/rqtl2/select-tissue.html diff --git a/qc_app/templates/rqtl2/summary-info.html b/uploader/templates/rqtl2/summary-info.html index 1be87fa..1be87fa 100644 --- a/qc_app/templates/rqtl2/summary-info.html +++ b/uploader/templates/rqtl2/summary-info.html diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html index 07c240f..07c240f 100644 --- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html +++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html index 93b1dc9..93b1dc9 100644 --- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html +++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html diff --git a/qc_app/templates/samples/select-population.html b/uploader/templates/samples/select-population.html index da19ddc..da19ddc 100644 --- a/qc_app/templates/samples/select-population.html +++ b/uploader/templates/samples/select-population.html diff --git a/qc_app/templates/samples/select-species.html b/uploader/templates/samples/select-species.html index edadc61..edadc61 100644 --- a/qc_app/templates/samples/select-species.html +++ b/uploader/templates/samples/select-species.html diff --git a/qc_app/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html index 09e2ecf..09e2ecf 100644 --- a/qc_app/templates/samples/upload-failure.html +++ b/uploader/templates/samples/upload-failure.html diff --git a/qc_app/templates/samples/upload-progress.html b/uploader/templates/samples/upload-progress.html index 7bb02be..7bb02be 100644 --- a/qc_app/templates/samples/upload-progress.html +++ b/uploader/templates/samples/upload-progress.html diff --git a/qc_app/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html index e62de57..e62de57 100644 --- a/qc_app/templates/samples/upload-samples.html +++ b/uploader/templates/samples/upload-samples.html diff --git a/qc_app/templates/samples/upload-success.html b/uploader/templates/samples/upload-success.html index cb745c3..cb745c3 100644 --- a/qc_app/templates/samples/upload-success.html +++ b/uploader/templates/samples/upload-success.html diff --git a/qc_app/templates/select_dataset.html b/uploader/templates/select_dataset.html index 2f07de8..2f07de8 100644 --- a/qc_app/templates/select_dataset.html +++ b/uploader/templates/select_dataset.html diff --git a/qc_app/templates/select_platform.html b/uploader/templates/select_platform.html index d9bc68f..d9bc68f 100644 --- a/qc_app/templates/select_platform.html +++ b/uploader/templates/select_platform.html diff --git a/qc_app/templates/select_species.html b/uploader/templates/select_species.html index 3b1a8a9..3b1a8a9 100644 --- a/qc_app/templates/select_species.html +++ b/uploader/templates/select_species.html diff --git a/qc_app/templates/select_study.html b/uploader/templates/select_study.html index 648ad4c..648ad4c 100644 --- a/qc_app/templates/select_study.html +++ b/uploader/templates/select_study.html diff --git a/qc_app/templates/stdout_output.html b/uploader/templates/stdout_output.html index 85345a9..85345a9 100644 --- a/qc_app/templates/stdout_output.html +++ b/uploader/templates/stdout_output.html diff --git a/qc_app/templates/unhandled_exception.html b/uploader/templates/unhandled_exception.html index 6e6a051..6e6a051 100644 --- a/qc_app/templates/unhandled_exception.html +++ b/uploader/templates/unhandled_exception.html diff --git a/qc_app/templates/upload_progress_indicator.html b/uploader/templates/upload_progress_indicator.html index e274e83..e274e83 100644 --- a/qc_app/templates/upload_progress_indicator.html +++ b/uploader/templates/upload_progress_indicator.html diff --git a/qc_app/templates/worker_failure.html b/uploader/templates/worker_failure.html index b65b140..b65b140 100644 --- a/qc_app/templates/worker_failure.html +++ b/uploader/templates/worker_failure.html diff --git a/qc_app/upload/__init__.py b/uploader/upload/__init__.py index 5f120d4..5f120d4 100644 --- a/qc_app/upload/__init__.py +++ b/uploader/upload/__init__.py diff --git a/qc_app/upload/rqtl2.py b/uploader/upload/rqtl2.py index 51d8321..6aed1f7 100644 --- a/qc_app/upload/rqtl2.py +++ b/uploader/upload/rqtl2.py @@ -27,20 +27,20 @@ from flask import ( from r_qtl import r_qtl2 -from qc_app import jobs -from qc_app.files import save_file, fullpath -from qc_app.dbinsert import species as all_species -from qc_app.db_utils import with_db_connection, database_connection - -from qc_app.db.platforms import platform_by_id, platforms_by_species -from qc_app.db.averaging import averaging_methods, averaging_method_by_id -from qc_app.db.tissues import all_tissues, tissue_by_id, create_new_tissue -from qc_app.db import ( +from uploader import jobs +from uploader.files import save_file, fullpath +from uploader.dbinsert import species as all_species +from uploader.db_utils import with_db_connection, database_connection + +from uploader.db.platforms import platform_by_id, platforms_by_species +from uploader.db.averaging import averaging_methods, averaging_method_by_id +from uploader.db.tissues import all_tissues, tissue_by_id, create_new_tissue +from uploader.db import ( species_by_id, save_population, populations_by_species, population_by_species_and_id,) -from qc_app.db.datasets import ( +from uploader.db.datasets import ( geno_dataset_by_id, geno_datasets_by_species_and_population, |