diff --git a/.github/linters/.pylintrc b/.github/linters/.pylintrc new file mode 100644 index 0000000..bf13f6b --- /dev/null +++ b/.github/linters/.pylintrc @@ -0,0 +1,572 @@ +[MASTER] + +# A comma-separated list of package or module names from where C extensions may +# be loaded. Extensions are loading into the active Python interpreter and may +# run arbitrary code +extension-pkg-whitelist= + +# Add files or directories to the blacklist. They should be base names, not +# paths. +ignore=CVS + +# Add files or directories matching the regex patterns to the blacklist. The +# regex matches against base names, not paths. +ignore-patterns= + +# Python code to execute, usually for sys.path manipulation such as +# pygtk.require(). +#init-hook= + +# Use multiple processes to speed up Pylint. +jobs=1 + +# List of plugins (as comma separated values of python modules names) to load, +# usually to register additional checkers. +load-plugins= + +# Pickle collected data for later comparisons. +persistent=yes + +# Specify a configuration file. +#rcfile= + +# When enabled, pylint would attempt to guess common misconfiguration and emit +# user-friendly hints instead of false-positive error messages +suggestion-mode=yes + +# Allow loading of arbitrary C extensions. Extensions are imported into the +# active Python interpreter and may run arbitrary code. +unsafe-load-any-extension=no + + +[MESSAGES CONTROL] + +# Only show warnings with the listed confidence levels. Leave empty to show +# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED +confidence= + +# Disable the message, report, category or checker with the given id(s). You +# can either give multiple identifiers separated by comma (,) or put this +# option multiple times (only on the command line, not in the configuration +# file where it should appear only once).You can also use "--disable=all" to +# disable everything first and then reenable specific checks. For example, if +# you want to run only the similarities checker, you can use "--disable=all +# --enable=similarities". If you want to run only the classes checker, but have +# no Warning level messages displayed, use"--disable=all --enable=classes +# --disable=W" +disable=print-statement, + parameter-unpacking, + unpacking-in-except, + old-raise-syntax, + backtick, + long-suffix, + old-ne-operator, + old-octal-literal, + import-star-module-level, + non-ascii-bytes-literal, + invalid-unicode-literal, + raw-checker-failed, + bad-inline-option, + locally-disabled, + locally-enabled, + file-ignored, + suppressed-message, + useless-suppression, + deprecated-pragma, + apply-builtin, + basestring-builtin, + buffer-builtin, + cmp-builtin, + coerce-builtin, + execfile-builtin, + file-builtin, + long-builtin, + raw_input-builtin, + reduce-builtin, + standarderror-builtin, + unicode-builtin, + xrange-builtin, + coerce-method, + delslice-method, + getslice-method, + setslice-method, + import-error, + no-absolute-import, + wrong-import-order, + wildcard-import, + no-name-in-module, + old-division, + dict-iter-method, + dict-view-method, + next-method-called, + metaclass-assignment, + indexing-exception, + raising-string, + reload-builtin, + oct-method, + hex-method, + nonzero-method, + cmp-method, + input-builtin, + round-builtin, + intern-builtin, + unichr-builtin, + map-builtin-not-iterating, + zip-builtin-not-iterating, + range-builtin-not-iterating, + filter-builtin-not-iterating, + using-cmp-argument, + eq-without-hash, + div-method, + idiv-method, + rdiv-method, + exception-message-attribute, + invalid-str-codec, + sys-max-int, + bad-python3-import, + deprecated-string-function, + deprecated-str-translate-call, + deprecated-itertools-function, + deprecated-types-field, + next-method-defined, + dict-items-not-iterating, + dict-keys-not-iterating, + dict-values-not-iterating, + deprecated-operator-function, + deprecated-urllib-function, + xreadlines-attribute, + deprecated-sys-function, + exception-escape, + comprehension-escape, + invalid-name, + broad-except, + superfluous-parens, + missing-module-docstring, + missing-class-docstring, + missing-function-docstring, + no-else-return, + useless-return, + unused-wildcard-import, + unused-argument, + unused-variable, + inconsistent-return-statements, + redefined-outer-name, + too-many-locals, + line-too-long, + bad-continuation, + trailing-newlines, + trailing-whitespace, + bad-whitespace + +# Enable the message, report, category or checker with the given id(s). You can +# either give multiple identifier separated by comma (,) or put this option +# multiple time (only on the command line, not in the configuration file where +# it should appear only once). See also the "--disable" option for examples. +enable=c-extension-no-member + + +[REPORTS] + +# Python expression which should return a note less than 10 (10 is the highest +# note). You have access to the variables errors warning, statement which +# respectively contain the number of errors / warnings messages and the total +# number of statements analyzed. This is used by the global evaluation report +# (RP0004). +evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10) + +# Template used to display messages. This is a python new-style format string +# used to format the message information. See doc for all details +#msg-template= + +# Set the output format. Available formats are text, parseable, colorized, json +# and msvs (visual studio).You can also give a reporter class, eg +# mypackage.mymodule.MyReporterClass. +output-format=text + +# Tells whether to display a full report or only the messages +reports=no + +# Activate the evaluation score. +score=yes + + +[REFACTORING] + +# Maximum number of nested blocks for function / method body +max-nested-blocks=5 + +# Complete name of functions that never returns. When checking for +# inconsistent-return-statements if a never returning function is called then +# it will be considered as an explicit return statement and no message will be +# printed. +never-returning-functions=optparse.Values,sys.exit + + +[SPELLING] + +# Limits count of emitted suggestions for spelling mistakes +max-spelling-suggestions=4 + +# Spelling dictionary name. Available dictionaries: none. To make it working +# install python-enchant package. +spelling-dict= + +# List of comma separated words that should not be checked. +spelling-ignore-words= + +# A path to a file that contains private dictionary; one word per line. +spelling-private-dict-file= + +# Tells whether to store unknown words to indicated private dictionary in +# --spelling-private-dict-file option instead of raising a message. +spelling-store-unknown-words=no + + +[FORMAT] + +# Expected format of line ending, e.g. empty (any line ending), LF or CRLF. +expected-line-ending-format= + +# Regexp for a line that is allowed to be longer than the limit. +ignore-long-lines=^\s*(# )??$ + +# Number of spaces of indent required inside a hanging or continued line. +indent-after-paren=4 + +# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1 +# tab). +indent-string=' ' + +# Maximum number of characters on a single line. +max-line-length=100 + +# Maximum number of lines in a module +max-module-lines=1000 + +# List of optional constructs for which whitespace checking is disabled. `dict- +# separator` is used to allow tabulation in dicts, etc.: {1 : 1,\n222: 2}. +# `trailing-comma` allows a space between comma and closing bracket: (a, ). +# `empty-line` allows space-only lines. +no-space-check=trailing-comma, + dict-separator + +# Allow the body of a class to be on the same line as the declaration if body +# contains single statement. +single-line-class-stmt=no + +# Allow the body of an if to be on the same line as the test if there is no +# else. +single-line-if-stmt=no + + +[TYPECHECK] + +# List of decorators that produce context managers, such as +# contextlib.contextmanager. Add to this list to register other decorators that +# produce valid context managers. +contextmanager-decorators=contextlib.contextmanager + +# List of members which are set dynamically and missed by pylint inference +# system, and so shouldn't trigger E1101 when accessed. Python regular +# expressions are accepted. +generated-members= + +# Tells whether missing members accessed in mixin class should be ignored. A +# mixin class is detected if its name ends with "mixin" (case insensitive). +ignore-mixin-members=yes + +# This flag controls whether pylint should warn about no-member and similar +# checks whenever an opaque object is returned when inferring. The inference +# can return multiple potential results while evaluating a Python object, but +# some branches might not be evaluated, which results in partial inference. In +# that case, it might be useful to still emit no-member and other checks for +# the rest of the inferred objects. +ignore-on-opaque-inference=yes + +# List of class names for which member attributes should not be checked (useful +# for classes with dynamically set attributes). This supports the use of +# qualified names. +ignored-classes=optparse.Values,thread._local,_thread._local + +# List of module names for which member attributes should not be checked +# (useful for modules/projects where namespaces are manipulated during runtime +# and thus existing member attributes cannot be deduced by static analysis. It +# supports qualified module names, as well as Unix pattern matching. +ignored-modules= + +# Show a hint with possible names when a member name was not found. The aspect +# of finding the hint is based on edit distance. +missing-member-hint=yes + +# The minimum edit distance a name should have in order to be considered a +# similar match for a missing member name. +missing-member-hint-distance=1 + +# The total number of similar names that should be taken in consideration when +# showing a hint for a missing member. +missing-member-max-choices=1 + + +[MISCELLANEOUS] + +# List of note tags to take in consideration, separated by a comma. +notes=FIXME, + XXX, + TODO + + +[LOGGING] + +# Logging modules to check that the string format arguments are in logging +# function parameter format +logging-modules=logging + + +[SIMILARITIES] + +# Ignore comments when computing similarities. +ignore-comments=yes + +# Ignore docstrings when computing similarities. +ignore-docstrings=yes + +# Ignore imports when computing similarities. +ignore-imports=no + +# Minimum lines number of a similarity. +min-similarity-lines=4 + + +[VARIABLES] + +# List of additional names supposed to be defined in builtins. Remember that +# you should avoid to define new builtins when possible. +additional-builtins= + +# Tells whether unused global variables should be treated as a violation. +allow-global-unused-variables=yes + +# List of strings which can identify a callback function by name. A callback +# name must start or end with one of those strings. +callbacks=cb_, + _cb + +# A regular expression matching the name of dummy variables (i.e. expectedly +# not used). +dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_ + +# Argument names that match this expression will be ignored. Default to name +# with leading underscore +ignored-argument-names=_.*|^ignored_|^unused_ + +# Tells whether we should check for unused import in __init__ files. +init-import=no + +# List of qualified module names which can have objects that can redefine +# builtins. +redefining-builtins-modules=six.moves,past.builtins,future.builtins,io,builtins + + +[BASIC] + +# Naming style matching correct argument names +argument-naming-style=snake_case + +# Regular expression matching correct argument names. Overrides argument- +# naming-style +#argument-rgx= + +# Naming style matching correct attribute names +attr-naming-style=snake_case + +# Regular expression matching correct attribute names. Overrides attr-naming- +# style +#attr-rgx= + +# Bad variable names which should always be refused, separated by a comma +bad-names=foo, + bar, + baz, + toto, + tutu, + tata + +# Naming style matching correct class attribute names +class-attribute-naming-style=any + +# Regular expression matching correct class attribute names. Overrides class- +# attribute-naming-style +#class-attribute-rgx= + +# Naming style matching correct class names +class-naming-style=PascalCase + +# Regular expression matching correct class names. Overrides class-naming-style +#class-rgx= + +# Naming style matching correct constant names +const-naming-style=UPPER_CASE + +# Regular expression matching correct constant names. Overrides const-naming- +# style +#const-rgx= + +# Minimum line length for functions/classes that require docstrings, shorter +# ones are exempt. +docstring-min-length=-1 + +# Naming style matching correct function names +function-naming-style=snake_case + +# Regular expression matching correct function names. Overrides function- +# naming-style +#function-rgx= + +# Good variable names which should always be accepted, separated by a comma +good-names=i, + j, + k, + ex, + Run, + _ + +# Include a hint for the correct naming format with invalid-name +include-naming-hint=no + +# Naming style matching correct inline iteration names +inlinevar-naming-style=any + +# Regular expression matching correct inline iteration names. Overrides +# inlinevar-naming-style +#inlinevar-rgx= + +# Naming style matching correct method names +method-naming-style=snake_case + +# Regular expression matching correct method names. Overrides method-naming- +# style +#method-rgx= + +# Naming style matching correct module names +module-naming-style=snake_case + +# Regular expression matching correct module names. Overrides module-naming- +# style +#module-rgx= + +# Colon-delimited sets of names that determine each other's naming style when +# the name regexes allow several styles. +name-group= + +# Regular expression which should only match function or class names that do +# not require a docstring. +no-docstring-rgx=^_ + +# List of decorators that produce properties, such as abc.abstractproperty. Add +# to this list to register other decorators that produce valid properties. +property-classes=abc.abstractproperty + +# Naming style matching correct variable names +variable-naming-style=snake_case + +# Regular expression matching correct variable names. Overrides variable- +# naming-style +#variable-rgx= + + +[IMPORTS] + +# Allow wildcard imports from modules that define __all__. +allow-wildcard-with-all=no + +# Analyse import fallback blocks. This can be used to support both Python 2 and +# 3 compatible code, which means that the block might have code that exists +# only in one or another interpreter, leading to false positives when analysed. +analyse-fallback-blocks=no + +# Deprecated modules which should not be used, separated by a comma +deprecated-modules=regsub, + TERMIOS, + Bastion, + rexec + +# Create a graph of external dependencies in the given file (report RP0402 must +# not be disabled) +ext-import-graph= + +# Create a graph of every (i.e. internal and external) dependencies in the +# given file (report RP0402 must not be disabled) +import-graph= + +# Create a graph of internal dependencies in the given file (report RP0402 must +# not be disabled) +int-import-graph= + +# Force import order to recognize a module as part of the standard +# compatibility libraries. +known-standard-library= + +# Force import order to recognize a module as part of a third party library. +known-third-party=enchant + + +[DESIGN] + +# Maximum number of arguments for function / method +max-args=5 + +# Maximum number of attributes for a class (see R0902). +max-attributes=7 + +# Maximum number of boolean expressions in a if statement +max-bool-expr=5 + +# Maximum number of branch for function / method body +max-branches=12 + +# Maximum number of locals for function / method body +max-locals=15 + +# Maximum number of parents for a class (see R0901). +max-parents=7 + +# Maximum number of public methods for a class (see R0904). +max-public-methods=20 + +# Maximum number of return / yield for function / method body +max-returns=6 + +# Maximum number of statements in function / method body +max-statements=50 + +# Minimum number of public methods for a class (see R0903). +min-public-methods=2 + + +[CLASSES] + +# List of method names used to declare (i.e. assign) instance attributes. +defining-attr-methods=__init__, + __new__, + setUp + +# List of member names, which should be excluded from the protected access +# warning. +exclude-protected=_asdict, + _fields, + _replace, + _source, + _make + +# List of valid names for the first argument in a class method. +valid-classmethod-first-arg=cls + +# List of valid names for the first argument in a metaclass class method. +valid-metaclass-classmethod-first-arg=mcs + + +[EXCEPTIONS] + +# Exceptions that will emit a warning when being caught. Defaults to +# "Exception" +overgeneral-exceptions=Exception diff --git a/.github/workflows/interface_test.yml b/.github/workflows/interface_test.yml new file mode 100644 index 0000000..8d40246 --- /dev/null +++ b/.github/workflows/interface_test.yml @@ -0,0 +1,36 @@ +name: YABA interface tests + +on: + push: + pull_request: + branches: [ master ] + +jobs: + interface_test: + + runs-on: ubuntu-latest + defaults: + run: + working-directory: interface + + strategy: + matrix: + node-version: [12.x, 14.x] + + steps: + - name: Checkout repository + uses: actions/checkout@v2 + + - name: Set up Node.js ${{ matrix.node-version }} + uses: actions/setup-node@v1 + with: + node-version: ${{ matrix.node-version }} + + - name: Install dependencies + run: npm install + + - name: Run the tests and generate coverage report + run: npm test -- --coverage + + - name: Upload coverage to Codecov + uses: codecov/codecov-action@v1 \ No newline at end of file diff --git a/.github/workflows/linter.yml b/.github/workflows/linter.yml new file mode 100644 index 0000000..1a394d3 --- /dev/null +++ b/.github/workflows/linter.yml @@ -0,0 +1,25 @@ +name: YABA Code Linter + +on: + push: + pull_request: + branches: [ master ] + +jobs: + lint: + + runs-on: ubuntu-latest + + steps: + - name: Checkout Code + uses: actions/checkout@v2 + + - name: Lint Code Base + uses: docker://github/super-linter:v3 + env: + PYTHON_PYLINT_CONFIG_FILE: .pylintrc + VALIDATE_ALL_CODEBASE: false + VALIDATE_PYTHON_PYLINT: true + VALIDATE_JAVASCRIPT_ES: true + DEFAULT_BRANCH: master + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file diff --git a/.github/workflows/py_tests.yml b/.github/workflows/py_tests.yml new file mode 100644 index 0000000..1dad83b --- /dev/null +++ b/.github/workflows/py_tests.yml @@ -0,0 +1,54 @@ +# This workflow will install Python dependencies, run tests and lint with a single version of Python +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: YABA app and client tests + +on: + push: + pull_request: + branches: [ master ] + +jobs: + py_test: + + runs-on: ubuntu-latest + strategy: + matrix: + code: [ app, client] + include: + - code: app + path: ./yaba_test/test_yaba.py + - code: client + path: ./yaba_client_test/test_yaba_client.py + + steps: + - name: Checkout Code + uses: actions/checkout@v2 + + - name: Set up Python 3.7 + uses: actions/setup-python@v2 + with: + python-version: 3.7 + + - name: Install dependencies + run: | + pip install --upgrade pip + pip install pytest + pip install pytest-cov + pip install docker-compose + + - name: Set-up the project + run: | + docker-compose up -d postgres + docker-compose run --rm bety initialize + docker-compose up -d + docker ps -a + docker logs betydb-yaba_yaba_api_1 + + - name: Test with pytest and generate coverage report + run: | + sleep 20 + pytest --cov= ${{ matrix.path }} --cov-report=xml + + - name: Upload coverage to Codecov + uses: codecov/codecov-action@v1 \ No newline at end of file diff --git a/.gitignore b/.gitignore index 87b4475..7f8551b 100644 --- a/.gitignore +++ b/.gitignore @@ -104,4 +104,4 @@ venv.bak/ .mypy_cache/ # node modules -node_modules/ \ No newline at end of file +node_modules/ diff --git a/app/Meta.py b/app/Meta.py index a722752..f433373 100644 --- a/app/Meta.py +++ b/app/Meta.py @@ -7,9 +7,7 @@ import traceback import logging import pandas as pd - -from flask import make_response,Response,jsonify -from flask import json +from flask import make_response,jsonify from db import * from werkzeug import secure_filename,FileStorage from sqlalchemy.exc import IntegrityError @@ -329,7 +327,7 @@ def insert_citations(username,fileName): insert_table(table='citations',data=data) msg = {'Message' : 'Successfully inserted', 'Table Affected' : 'Citations', - 'Lines Inserted': data.shape[0]} + 'Lines Inserted': data.shape[0]} return make_response(jsonify(msg), 201) @@ -379,7 +377,7 @@ def insert_experimentSites(fileName): insert_table(table='experiments_sites',data=new_data) msg = {'Message' : 'Successfully inserted', 'Table Affected' : 'Experiments_sites', - 'Lines Inserted': data.shape[0]} + 'Lines Inserted': data.shape[0]} return make_response(jsonify(msg), 201) @@ -431,7 +429,7 @@ def insert_experimentTreatments(fileName): insert_table(table='experiments_treatments',data=new_data) msg = {'Message' : 'Successfully inserted', 'Table Affected' : 'Experiments_treatments', - 'Lines Inserted': data.shape[0]} + 'Lines Inserted': data.shape[0]} return make_response(jsonify(msg), 201) @@ -535,14 +533,12 @@ def insert_citationsSites(fileName): insert_table(table='citations_sites',data=new_data) msg = {'Message' : 'Successfully inserted', 'Table Affected' : 'Citations_sites', - 'col' : columns, 'Lines Inserted': data.shape[0]} return make_response(jsonify(msg), 201) else: msg = {'Message' : 'File not acceptable and Check the format of file or columns', - 'col' : columns, 'Table':'citations_sites'} return make_response(jsonify(msg), 400) diff --git a/app/requirements.txt b/app/requirements.txt index 29de8a6..ccdf53a 100644 --- a/app/requirements.txt +++ b/app/requirements.txt @@ -2,7 +2,7 @@ requests==2.20.0 psycopg2-binary WSGIserver gevent -pandas +pandas==0.24.2 connexion==2.2.0 Flask==1.0 Werkzeug==0.15.3 diff --git a/app/server.py b/app/server.py index 61e6ef8..063cd9e 100644 --- a/app/server.py +++ b/app/server.py @@ -6,6 +6,7 @@ import connexion import json from time import sleep +from flask import Response # Create the application instance app = connexion.App(__name__, specification_dir="./") diff --git a/client/client.py b/client/client.py index 12cc129..5c85cb9 100644 --- a/client/client.py +++ b/client/client.py @@ -3,14 +3,12 @@ ################# import requests -from flask import Flask, g, render_template,request,redirect,Response,flash,jsonify, make_response -from flask import request +from flask import Flask, render_template,request,redirect,Response,flash import logging -import json from time import sleep -import sys -from flask_cors import CORS, cross_origin + +from flask_cors import CORS # Create app app = Flask(__name__) @@ -18,7 +16,8 @@ # The maximum allowed payload to 16 megabytes. app.config['MAX_CONTENT_LENGTH'] = 16 * 1024 * 1024 -cors = CORS(app, resources={r'/*': {'origins': '*'}}) +cors = CORS(app, resources={r'/*': {'origins': 'http://localhost:3001'}}) + logging.getLogger('flask_cors').level = logging.DEBUG ALLOWED_EXTENSIONS = set(['csv', 'xls','xlsx']) diff --git a/client/requirements.txt b/client/requirements.txt index 5f41371..e09aaca 100644 --- a/client/requirements.txt +++ b/client/requirements.txt @@ -1,2 +1,3 @@ Flask==1.0 requests==2.20.0 +flask-cors \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index abb7a22..5bd11b3 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -48,6 +48,35 @@ services: - 6001:6000 depends_on: - yaba_api + + yaba_visualization: + build: ./visualization + networks: + - bety + volumes: + - './visualization:/code' + - '/code/node_modules' + ports: + - 8008:8075 + depends_on: + - postgres + + yaba_interface: + build: ./interface + networks: + - bety + volumes: + - './interface:/code' + - '/code/node_modules' + ports: + - 3001:3000 + environment: + - CHOKIDAR_USEPOLLING=true + depends_on: + - yaba_client + - yaba_visualization + stdin_open: true + volumes: postgres: diff --git a/interface/.dockerignore b/interface/.dockerignore new file mode 100644 index 0000000..b512c09 --- /dev/null +++ b/interface/.dockerignore @@ -0,0 +1 @@ +node_modules \ No newline at end of file diff --git a/interface/Dockerfile b/interface/Dockerfile new file mode 100644 index 0000000..1ade404 --- /dev/null +++ b/interface/Dockerfile @@ -0,0 +1,16 @@ +FROM node:12.18.2-alpine + +COPY . /code + +WORKDIR /code + +ENV PATH /code/node_modules/.bin:$PATH + +RUN npm install --silent + +RUN npm install react-scripts@1.1.1 -g --silent + +EXPOSE 3000 + +# start app +CMD ["npm", "start"] \ No newline at end of file diff --git a/interface/public/index.html b/interface/public/index.html index 8b9861a..7357cbc 100644 --- a/interface/public/index.html +++ b/interface/public/index.html @@ -2,14 +2,14 @@ - + - + - React App + BETYdb-YABA Interface diff --git a/interface/src/App.test.js b/interface/src/App.test.js deleted file mode 100644 index 4db7ebc..0000000 --- a/interface/src/App.test.js +++ /dev/null @@ -1,9 +0,0 @@ -import React from 'react'; -import { render } from '@testing-library/react'; -import App from './App'; - -test('renders learn react link', () => { - const { getByText } = render(); - const linkElement = getByText(/learn react/i); - expect(linkElement).toBeInTheDocument(); -}); diff --git a/interface/src/components/grid.js b/interface/src/components/grid.js index 0bca424..24c37fa 100644 --- a/interface/src/components/grid.js +++ b/interface/src/components/grid.js @@ -31,8 +31,8 @@ class Grid extends Component{ if(!label.includes(data[i][type])){ label.push(data[i][type]) } - } - + } + color= getRandomColors(label.length) let plots = new Array(); let xpos = 1; //starting xpos and ypos at 1 so the stroke will show when we make the grid below diff --git a/interface/src/components/requests.js b/interface/src/components/requests.js index 10f2603..5a135e6 100644 --- a/interface/src/components/requests.js +++ b/interface/src/components/requests.js @@ -29,7 +29,7 @@ export function getVisualData(files, type, username){ params= 'getTreatmentSites' } - let res= fetch(`http://localhost:3001/${params}`, { + let res= fetch(`http://localhost:8008/${params}`, { method: 'POST', body: formData, redirect: 'follow' @@ -48,7 +48,7 @@ export function getGeoJSON(file){ formData.append("shp_file", file); - let res= fetch("http://localhost:3001/getGeoJSON", { + let res= fetch("http://localhost:8008/getGeoJSON", { method: 'POST', body: formData, redirect: 'follow' @@ -98,7 +98,7 @@ function getGeoFile(zip_file, file_type){ redirect: 'follow' }; - const res = fetch("http://localhost:3001/getGeoFile", requestOptions) + const res = fetch("http://localhost:8008/getGeoFile", requestOptions) .then(response => new File([response.blob()], `${file_type}_file.${file_type}`)) .catch(error => { throw Error(error) diff --git a/interface/src/setupTests.js b/interface/src/setupTests.js index bf5489f..51f6616 100644 --- a/interface/src/setupTests.js +++ b/interface/src/setupTests.js @@ -5,4 +5,4 @@ import '@testing-library/jest-dom/extend-expect'; import { configure } from 'enzyme'; import Adapter from 'enzyme-adapter-react-16'; -configure({ adapter: new Adapter() }); \ No newline at end of file +configure({ adapter: new Adapter() }); diff --git a/visualization/.dockerignore b/visualization/.dockerignore new file mode 100644 index 0000000..b512c09 --- /dev/null +++ b/visualization/.dockerignore @@ -0,0 +1 @@ +node_modules \ No newline at end of file diff --git a/visualization/Dockerfile b/visualization/Dockerfile new file mode 100644 index 0000000..b0abd15 --- /dev/null +++ b/visualization/Dockerfile @@ -0,0 +1,14 @@ +FROM node:12.18.2-alpine + +COPY . /code + +WORKDIR /code + +ENV PATH /code/node_modules/.bin:$PATH + +RUN npm install --silent + +EXPOSE 8075 + +# start app +CMD ["npm", "start"] \ No newline at end of file diff --git a/visualization/index.js b/visualization/index.js index 12b42e9..859c071 100644 --- a/visualization/index.js +++ b/visualization/index.js @@ -1,6 +1,7 @@ const express = require('express') const app = express() -const port = 3001 +const port = 8075 +const host = '0.0.0.0' const { getCultivarSites, getExperimentSites, getTreatmentSites } = require('./pg_joins') const { shapeParser }= require('./shape-parser') const { sheetToCsv }= require('./sheet-parser') @@ -13,7 +14,7 @@ const path= require('path') app.use(express.static('dist')) app.use(express.json()) app.use(function (req, res, next) { - res.setHeader('Access-Control-Allow-Origin', 'http://localhost:3000'); + res.setHeader('Access-Control-Allow-Origin', 'http://localhost:3001'); res.setHeader('Access-Control-Allow-Methods', 'GET,POST,PUT,DELETE,OPTIONS'); res.setHeader('Access-Control-Allow-Headers', 'Content-Type, Access-Control-Allow-Headers'); next(); @@ -169,6 +170,6 @@ app.post('/sheetToCsv', async(req, res) => { let csvFile= await sheetToCsv(sheet) }) -app.listen(port, () => { +app.listen(port, host,() => { console.log(`App running on port ${port}.`) }) \ No newline at end of file diff --git a/visualization/pg_joins.js b/visualization/pg_joins.js index f826cd8..9d0443a 100644 --- a/visualization/pg_joins.js +++ b/visualization/pg_joins.js @@ -5,8 +5,8 @@ const pool = new Pool({ user: 'bety', database: 'bety', password: '', - host: 'localhost', - port: 9000, + host: 'postgres', + port: 5432, }); const fetch_Id= async (client, value,table)=>{