diff --git a/README.md b/README.md index caef7f86ac..811157100a 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# Augur NEW Release v0.51.0 +# Augur NEW Release v0.51.1 [![first-timers-only](https://img.shields.io/badge/first--timers--only-friendly-blue.svg?style=flat-square)](https://www.firsttimersonly.com/) We follow the [First Timers Only](https://www.firsttimersonly.com/) philosophy of tagging issues for first timers only, and walking one newcomer through the resolution process weekly. [You can find these issues tagged with "first timers only" on our issues list.](https://github.com/chaoss/augur/labels/first-timers-only). @@ -8,7 +8,7 @@ ### [If you want to jump right in, updated docker build/compose and bare metal installation instructions are available here](docs/new-install.md) -Augur is now releasing a dramatically improved new version to the main branch. It is also available here: https://github.com/chaoss/augur/releases/tag/v0.51.0 +Augur is now releasing a dramatically improved new version to the main branch. It is also available here: https://github.com/chaoss/augur/releases/tag/v0.51.1 - The `main` branch is a stable version of our new architecture, which features: - Dramatic improvement in the speed of large scale data collection (100,000+ repos). All data is obtained for 100k+ repos within 2 weeks. - A new job management architecture that uses Celery and Redis to manage queues, and enables users to run a Flower job monitoring dashboard diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 51220fcf12..dfaeb81f7f 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -2,28 +2,19 @@ """ Creates routes for user functionality """ +from augur.api.routes import AUGUR_API_VERSION import logging -import requests -import os -import base64 -import time import secrets -import pandas as pd -from flask import request, Response, jsonify, session +from flask import request, jsonify, session from flask_login import login_user, logout_user, current_user, login_required from werkzeug.security import check_password_hash -from sqlalchemy.sql import text from sqlalchemy.orm import sessionmaker -from sqlalchemy.orm.exc import NoResultFound from augur.application.db.session import DatabaseSession -from augur.tasks.github.util.github_task_session import GithubTaskSession -from augur.util.repo_load_controller import RepoLoadController from augur.api.util import api_key_required from augur.api.util import ssl_required -from augur.application.db.models import User, UserRepo, UserGroup, UserSessionToken, ClientApplication, RefreshToken -from augur.application.config import get_development_flag +from augur.application.db.models import User, UserSessionToken, RefreshToken from augur.tasks.init.redis_connection import redis_connection as redis from ..server import app, engine @@ -31,9 +22,6 @@ current_user: User = current_user Session = sessionmaker(bind=engine) -from augur.api.routes import AUGUR_API_VERSION - - @app.route(f"/{AUGUR_API_VERSION}/user/validate", methods=['POST']) @ssl_required def validate_user(): @@ -51,7 +39,7 @@ def validate_user(): return jsonify({"status": "Invalid username"}) checkPassword = check_password_hash(user.login_hashword, password) - if checkPassword == False: + if not checkPassword: return jsonify({"status": "Invalid password"}) @@ -89,9 +77,9 @@ def generate_session(application): code = request.args.get("code") or request.form.get("code") if not code: return jsonify({"status": "Missing argument: code"}), 400 - + grant_type = request.args.get("grant_type") or request.form.get("grant_type") - + if "code" not in grant_type: return jsonify({"status": "Invalid grant type"}) @@ -131,7 +119,7 @@ def refresh_session(application): if not refresh_token_str: return jsonify({"status": "Missing argument: refresh_token"}), 400 - + if request.args.get("grant_type") != "refresh_token": return jsonify({"status": "Invalid grant type"}) @@ -139,17 +127,17 @@ def refresh_session(application): refresh_token = session.query(RefreshToken).filter(RefreshToken.id == refresh_token_str).first() if not refresh_token: - return jsonify({"status": "Invalid refresh token"}) + return jsonify({"status": "Invalid refresh token"}), 400 if refresh_token.user_session.application != application: - return jsonify({"status": "Invalid application"}) + return jsonify({"status": "Invalid application"}), 400 user_session = refresh_token.user_session user = user_session.user new_user_session_token = UserSessionToken.create(session, user.user_id, user_session.application.id).token new_refresh_token_id = RefreshToken.create(session, new_user_session_token).id - + session.delete(refresh_token) session.delete(user_session) session.commit() @@ -327,11 +315,11 @@ def group_repos(): result_dict = result[1] if result[0] is not None: - + for repo in result[0]: repo["base64_url"] = str(repo["base64_url"].decode()) - result_dict.update({"repos": result[0]}) + result_dict.update({"repos": result[0]}) return jsonify(result_dict) @@ -436,7 +424,7 @@ def toggle_user_group_favorite(): Returns ------- dict - A dictionairy with key of 'status' that indicates the success or failure of the operation + A dictionary with key of 'status' that indicates the success or failure of the operation """ group_name = request.args.get("group_name") diff --git a/augur/api/view/augur_view.py b/augur/api/view/augur_view.py index 268c1bed57..b39d698452 100644 --- a/augur/api/view/augur_view.py +++ b/augur/api/view/augur_view.py @@ -29,7 +29,7 @@ def page_not_found(error): if AUGUR_API_VERSION in str(request.path): return jsonify({"status": "Not Found"}), 404 - return render_template('index.j2', title='404', api_url=getSetting('serving')), 404 + return render_template('index.j2', title='404'), 404 @app.errorhandler(405) def unsupported_method(error): diff --git a/augur/api/view/init.py b/augur/api/view/init.py index 210dc60e08..cbe6d139ac 100644 --- a/augur/api/view/init.py +++ b/augur/api/view/init.py @@ -8,8 +8,6 @@ # load configuration files and initialize globals configFile = Path(env.setdefault("CONFIG_LOCATION", "config.yml")) -version = {"major": 0, "minor": 0.1, "series": "Alpha"} - report_requests = {} settings = {} @@ -22,7 +20,6 @@ def init_settings(): settings["pagination_offset"] = 25 settings["reports"] = "reports.yml" settings["session_key"] = secrets.token_hex() - settings["version"] = version def write_settings(current_settings): current_settings["caching"] = str(current_settings["caching"]) @@ -33,55 +30,6 @@ def write_settings(current_settings): with open(configFile, 'w') as file: yaml.dump(current_settings, file) -""" ---------------------------------------------------------------- -""" -def version_check(current_settings): - def to_version_string(version_object): - if version_object is None: - return "Undefined_version" - return f'{version_object["major"]}-{version_object["minor"]}-{version_object["series"]}' - - def update_from(old): - if old == None: - if "pagination_offset" not in current_settings: - current_settings["pagination_offset"] = current_settings.pop("paginationOffset") - if "session_key" not in current_settings: - current_settings["session_key"] = secrets.token_hex() - - else: - raise ValueError(f"Updating from {to_version_string(old)} to {to_version_string(version)} is unsupported") - - current_settings["version"] = version - write_settings(current_settings) - logger.info(f"Configuration updated from {to_version_string(old)} to {to_version_string(version)}") - - def compare_versions(old, new): - if old["major"] < new["major"]: - return -1, old["series"] == new["series"] - elif old["major"] > new["major"]: - return 1, old["series"] == new["series"] - elif old["minor"] < new["minor"]: - return -1, old["series"] == new["series"] - elif old["minor"] > new["minor"]: - return 1, old["series"] == new["series"] - return 0, old["series"] == new["series"] - - if "version" not in current_settings: - update_from(None) - - version_diff = compare_versions(current_settings["version"], version) - - if current_settings["version"] == version: - return - elif version_diff[0] == -1: - update_from(current_settings["version"]) - elif version_diff[0] == 1: - raise ValueError("Downgrading configuration versions is unsupported: " + - f"from {to_version_string(current_settings['version'])} to {to_version_string(version)}") - - global settings - settings = current_settings - # default reports definition reports = { "pull_request_reports":[ diff --git a/augur/api/view/routes.py b/augur/api/view/routes.py index 3e62dbfd94..8a9fc0597c 100644 --- a/augur/api/view/routes.py +++ b/augur/api/view/routes.py @@ -79,11 +79,7 @@ def repo_table_view(): else: data = get_all_repos(page = page, sort = sorting, direction = direction, search=query)[0] page_count = (get_all_repos_count(search = query)[0] or 0) // pagination_offset - - #if not cacheFileExists("repos.json"): - # return renderLoading("repos/views/table", query, "repos.json") - # return renderRepos("table", query, data, sorting, rev, page, True) return render_module("repos-table", title="Repos", repos=data, query_key=query, activePage=page, pages=page_count, offset=pagination_offset, PS="repo_table_view", reverse = rev, sorting = sorting) """ ---------------------------------------------------------------- @@ -102,31 +98,6 @@ def repo_card_view(): return renderRepos("card", query, data, filter = True) -""" ---------------------------------------------------------------- -groups: - This route returns the groups table view, listing all the current - groups in the backend -""" -# @app.route('/groups') -# @app.route('/groups/') -# def repo_groups_view(group=None): -# query = request.args.get('q') -# page = request.args.get('p') - -# if(group is not None): -# query = group - -# if(query is not None): -# buffer = [] -# data = requestJson("repos") -# for repo in data: -# if query == str(repo["repo_group_id"]) or query in repo["rg_name"]: -# buffer.append(repo) -# return renderRepos("table", query, buffer, page = page, pageSource = "repo_groups_view") -# else: -# groups = requestJson("repo-groups") -# return render_template('index.html', body="groups-table", title="Groups", groups=groups, query_key=query, api_url=getSetting('serving')) - """ ---------------------------------------------------------------- status: This route returns the status view, which displays information @@ -346,13 +317,6 @@ def user_group_view(group = None): page_count = current_user.get_group_repo_count(group, search = query)[0] or 0 page_count //= pagination_offset - # if not data: - # return render_message("Error Loading Group", "Either the group you requested does not exist, the group has no repos, or an unspecified error occurred.") - - #if not cacheFileExists("repos.json"): - # return renderLoading("repos/views/table", query, "repos.json") - - # return renderRepos("table", None, data, sort, rev, params.get("page"), True) return render_module("user-group-repos-table", title="Repos", repos=data, query_key=query, activePage=params["page"], pages=page_count, offset=pagination_offset, PS="user_group_view", reverse = rev, sorting = params.get("sort"), group=group) @app.route('/error') diff --git a/augur/api/view/server/User.py b/augur/api/view/server/User.py deleted file mode 100644 index 4889922ce1..0000000000 --- a/augur/api/view/server/User.py +++ /dev/null @@ -1,276 +0,0 @@ -from flask_login import UserMixin -# I'm using requests here to avoid circular integration with utils -import requests, time, re - -""" ---------------------------------------------------------------- -""" -class User(UserMixin): - # User.api is set in utils.py - # User.logger is set in utils.py - - @property - def is_authenticated(self): - return self._is_authenticated - - @is_authenticated.setter - def is_authenticated(self, val): - self._is_authenticated = val - - @property - def is_active(self): - return self._is_active - - @is_active.setter - def is_active(self, val): - self._is_active = val - - @property - def is_anoymous(self): - return self._is_anoymous - - @is_anoymous.setter - def is_anoymous(self, val): - self._is_anoymous = val - - @property - def exists(self): - return self._exists - - @property - def default_group(self): - if not self.is_authenticated: - return None - elif self._default_group: - return self._default_group - - group_name = self.id + "_default" - groups = self.get_groups() - - if group_name not in groups: - if not self.add_repo_group(group_name): - User.logger.warning("Default user group does not exist, and could not be created") - return None - - self._default_group = group_name - return group_name - - def __init__(self, id): - # flask_login requires that the id be of type string - self.id = str(id) - self._exists = False - self._is_anonymous = False - self._is_authenticated = False - self._is_active = False - self._default_group = None - - # Query the server for the existence of this user - self.query_user() - - def query_user(self): - if self._exists: - # User has already been queried and verified to exist - return True - - endpoint = User.api + "/user/query" - - response = requests.post(endpoint, params = {"username": self.id}) - - if response.status_code == 200 and response.json().get("status") == True: - self._exists = True - return True - - return False - - def get_id(self): - return self.id - - def query_repos(self, group = None): - endpoint = User.api + "/user/repos" - - if not group: - group = self.default_group - - response = requests.post(endpoint, params = {"username": self.id}) - - if response.status_code == 200: - data = response.json() - if data.get("status") == "success": - return data.get("repo_ids") - else: - User.logger.warning(f"Could not get user repos: {data.get('status')}") - else: - User.logger.warning(f"Could not get user repos: {response.status_code}") - - def try_add_url(self, url, group = None): - repo = re.search("https?:\/\/github\.com\/([A-Za-z0-9 \- _]+)\/([A-Za-z0-9 \- _]+)(.git)?\/?$", url) - org = re.search("https?:\/\/github\.com\/([A-Za-z0-9 \- _]+)\/?$", url) - - if repo: - return self.add_repo(url, group) - elif org: - return self.add_org(url, group) - - return False - - def add_repo(self, url, group = None): - endpoint = User.api + "/user/add_repo" - - if not group: - group = self.default_group - - response = requests.post(endpoint, params = {"username": self.id, "repo_url": url}) - - if response.status_code == 200: - data = response.json() - if data.get("status") == "Repo Added": - return True - else: - User.logger.warning(f"Could not add user repo {url}: {data.get('status')}") - else: - User.logger.warning(f"Could not add user repo {url}: {response.status_code}") - - return False - - def add_org(self, url, group = None): - endpoint = User.api + "/user/add_org" - - response = requests.post(endpoint, params = {"username": self.id, "org_url": url}) - - if response.status_code == 200: - data = response.json() - if data.get("status") == "Org repos added": - return True - else: - User.logger.warning(f"Could not add user org {url}: {data.get('status')}") - else: - User.logger.warning(f"Could not add user org {url}: {response.status_code}") - - return False - - def get_groups(self): - endpoint = User.api + "/user/groups" - - response = requests.post(endpoint, params = {"username": self.id}) - - if response.status_code == 200: - return response.json() - else: - data = response.json() - User.logger.warning(f"Could not get user groups: {data.get('status')}") - - def add_repo_group(self, group_name): - endpoint = User.api + "/user/add_group" - - response = requests.post(endpoint, params = {"username": self.id, "group_name": group_name}) - - if response.status_code == 200: - data = response.json() - if data.get("status") == "Group created": - return True - else: - User.logger.warning(f"Could not add user group: {data.get('status')}") - else: - User.logger.warning(f"Could not add user group: {response.status_code}") - - def remove_repo_group(self, group_name): - endpoint = User.api + "/user/remove_group" - - response = requests.post(endpoint, params = {"username": self.id, "group_name": group_name}) - - if response.status_code == 200: - data = response.json() - if data.get("status") == "Group deleted": - return True - else: - User.logger.warning(f"Could not remove user group: {data.get('status')}") - else: - User.logger.warning(f"Could not remove user group: {response.status_code}") - - def select_group(self, group_name, **kwargs): - endpoint = User.api + "/user/group_repos" - - kwargs["username"] = self.id - kwargs["group_name"] = group_name - - response = requests.post(endpoint, params = kwargs) - - if response.status_code == 200: - return response.json() - elif response.status_code == 400: - data = response.json() - User.logger.warning(f"Could not select user group {group_name}: {data.get('status')}") - else: - User.logger.warning(f"Could not select user group {group_name}: {response.status_code}") - - def register(self, request): - endpoint = User.api + "/user/create" - - data = request.form.to_dict() - - # admin creation is CLI only for now - if "create_admin" in data: - data.pop("create_admin") - - response = requests.post(endpoint, params = request.form.to_dict()) - - if response.status_code == 200: - return True - elif response.status_code != 200: - User.logger.debug(f"Could not register user: {response.status_code}") - else: # :/ - User.logger.debug(f"Could not register user: {response.json()['status']}") - - return False - - def validate(self, request): - endpoint = User.api + "/user/validate" - - response = requests.post(endpoint, params = request.form.to_dict()) - - if response.status_code == 200 and response.json()["status"] == "Validated": - self._is_authenticated = True - self._is_active = True - return True - elif response.status_code != 200: - User.logger.debug(f"Could not validate user: {response.status_code}") - else: - User.logger.debug(f"Could not validate user: {response.json()['status']}") - - - # Avoid abuse by malicious actors - time.sleep(2) - return False - - def update_password(self, request): - endpoint = User.api + "/user/update" - - data = request.form.to_dict() - data["username"] = self.id - - response = requests.post(endpoint, params = data) - - if response.status_code == 200 and "Updated" in response.json()["status"]: - return True - elif response.status_code != 200: - User.logger.debug(f"Could not update user password: {response.status_code}") - else: - User.logger.debug(f"Could not update user password: {response.json()['status']}") - - return False - - def delete(self): - endpoint = User.api + "/user/remove" - - response = requests.delete(endpoint, params = {"username": self.id}) - - if response.status_code == 200: - return True - elif response.status_code != 200: - User.logger.debug(f"Could not remove user: {response.status_code}") - else: - User.logger.debug(f"Could not remove user: {response.json()['status']}") - - return False - - def __str__(self) -> str: - return f"" diff --git a/augur/api/view/server/__init__.py b/augur/api/view/server/__init__.py index 287457c4fd..2a54a556f7 100644 --- a/augur/api/view/server/__init__.py +++ b/augur/api/view/server/__init__.py @@ -1,4 +1,3 @@ from .Environment import Environment -from .User import User from .ServerThread import ServerThread from .LoginException import LoginException diff --git a/augur/api/view/url_converters.py b/augur/api/view/url_converters.py index 4d43a411f6..d7b473ea1e 100644 --- a/augur/api/view/url_converters.py +++ b/augur/api/view/url_converters.py @@ -11,9 +11,9 @@ def to_url(self, values): class BoolConverter(BaseConverter): def to_python(self, value): - if value == "False": + if value.lower() in ["false", "f", "n", "0"]: return False - elif value == "True": + elif value.lower() in ["true", "t", "y", "1"]: return True def to_url(self, value): diff --git a/augur/api/view/utils.py b/augur/api/view/utils.py index a8e6998f9a..2289355743 100644 --- a/augur/api/view/utils.py +++ b/augur/api/view/utils.py @@ -2,7 +2,6 @@ from concurrent.futures import ThreadPoolExecutor from flask import render_template, flash, url_for, Flask from .init import * -from .server import User from ..server import app, db_session from augur.application.config import AugurConfig import urllib.request, urllib.error, json, os, math, yaml, urllib3, time, logging, re @@ -13,72 +12,6 @@ config = AugurConfig(logger, db_session) -def parse_url(url): - from urllib.parse import urlparse - - # localhost is not a valid host - if "localhost" in url: - url = url.replace("localhost", "127.0.0.1") - - if not url.startswith("http"): - url = f"http://{url}" - - parts = urlparse(url) - directories = parts.path.strip('/').split('/') - queries = parts.query.strip('&').split('&') - - elements = { - 'scheme': parts.scheme, - 'netloc': parts.netloc, - 'path': parts.path, - 'params': parts.params, - 'query': parts.query, - 'fragment': parts.fragment - } - - return elements, directories, queries - -def validate_api_url(url): - from urllib.parse import urlunparse - - parts = parse_url(url)[0] - - if not parts["scheme"]: - parts["scheme"] = "http" - - staged_url = urlunparse(parts.values()) - - def is_status_ok(): - try: - with urllib.request.urlopen(staged_url) as request: - response = json.loads(request.read().decode()) - if "status" in response: - return request.url - except Exception as e: - logger.error(f"Error during serving URL verification: {str(e)}") - - return False - - status = is_status_ok() - if not status: - if "/api/unstable" not in parts["path"]: - # The URL does not point directly to the API - # try once more with a new suffix - parts["path"] = str(Path(parts["path"]).joinpath("api/unstable")) - staged_url = urlunparse(parts.values()) - - status = is_status_ok() - if not status: - # The URL does not point to a valid augur instance - return "" - else: - return status - else: - return "" - - return status - - """ ---------------------------------------------------------------- loadSettings: This function attempts to load the application settings from the config file @@ -121,14 +54,6 @@ def loadSettings(): # Use the resolved path for cache directory access settings["caching"] = cachePath - staged_url = validate_api_url(settings["serving"]) - if staged_url: - settings["serving"] = re.sub("/$", "", staged_url) - settings["valid"] = True - else: - settings["valid"] = False - raise ValueError(f"The provided serving URL is not valid: {settings['serving']}") - """ ---------------------------------------------------------------- """ def getSetting(key, section = "View"): @@ -141,11 +66,6 @@ def getSetting(key, section = "View"): loadSettings() -User.api = getSetting("serving") -User.logger = logger - -version_check(settings) - """ ---------------------------------------------------------------- """ def loadReports(): @@ -195,9 +115,6 @@ def cacheFileExists(filename): else: return False -def stripStatic(url): - return url.replace("static/", "") - """ ---------------------------------------------------------------- """ def toCacheFilename(endpoint, append = True): @@ -209,67 +126,6 @@ def toCacheFilepath(endpoint, append = True): def toCacheURL(endpoint): return getSetting('approot') + str(toCacheFilepath(endpoint)) -""" ---------------------------------------------------------------- -requestJson: - Attempts to load JSON data from cache for the given endpoint. - If no cache file is found, a request is made to the URL for - the given endpoint and, if successful, the resulting JSON is - cached for future use. Cached files will be stored with all - '/' characters replaced with '.' for filesystem compatibility. - -@PARAM: endpoint: String - A String representation of the requested - json endpoint (relative to the api root). - -@RETURN: data: JSON - An object representing the JSON data read - from either the cache file or the enpoint - URL. Will return None if an error isreturn None - encountered. -""" -def requestJson(endpoint, cached = True): - filename = toCacheFilepath(endpoint) - requestURL = getSetting('serving') + "/" + endpoint - logger.info(f'requesting json from: {endpoint}') - try: - if cached and cacheFileExists(filename): - with open(filename) as f: - data = json.load(f) - else: - with urllib.request.urlopen(requestURL) as url: - if url.getcode() != 200: - raise urllib.error.HTTPError(code = url.getcode()) - - data = json.loads(url.read().decode()) - - if cached: - with open(filename, 'w') as f: - json.dump(data, f) - if filename in cache_files_requested: - cache_files_requested.remove(filename) - return data - except Exception as err: - logger.error("An exception occurred while fulfilling a json request") - logger.error(err) - return False, str(err) - -""" ---------------------------------------------------------------- -""" -def requestPNG(endpoint): - filename = toCacheFilepath(endpoint) - requestURL = getSetting('serving') + "/" + endpoint - try: - if cacheFileExists(filename): - return toCacheURL(endpoint) - else: - urllib.request.urlretrieve(requestURL, filename) - if filename in cache_files_requested: - cache_files_requested.remove(filename) - return toCacheURL(endpoint) - except Exception as err: - logger.error("An exception occurred while fulfilling a png request") - logger.error(err) - """ ---------------------------------------------------------------- """ def download(url, cmanager, filename, image_cache, image_id, repo_id = None): @@ -440,19 +296,5 @@ def render_message(messageTitle, messageBody = None, title = None, redirect = No """ ---------------------------------------------------------------- """ def render_module(module, **args): - # args.setdefault("title", "Augur View") - args.setdefault("api_url", getSetting("serving")) args.setdefault("body", module) - - if not getSetting("valid"): - args.setdefault("invalid", True) - return render_template('index.j2', **args) - -""" ---------------------------------------------------------------- - No longer used -""" -# My attempt at a loading page -def renderLoading(dest, query, request): - cache_files_requested.append(request) - return render_template('index.j2', body="loading", title="Loading", d=dest, query_key=query, api_url=getSetting('serving')) diff --git a/augur/application/cli/backend.py b/augur/application/cli/backend.py index aaede20d0a..548c1eeff4 100644 --- a/augur/application/cli/backend.py +++ b/augur/application/cli/backend.py @@ -21,6 +21,7 @@ from augur import instance_id from augur.tasks.start_tasks import augur_collection_monitor, CollectionState, create_collection_status_records from augur.tasks.git.facade_tasks import clone_repos +from augur.tasks.data_analysis.contributor_breadth_worker.contributor_breadth_worker import contributor_breadth_model from augur.tasks.init.redis_connection import redis_connection from augur.application.db.models import Repo, CollectionStatus, UserRepo from augur.application.db.session import DatabaseSession @@ -85,7 +86,7 @@ def start(disable_collection, development, port): logger.info(f'Augur is running at: {"http" if development else "https"}://{host}:{port}') processes = start_celery_worker_processes(float(worker_vmem_cap), disable_collection) - time.sleep(5) + if os.path.exists("celerybeat-schedule.db"): logger.info("Deleting old task schedule") os.remove("celerybeat-schedule.db") @@ -104,6 +105,8 @@ def start(disable_collection, development, port): create_collection_status_records.si().apply_async() time.sleep(3) + contributor_breadth_model.si().apply_async() + # start cloning repos when augur starts clone_repos.si().apply_async() @@ -147,6 +150,7 @@ def start_celery_worker_processes(vmem_cap_ratio, disable_collection=False): available_memory_in_bytes = psutil.virtual_memory().total * vmem_cap_ratio available_memory_in_megabytes = available_memory_in_bytes / (1024 ** 2) max_process_estimate = available_memory_in_megabytes // 500 + sleep_time = 0 #Get a subset of the maximum procesess available using a ratio, not exceeding a maximum value def determine_worker_processes(ratio,maximum): @@ -155,6 +159,7 @@ def determine_worker_processes(ratio,maximum): frontend_worker = f"celery -A augur.tasks.init.celery_app.celery_app worker -l info --concurrency=1 -n frontend:{uuid.uuid4().hex}@%h -Q frontend" max_process_estimate -= 1 process_list.append(subprocess.Popen(frontend_worker.split(" "))) + sleep_time += 6 if not disable_collection: @@ -162,18 +167,21 @@ def determine_worker_processes(ratio,maximum): scheduling_worker = f"celery -A augur.tasks.init.celery_app.celery_app worker -l info --concurrency=2 -n scheduling:{uuid.uuid4().hex}@%h -Q scheduling" max_process_estimate -= 2 process_list.append(subprocess.Popen(scheduling_worker.split(" "))) + sleep_time += 6 #60% of estimate, Maximum value of 45 core_num_processes = determine_worker_processes(.6, 45) logger.info(f"Starting core worker processes with concurrency={core_num_processes}") core_worker = f"celery -A augur.tasks.init.celery_app.celery_app worker -l info --concurrency={core_num_processes} -n core:{uuid.uuid4().hex}@%h" process_list.append(subprocess.Popen(core_worker.split(" "))) + sleep_time += 6 #20% of estimate, Maximum value of 25 secondary_num_processes = determine_worker_processes(.2, 25) logger.info(f"Starting secondary worker processes with concurrency={secondary_num_processes}") secondary_worker = f"celery -A augur.tasks.init.celery_app.celery_app worker -l info --concurrency={secondary_num_processes} -n secondary:{uuid.uuid4().hex}@%h -Q secondary" process_list.append(subprocess.Popen(secondary_worker.split(" "))) + sleep_time += 6 #15% of estimate, Maximum value of 20 facade_num_processes = determine_worker_processes(.2, 20) @@ -181,6 +189,9 @@ def determine_worker_processes(ratio,maximum): facade_worker = f"celery -A augur.tasks.init.celery_app.celery_app worker -l info --concurrency={facade_num_processes} -n facade:{uuid.uuid4().hex}@%h -Q facade" process_list.append(subprocess.Popen(facade_worker.split(" "))) + sleep_time += 6 + + time.sleep(sleep_time) return process_list diff --git a/augur/application/db/models/augur_operations.py b/augur/application/db/models/augur_operations.py index e2100196dc..a2e3a6c4d8 100644 --- a/augur/application/db/models/augur_operations.py +++ b/augur/application/db/models/augur_operations.py @@ -1,24 +1,20 @@ -# coding: utf-8 +# encoding: utf-8 from sqlalchemy import BigInteger, SmallInteger, Column, Index, Integer, String, Table, text, UniqueConstraint, Boolean, ForeignKey, update, CheckConstraint -from sqlalchemy.dialects.postgresql import TIMESTAMP, UUID +from sqlalchemy.dialects.postgresql import TIMESTAMP from sqlalchemy.orm.exc import NoResultFound, MultipleResultsFound from sqlalchemy.exc import IntegrityError from sqlalchemy.orm import relationship -from sqlalchemy.sql import text as sql_text from werkzeug.security import generate_password_hash, check_password_hash -from typing import List, Any, Dict +from typing import List -import logging +import logging import secrets import traceback -import importlib from augur.application.db.models import Repo, RepoGroup from augur.application.db.session import DatabaseSession from augur.application.db.models.base import Base - - FRONTEND_REPO_GROUP_NAME = "Frontend Repos" logger = logging.getLogger(__name__) @@ -39,15 +35,15 @@ def retrieve_owner_repos(session, owner: str) -> List[str]: OWNER_INFO_ENDPOINT = f"https://api.github.com/users/{owner}" ORG_REPOS_ENDPOINT = f"https://api.github.com/orgs/{owner}/repos?per_page=100" USER_REPOS_ENDPOINT = f"https://api.github.com/users/{owner}/repos?per_page=100" - + if not session.oauths.list_of_keys: return None, {"status": "No valid github api keys to retrieve data with"} - + # determine whether the owner is a user or an organization data, _ = retrieve_dict_from_endpoint(logger, session.oauths, OWNER_INFO_ENDPOINT) if not data: return None, {"status": "Invalid owner"} - + owner_type = data["type"] @@ -57,11 +53,11 @@ def retrieve_owner_repos(session, owner: str) -> List[str]: url = ORG_REPOS_ENDPOINT else: return None, {"status": f"Invalid owner type: {owner_type}"} - - + + # collect repo urls for the given owner repos = [] - for page_data, page in GithubPaginator(url, session.oauths, logger).iter_pages(): + for page_data in GithubPaginator(url, session.oauths, logger).iter_pages(): if page_data is None: break @@ -72,7 +68,7 @@ def retrieve_owner_repos(session, owner: str) -> List[str]: return repo_urls, {"status": "success", "owner_type": owner_type} - + metadata = Base.metadata t_all = Table( @@ -266,7 +262,7 @@ class User(Base): tool_version = Column(String) data_source = Column(String) data_collection_date = Column(TIMESTAMP(precision=0), server_default=text("CURRENT_TIMESTAMP")) - + __tablename__ = 'users' __table_args__ = ( UniqueConstraint('email', name='user-unique-email'), @@ -333,8 +329,8 @@ def get_user(session, username: str): return user except NoResultFound: return None - - @staticmethod + + @staticmethod def get_by_id(session, user_id: int): if not isinstance(user_id, int): @@ -344,12 +340,12 @@ def get_by_id(session, user_id: int): return user except NoResultFound: return None - + @staticmethod def create_user(username: str, password: str, email: str, first_name:str, last_name:str, admin=False): if username is None or password is None or email is None or first_name is None or last_name is None: - return False, {"status": "Missing field"} + return False, {"status": "Missing field"} with DatabaseSession(logger) as session: @@ -371,7 +367,7 @@ def create_user(username: str, password: str, email: str, first_name:str, last_n return False, {"status": "Failed to add default group for the user"} return True, {"status": "Account successfully created"} - except AssertionError as exception_message: + except AssertionError as exception_message: return False, {"Error": f"{exception_message}."} def delete(self, session): @@ -410,7 +406,7 @@ def update_email(self, session, new_email): if not new_email: print("Need new email to update the email") return False, {"status": "Missing argument"} - + existing_user = session.query(User).filter(User.email == new_email).first() if existing_user is not None: @@ -454,7 +450,7 @@ def remove_group(self, group_name): return result def add_repo(self, group_name, repo_url): - + from augur.tasks.github.util.github_task_session import GithubTaskSession from augur.tasks.github.util.github_api_key_handler import NoValidKeysError try: @@ -497,20 +493,20 @@ def get_group_names(self, search=None, reversed=False): group_names = [group.name for group in user_groups] else: group_names = [group.name for group in user_groups if search.lower() in group.name.lower()] - + group_names.sort(reverse = reversed) return group_names, {"status": "success"} - + def get_groups_info(self, search=None, reversed=False, sort="group_name"): (groups, result) = self.get_groups() if search is not None: groups = [group for group in groups if search.lower() in group.name.lower()] - + for group in groups: group.count = self.get_group_repo_count(group.name)[0] - + def sorting_function(group): if sort == "group_name": return group.name @@ -518,7 +514,7 @@ def sorting_function(group): return group.count elif sort == "favorited": return group.favorited - + groups = sorted(groups, key=sorting_function, reverse=reversed) return groups, {"status": "success"} @@ -612,7 +608,7 @@ def get_favorite_groups(self, session): return None, {"status": "Error when trying to get favorite groups"} return groups, {"status": "Success"} - + @staticmethod def compute_hashsed_password(password): return generate_password_hash(password, method='pbkdf2:sha512', salt_length=32) @@ -621,7 +617,7 @@ def compute_hashsed_password(password): class UserGroup(Base): group_id = Column(BigInteger, primary_key=True) - user_id = Column(Integer, + user_id = Column(Integer, ForeignKey("augur_operations.users.user_id", name="user_group_user_id_fkey") ) name = Column(String, nullable=False) @@ -797,7 +793,7 @@ def add(session, url: List[str], user_id: int, group_name=None, group_id=None, f if not group_name and not group_id: return False, {"status": "Need group name or group id to add a repo"} - + if from_org_list and not repo_type: return False, {"status": "Repo type must be passed if the repo is from an organization's list of repos"} @@ -806,21 +802,21 @@ def add(session, url: List[str], user_id: int, group_name=None, group_id=None, f group_id = UserGroup.convert_group_name_to_id(session, user_id, group_name) if group_id is None: return False, {"status": "Invalid group name"} - + if not from_org_list: result = Repo.is_valid_github_repo(session, url) if not result[0]: return False, {"status": result[1]["status"], "repo_url": url} - + repo_type = result[1]["repo_type"] - + # if no repo_group_id is passed then assign the repo to the frontend repo group if repo_group_id is None: frontend_repo_group = session.query(RepoGroup).filter(RepoGroup.rg_name == FRONTEND_REPO_GROUP_NAME).first() if not frontend_repo_group: - return False, {"status": "Could not find repo group with name 'Frontend Repos'", "repo_url": url} - + return False, {"status": "Could not find repo group with name 'Frontend Repos'", "repo_url": url} + repo_group_id = frontend_repo_group.repo_group_id @@ -877,7 +873,7 @@ def add_org_repos(session, url: List[str], user_id: int, group_name: int): group_id = UserGroup.convert_group_name_to_id(session, user_id, group_name) if group_id is None: return False, {"status": "Invalid group name"} - + # parse github owner url to get owner name owner = Repo.parse_github_org_url(url) if not owner: @@ -888,10 +884,10 @@ def add_org_repos(session, url: List[str], user_id: int, group_name: int): # if the result is returns None or [] if not result[0]: return False, result[1] - + repos = result[0] type = result[1]["owner_type"] - + # get repo group if it exists try: repo_group = RepoGroup.get_by_name(session, owner) @@ -921,7 +917,7 @@ def add_org_repos(session, url: List[str], user_id: int, group_name: int): if not result[0]: failed_repos.append(repo) - # Update repo group id to new org's repo group id if the repo + # Update repo group id to new org's repo group id if the repo # is a part of the org and existed before org added update_stmt = ( update(Repo) @@ -931,7 +927,7 @@ def add_org_repos(session, url: List[str], user_id: int, group_name: int): ) session.execute(update_stmt) session.commit() - + failed_count = len(failed_repos) if failed_count > 0: # this should never happen because an org should never return invalid repos @@ -959,11 +955,11 @@ class UserSessionToken(Base): @staticmethod def create(session, user_id, application_id, seconds_to_expire=86400): - import time + import time user_session_token = secrets.token_hex() expiration = int(time.time()) + seconds_to_expire - + user_session = UserSessionToken(token=user_session_token, user_id=user_id, application_id = application_id, expiration=expiration) session.add(user_session) @@ -999,12 +995,13 @@ class ClientApplication(Base): sessions = relationship("UserSessionToken") subscriptions = relationship("Subscription") + def __eq__(self, other): + return isinstance(other, ClientApplication) and str(self.id) == str(other.id) + @staticmethod def get_by_id(session, client_id): - return session.query(ClientApplication).filter(ClientApplication.id == client_id).first() - class Subscription(Base): __tablename__ = "subscriptions" __table_args__ = ( @@ -1150,7 +1147,7 @@ class CollectionStatus(Base): issue_pr_sum = Column(BigInteger) commit_sum = Column(BigInteger) - + repo = relationship("Repo", back_populates="collection_status") @staticmethod @@ -1173,7 +1170,7 @@ def insert(session, repo_id): session.logger.error( ''.join(traceback.format_exception(None, e, e.__traceback__))) - + record = { "repo_id": repo_id, "issue_pr_sum": pr_issue_count, diff --git a/augur/tasks/data_analysis/contributor_breadth_worker/contributor_breadth_worker.py b/augur/tasks/data_analysis/contributor_breadth_worker/contributor_breadth_worker.py index f8b6a9a585..44a6761cf9 100644 --- a/augur/tasks/data_analysis/contributor_breadth_worker/contributor_breadth_worker.py +++ b/augur/tasks/data_analysis/contributor_breadth_worker/contributor_breadth_worker.py @@ -2,9 +2,10 @@ import logging, json import pandas as pd import sqlalchemy as s +from datetime import datetime from augur.tasks.init.celery_app import celery_app as celery -from augur.application.db.session import DatabaseSession +from augur.tasks.github.util.github_task_session import GithubTaskManifest from augur.tasks.github.util.github_paginator import GithubPaginator from augur.application.db.models import ContributorRepo @@ -14,13 +15,6 @@ ### Logic: For each unique platform contributor, gather non duplicate events, using the GitHub "id" ### for the event API (GitLab coming!) - -###################### -# -# IN PROGRESS -# -###################### - @celery.task def contributor_breadth_model() -> None: @@ -33,101 +27,78 @@ def contributor_breadth_model() -> None: data_source = 'GitHub API' - ## Get all the contributors currently in the database - #!/usr/bin/env python3 - - #cntrb_key = gh_login - cntrb_login_query = s.sql.text(""" SELECT DISTINCT gh_login, cntrb_id FROM augur_data.contributors WHERE gh_login IS NOT NULL """) - - current_cntrb_logins = json.loads(pd.read_sql(cntrb_login_query, engine, params={}).to_json(orient="records")) - - ## We need a list of all contributors so we can iterate through them to gather events - ## We need a list of event ids to avoid insertion of duplicate events. We ignore the event - ## If it already exists + result = engine.execute(cntrb_login_query) - logger.info(f"Contributor Logins are: {current_cntrb_logins}") + current_cntrb_logins = [dict(row) for row in result] - ######################################################## - #### List of existing contributor ids and their corresponding gh_login - #### is contained in the `current_cntrb_logins` variable - ######################################################## + cntrb_newest_events_query = s.sql.text(""" + SELECT c.gh_login, MAX(cr.created_at) as newest_event_date + FROM contributor_repo AS cr + JOIN contributors AS c ON cr.cntrb_id = c.cntrb_id + GROUP BY c.gh_login; + """) - ######################################################## - #### Define the action map for events to avoid duplicates - #### Query event_ids so a list of existing events are - #### Available for duplicate checking - ######################################################## - - action_map = { - 'insert': { - 'source': ['id'], - 'augur': ['event_id'] - } - } + cntrb_newest_events_list = engine.execute(cntrb_newest_events_query) + cntrb_newest_events_list = [dict(row) for row in cntrb_newest_events_list] - # Eliminate any duplicate event_ids from what will be inserted - # Because of Bulk Insert - # keyVal = event_id + cntrb_newest_events_map = {} + for cntrb_event in cntrb_newest_events_list: - ######################################################## - # Query for existing event ids to avoid duplication - ######################################################## + gh_login = cntrb_event["gh_login"] + newest_event_date = cntrb_event["newest_event_date"] + + cntrb_newest_events_map[gh_login] = newest_event_date - dup_query = s.sql.text(""" - SELECT DISTINCT event_id - FROM augur_data.contributor_repo - WHERE 1 = 1 - """) - current_event_ids = json.loads(pd.read_sql(dup_query, engine, params={}).to_json(orient="records")) + with GithubTaskManifest(logger) as manifest: - #Convert list of dictionaries to regular list of 'event_ids'. - #The only values that the sql query returns are event_ids so - #it makes no sense to be a list of many dicts of one key. - current_event_ids = [value for elem in current_event_ids for value in elem.values()] + index = 1 + total = len(current_cntrb_logins) + for cntrb in current_cntrb_logins: - logger.info(f"current event ids are: {current_event_ids}") + print(f"Processing cntrb {index} of {total}") + index += 1 - for cntrb in current_cntrb_logins: + repo_cntrb_url = f"https://api.github.com/users/{cntrb['gh_login']}/events" - repo_cntrb_url = f"https://api.github.com/users/{cntrb['gh_login']}/events" - # source_cntrb_repos seemed like not exactly what the variable is for; its a list of actions for - # each Github gh_login value already in our database + newest_event_in_db = datetime(1970, 1, 1) + if cntrb["gh_login"] in cntrb_newest_events_map: + newest_event_in_db = cntrb_newest_events_map[cntrb["gh_login"]] + - with DatabaseSession(logger, engine) as session: cntrb_events = [] - for page_data, page in GithubPaginator(repo_cntrb_url, session.oauths, logger).iter_pages(): + for page_data, page in GithubPaginator(repo_cntrb_url, manifest.key_auth, logger).iter_pages(): - if page_data: + if page_data: cntrb_events += page_data - process_contributor_events(cntrb, cntrb_events, current_event_ids, logger) + oldest_event_on_page = datetime.strptime(page_data[-1]["created_at"], "%Y-%m-%dT%H:%M:%SZ") + if oldest_event_on_page < newest_event_in_db: + print("Found cntrb events we already have...skipping the rest") + break + + if len(cntrb_events) == 0: + logger.info("There are no cntrb events, or new events for this user.\n") + continue - # source_cntrb_events = self.paginate_endpoint(repo_cntrb_url, action_map=action_map, - # table=self.contributor_repo_table) + events = process_contributor_events(cntrb, cntrb_events, logger, tool_source, tool_version, data_source) -def process_contributor_events(cntrb, cntrb_events, current_event_ids, logger): + logger.info(f"Inserting {len(events)} events") + natural_keys = ["event_id", "tool_version"] + manifest.augur_db.insert_data(events, ContributorRepo, natural_keys) - if not cntrb_events: - logger.info("There are no events, or new events for this user.\n") - return - ## current_event_ids are the ones ALREADY IN THE AUGUR DB. SKIP THOSE. - ## source_cntrb_events are the ones the API pulls. +def process_contributor_events(cntrb, cntrb_events, logger, tool_source, tool_version, data_source): + cntrb_repos_insert = [] for event_id_api in cntrb_events: - logger.info(f"Keys of event_id_api: {event_id_api.keys()}") - #logger.info(f"Keys of current_event_ids: {current_event_ids.keys()}") - if int(event_id_api['id']) in current_event_ids: - continue - cntrb_repos_insert.append({ "cntrb_id": cntrb['cntrb_id'], @@ -138,23 +109,8 @@ def process_contributor_events(cntrb, cntrb_events, current_event_ids, logger): "repo_name": event_id_api['repo']['name'], "gh_repo_id": event_id_api['repo']['id'], "cntrb_category": event_id_api['type'], - "event_id": event_id_api['id'], + "event_id": int(event_id_api['id']), "created_at": event_id_api['created_at'] }) - - - # else: - # # Print the message if the value does not exist - # logger.info(f"event_id is found in JSON data {current_event_ids[event_id]}.") - - ######################################################## - # Do the Inserts - ######################################################## - - #cntrb_repos_insert = [] - #cntrb_ids_idx = pd.Index(cntrb_ids, name=contributors) - - cntrb_repo_insert_result, cntrb_repo_update_result = self.bulk_insert(self.contributor_repo_table, - unique_columns='event_id', insert=cntrb_repos_insert) - + return cntrb_repos_insert diff --git a/augur/tasks/git/dependency_libyear_tasks/core.py b/augur/tasks/git/dependency_libyear_tasks/core.py index 610342afc8..f4ebdd4b3b 100644 --- a/augur/tasks/git/dependency_libyear_tasks/core.py +++ b/augur/tasks/git/dependency_libyear_tasks/core.py @@ -11,18 +11,25 @@ from augur.application.db.util import execute_session_query from urllib.parse import quote from augur.tasks.git.dependency_libyear_tasks.libyear_util.util import get_deps_libyear_data +from augur.tasks.git.util.facade_worker.facade_worker.utilitymethods import get_absolute_repo_path def deps_libyear_model( session, repo_id,repo_git,repo_group_id): """ Data collection and storage method """ session.logger.info(f"This is the libyear deps model repo: {repo_git}") - result = re.search(r"https:\/\/(github\.com\/[A-Za-z0-9 \- _]+\/)([A-Za-z0-9 \- _ .]+)$", repo_git).groups() + #result = re.search(r"https:\/\/(github\.com\/[A-Za-z0-9 \- _]+\/)([A-Za-z0-9 \- _ .]+)$", repo_git).groups() + + #relative_repo_path = f"{repo_group_id}/{result[0]}{result[1]}" + query = session.query(Repo).filter( + Repo.repo_git == repo_git) + + result = execute_session_query(query, 'one') - relative_repo_path = f"{repo_group_id}/{result[0]}{result[1]}" config = AugurConfig(session.logger, session) - absolute_repo_path = config.get_section("Facade")['repo_directory'] + relative_repo_path#self.config['repo_directory'] + relative_repo_path + absolute_repo_path = get_absolute_repo_path(config.get_section("Facade")['repo_directory'],repo_id,result.repo_path,result.repo_name) + #config.get_section("Facade")['repo_directory'] + relative_repo_path#self.config['repo_directory'] + relative_repo_path generate_deps_libyear_data(session,repo_id, absolute_repo_path) diff --git a/augur/tasks/init/celery_app.py b/augur/tasks/init/celery_app.py index 69abc837aa..ac6e18fc64 100644 --- a/augur/tasks/init/celery_app.py +++ b/augur/tasks/init/celery_app.py @@ -58,7 +58,8 @@ class CollectionState(Enum): 'augur.tasks.data_analysis.clustering_worker.tasks', 'augur.tasks.data_analysis.discourse_analysis.tasks', 'augur.tasks.data_analysis.pull_request_analysis_worker.tasks', - 'augur.tasks.data_analysis.insight_worker.tasks'] + 'augur.tasks.data_analysis.insight_worker.tasks', + 'augur.tasks.data_analysis.contributor_breadth_worker.contributor_breadth_worker'] materialized_view_tasks = ['augur.tasks.db.refresh_materialized_views'] @@ -139,7 +140,8 @@ def on_failure(self,exc,task_id,args,kwargs,einfo): 'augur.tasks.git.dependency_tasks.tasks.process_ossf_dependency_metrics': {'queue': 'secondary'}, 'augur.tasks.git.dependency_tasks.tasks.process_dependency_metrics': {'queue': 'facade'}, 'augur.tasks.git.dependency_libyear_tasks.tasks.process_libyear_dependency_metrics': {'queue': 'facade'}, - 'augur.tasks.frontend.*': {'queue': 'frontend'} + 'augur.tasks.frontend.*': {'queue': 'frontend'}, + 'augur.tasks.data_analysis.contributor_breadth_worker.*': {'queue': 'secondary'}, } #Setting to be able to see more detailed states of running tasks @@ -204,6 +206,7 @@ def setup_periodic_tasks(sender, **kwargs): from augur.tasks.start_tasks import non_repo_domain_tasks from augur.tasks.git.facade_tasks import clone_repos from augur.tasks.db.refresh_materialized_views import refresh_materialized_views + from augur.tasks.data_analysis.contributor_breadth_worker.contributor_breadth_worker import contributor_breadth_model with DatabaseEngine() as engine, DatabaseSession(logger, engine) as session: @@ -225,6 +228,10 @@ def setup_periodic_tasks(sender, **kwargs): logger.info(f"Scheduling update of collection weights on midnight each day") sender.add_periodic_task(crontab(hour=0, minute=0),augur_collection_update_weights.s()) + logger.info(f"Scheduling contributor breadth every 30 days") + thirty_days_in_seconds = 30*24*60*60 + sender.add_periodic_task(thirty_days_in_seconds, contributor_breadth_model.s()) + @after_setup_logger.connect def setup_loggers(*args,**kwargs): diff --git a/augur/templates/index.j2 b/augur/templates/index.j2 index 89cd6734c3..ba934533ff 100644 --- a/augur/templates/index.j2 +++ b/augur/templates/index.j2 @@ -39,10 +39,8 @@ {% include 'navbar.j2' %}
- {% if invalid %} -

Invalid API URL

-

The API URL [{{ api_url or 'unspecified'}}] is invalid

- {% elif body %} + {% if body %} + {# Load the provided module #} {% include '%s.j2' % body ignore missing %} {% else %}

404 - Page Not Found

@@ -54,7 +52,6 @@

This is a beta build of Augur-View. Experimental frontend features may not be fully functional.

- {#

Currently serving: {{api_url or 'api_url unspecified'}}

#}
diff --git a/docker/backend/Dockerfile b/docker/backend/Dockerfile index 504e0946fa..0b63b5a705 100644 --- a/docker/backend/Dockerfile +++ b/docker/backend/Dockerfile @@ -2,7 +2,7 @@ FROM python:3.8.11-slim-buster LABEL maintainer="outdoors@acm.org" -LABEL version="0.51.0" +LABEL version="0.51.1" ENV DEBIAN_FRONTEND=noninteractive diff --git a/docker/database/Dockerfile b/docker/database/Dockerfile index 83e1df4f7e..e6899a7713 100644 --- a/docker/database/Dockerfile +++ b/docker/database/Dockerfile @@ -2,7 +2,7 @@ FROM postgres:12 LABEL maintainer="outdoors@acm.org" -LABEL version="0.51.0" +LABEL version="0.51.1" ENV POSTGRES_DB "test" ENV POSTGRES_USER "augur" diff --git a/docs/augur-0.5.0.ndm2 b/docs/augur-0.5.0.ndm2 deleted file mode 100644 index a304b4d8ec..0000000000 --- a/docs/augur-0.5.0.ndm2 +++ /dev/null @@ -1,63372 +0,0 @@ -{ - "paper": { - "name": "A4", - "leftMargin": 0.5, - "rightMargin": 0.5, - "topMargin": 0.5, - "bottomMargin": 0.5, - "isPortriat": true - }, - "modelVersion": 2.01, - "defaultSchema": "public", - "server": { - "objectType": "Server_PGSQL", - "name": "Default", - "uuid": "", - "serverVersion": 120000, - "edition": "Default", - "catalogs": [ - { - "objectType": "Catalog_PGSQL", - "name": "Default", - "schemas": [ - { - "objectType": "Schema_PGSQL", - "name": "public", - "comment": "", - "tables": [], - "views": [] - }, - { - "objectType": "Schema_PGSQL", - "name": "augur_data", - "comment": "", - "tables": [ - { - "objectType": "TableNormal_PGSQL", - "name": "_temp_repolist", - "comment": "", - "tablespace": "", - "isUnlogged": false, - "owner": "augur", - "inheritFromTables": [], - "hasOIDs": false, - "fillFactor": -1, - "oldName": "_temp_repolist", - "oid": 551824533, - "rows": 158, - "isInheritTables": false, - "cluster": "", - "ACL": "{augur=arwdDxt/augur,cali=r/augur,austin=r/augur}", - "isPartition": false, - "partitioningStrategy": "None", - "partitionOfSchema": "", - "partitionOfTable": "", - "partitionListValues": [], - "partitionRangeFromValues": [], - "partitionRangeToValues": [], - "foreignServer": "", - "foreignOptionDisplay": "", - "fields": [ - { - "objectType": "TableField_PGSQL", - "name": "repo_git", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "repo_git", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 1, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - } - ], - "indexes": [], - "rules": [], - "foreignKeys": [], - "uniques": [], - "checks": [], - "excludes": [], - "triggers": [], - "partitionKeys": [], - "partitions": [] - }, - { - "objectType": "TableNormal_PGSQL", - "name": "analysis_log", - "comment": "", - "tablespace": "", - "isUnlogged": false, - "owner": "augur", - "inheritFromTables": [], - "hasOIDs": false, - "fillFactor": -1, - "oldName": "analysis_log", - "oid": 528434861, - "rows": 790981, - "isInheritTables": false, - "cluster": "", - "ACL": "{augur=arwdDxt/augur,cali=r/augur,austin=r/augur}", - "isPartition": false, - "partitioningStrategy": "None", - "partitionOfSchema": "", - "partitionOfTable": "", - "partitionListValues": [], - "partitionRangeFromValues": [], - "partitionRangeToValues": [], - "foreignServer": "", - "foreignOptionDisplay": "", - "fields": [ - { - "objectType": "TableField_PGSQL", - "name": "repos_id", - "type": "int4", - "length": 32, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": false, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "repos_id", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 1, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "status", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": false, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "status", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 2, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "date_attempted", - "type": "timestamp", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": false, - "defaultType": "Others", - "defaultValue": "CURRENT_TIMESTAMP", - "comment": "", - "oldName": "date_attempted", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 3, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - } - ], - "indexes": [ - { - "objectType": "Index_PGSQL", - "name": "repos_id", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "BTree", - "tableSpaceName": "", - "constraint": "", - "oldName": "repos_id", - "oid": 528434868, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "analysis_log", - "size": "17400", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "repos_id", - "collation": "", - "opClass": "int4_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "repos_id", - "collationSchema": "" - } - ] - } - ], - "rules": [], - "foreignKeys": [], - "uniques": [], - "checks": [], - "excludes": [], - "triggers": [], - "partitionKeys": [], - "partitions": [] - }, - { - "objectType": "TableNormal_PGSQL", - "name": "chaoss_metric_status", - "comment": "This table used to track CHAOSS Metric implementations in Augur, but due to the constantly changing location of that information, it is for the moment not actively populated. 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"comment": "“web_url” value from these API calls to GitLab, all for the same user\n\nhttps://gitlab.com/api/v4/users?username=computationalmystic\nhttps://gitlab.com/api/v4/users?search=s@goggins.com\nhttps://gitlab.com/api/v4/users?search=outdoors@acm.org\n\n[\n {\n \"id\": 5481034,\n \"name\": \"sean goggins\",\n \"username\": \"computationalmystic\",\n \"state\": \"active\",\n \"avatar_url\": \"https://secure.gravatar.com/avatar/fb1fb43953a6059df2fe8d94b21d575c?s=80&d=identicon\",\n \"web_url\": \"https://gitlab.com/computationalmystic\"\n }\n]", - "oldName": "gl_web_url", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 36, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "gl_avatar_url", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "“avatar_url” value from these API calls to GitLab, all for the same user\n\nhttps://gitlab.com/api/v4/users?username=computationalmystic\nhttps://gitlab.com/api/v4/users?search=s@goggins.com\nhttps://gitlab.com/api/v4/users?search=outdoors@acm.org\n\n[\n {\n \"id\": 5481034,\n \"name\": \"sean goggins\",\n \"username\": \"computationalmystic\",\n \"state\": \"active\",\n \"avatar_url\": \"https://secure.gravatar.com/avatar/fb1fb43953a6059df2fe8d94b21d575c?s=80&d=identicon\",\n \"web_url\": \"https://gitlab.com/computationalmystic\"\n }\n]", - "oldName": "gl_avatar_url", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 37, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "gl_state", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "“state” value from these API calls to GitLab, all for the same user\n\nhttps://gitlab.com/api/v4/users?username=computationalmystic\nhttps://gitlab.com/api/v4/users?search=s@goggins.com\nhttps://gitlab.com/api/v4/users?search=outdoors@acm.org\n\n[\n {\n \"id\": 5481034,\n \"name\": \"sean goggins\",\n \"username\": \"computationalmystic\",\n \"state\": \"active\",\n \"avatar_url\": \"https://secure.gravatar.com/avatar/fb1fb43953a6059df2fe8d94b21d575c?s=80&d=identicon\",\n \"web_url\": \"https://gitlab.com/computationalmystic\"\n }\n]", - "oldName": "gl_state", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 38, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "gl_username", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "“username” value from these API calls to GitLab, all for the same user\n\nhttps://gitlab.com/api/v4/users?username=computationalmystic\nhttps://gitlab.com/api/v4/users?search=s@goggins.com\nhttps://gitlab.com/api/v4/users?search=outdoors@acm.org\n\n[\n {\n \"id\": 5481034,\n \"name\": \"sean goggins\",\n \"username\": \"computationalmystic\",\n \"state\": \"active\",\n \"avatar_url\": \"https://secure.gravatar.com/avatar/fb1fb43953a6059df2fe8d94b21d575c?s=80&d=identicon\",\n \"web_url\": \"https://gitlab.com/computationalmystic\"\n }\n]", - "oldName": "gl_username", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 39, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "gl_full_name", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "“name” value from these API calls to GitLab, all for the same user\n\nhttps://gitlab.com/api/v4/users?username=computationalmystic\nhttps://gitlab.com/api/v4/users?search=s@goggins.com\nhttps://gitlab.com/api/v4/users?search=outdoors@acm.org\n\n[\n {\n \"id\": 5481034,\n \"name\": \"sean goggins\",\n \"username\": \"computationalmystic\",\n \"state\": \"active\",\n \"avatar_url\": \"https://secure.gravatar.com/avatar/fb1fb43953a6059df2fe8d94b21d575c?s=80&d=identicon\",\n \"web_url\": \"https://gitlab.com/computationalmystic\"\n }\n]", - "oldName": "gl_full_name", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 40, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "gl_id", - "type": "int8", - "length": 64, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "\"id\" value from these API calls to GitLab, all for the same user\n\nhttps://gitlab.com/api/v4/users?username=computationalmystic\nhttps://gitlab.com/api/v4/users?search=s@goggins.com\nhttps://gitlab.com/api/v4/users?search=outdoors@acm.org\n\n[\n {\n \"id\": 5481034,\n \"name\": \"sean goggins\",\n \"username\": \"computationalmystic\",\n \"state\": \"active\",\n \"avatar_url\": \"https://secure.gravatar.com/avatar/fb1fb43953a6059df2fe8d94b21d575c?s=80&d=identicon\",\n \"web_url\": \"https://gitlab.com/computationalmystic\"\n }\n]", - "oldName": "gl_id", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 41, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "tool_source", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "tool_source", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 42, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "tool_version", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "tool_version", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 43, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "data_source", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "data_source", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 44, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "data_collection_date", - "type": "timestamp", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": true, - "defaultType": "Others", - "defaultValue": "CURRENT_TIMESTAMP", - "comment": "", - "oldName": "data_collection_date", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 45, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "cntrb_id", - "type": "uuid", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": false, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "cntrb_id", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 46, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - } - ], - "indexes": [ - { - "objectType": "Index_PGSQL", - "name": "cnt-fullname", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "Hash", - "tableSpaceName": "", - "constraint": "", - "oldName": "cnt-fullname", - "oid": 528434995, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "contributors", - "size": "16400", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "cntrb_full_name", - "collation": "default", - "opClass": "text_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "cntrb_full_name", - "collationSchema": "pg_catalog" - } - ] - }, - { - "objectType": "Index_PGSQL", - "name": "cntrb-theemail", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "Hash", - "tableSpaceName": "", - "constraint": "", - "oldName": "cntrb-theemail", - "oid": 528434996, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "contributors", - "size": "16400", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "cntrb_email", - "collation": "default", - "opClass": "text_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "cntrb_email", - "collationSchema": "pg_catalog" - } - ] - }, - { - "objectType": "Index_PGSQL", - "name": "cntrb_canonica-idx11", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "BTree", - "tableSpaceName": "", - "constraint": "", - "oldName": "cntrb_canonica-idx11", - "oid": 528434997, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "contributors", - "size": "13800", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "cntrb_canonical", - "collation": "default", - "opClass": "text_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "cntrb_canonical", - "collationSchema": "pg_catalog" - } - ] - }, - { - "objectType": "Index_PGSQL", - "name": "cntrb_login_platform_index", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "BTree", - "tableSpaceName": "", - "constraint": "", - "oldName": "cntrb_login_platform_index", - "oid": 528434998, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "contributors", - "size": "15936", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "cntrb_login", - "collation": "default", - "opClass": "text_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "cntrb_login", - "collationSchema": "pg_catalog" - } - ] - }, - { - "objectType": "Index_PGSQL", - "name": "contributor_worker_email_finder", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "BRIN", - "tableSpaceName": "", - "constraint": "", - "oldName": "contributor_worker_email_finder", - "oid": 528435000, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "contributors", - "size": "48", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "cntrb_email", - "collation": "default", - "opClass": "text_minmax_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "cntrb_email", - "collationSchema": "pg_catalog" - } - ] - }, - { - "objectType": "Index_PGSQL", - "name": "contributor_worker_fullname_finder", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "BRIN", - "tableSpaceName": "", - "constraint": "", - "oldName": "contributor_worker_fullname_finder", - "oid": 528435002, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "contributors", - "size": "40", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "cntrb_full_name", - "collation": "default", - "opClass": "text_minmax_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "cntrb_full_name", - "collationSchema": "pg_catalog" - } - ] - }, - { - "objectType": "Index_PGSQL", - "name": "contributors_idx_cntrb_email3", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "BTree", - "tableSpaceName": "", - "constraint": "", - "oldName": "contributors_idx_cntrb_email3", - "oid": 528435003, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "contributors", - "size": "12984", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "cntrb_email", - "collation": "default", - "opClass": "text_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "cntrb_email", - "collationSchema": "pg_catalog" - } - ] - }, - { - "objectType": "Index_PGSQL", - "name": "login", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "BTree", - "tableSpaceName": "", - "constraint": "", - "oldName": "login", - "oid": 528435004, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "contributors", - "size": "15936", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "cntrb_login", - "collation": "default", - "opClass": "text_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "cntrb_login", - "collationSchema": "pg_catalog" - } - ] - }, - { - "objectType": "Index_PGSQL", - "name": "login-contributor-idx", - "comment": "", - "isClustered": false, - "isConcurrently": false, - "isUnique": false, - "fastUpdate": "", - "buffering": "", - "fillFactor": -1, - "method": "BTree", - "tableSpaceName": "", - "constraint": "", - "oldName": "login-contributor-idx", - "oid": 528435005, - "owner": "augur", - "brinPagesPerRange": -1, - "ginPendingListLimit": -1, - "tableName": "contributors", - "size": "15936", - "fields": [ - { - "objectType": "IndexField_PGSQL", - "name": "cntrb_login", - "collation": "default", - "opClass": "text_ops", - "opClassSchema": "pg_catalog", - "order": "ASC", - "nullSort": "NULLS LAST", - "oldName": "cntrb_login", - "collationSchema": "pg_catalog" - } - ] - } - ], - "rules": [], - "primaryKey": { - "objectType": "PrimaryKey_PGSQL", - "name": "contributors-pk", - "fields": [ - "cntrb_id" - ], - "fillFactor": -1, - "indexTablespace": "", - "comment": "", - "isDeferrable": false, - "isDeferred": false, - "oldName": "contributors-pk" - }, - "foreignKeys": [], - "uniques": [ - { - "objectType": "Unique_PGSQL", - "name": "GH-UNIQUE-C", - "fields": [ - "gh_login" - ], - "fillFactor": -1, - "indexTablespace": "", - "comment": "", - "isDeferrable": true, - "isDeferred": true, - "oldName": "GH-UNIQUE-C" - }, - { - "objectType": "Unique_PGSQL", - "name": "GL-UNIQUE-B", - "fields": [ - "gl_id" - ], - "fillFactor": -1, - "indexTablespace": "", - "comment": "", - "isDeferrable": true, - "isDeferred": true, - "oldName": "GL-UNIQUE-B" - }, - { - "objectType": "Unique_PGSQL", - "name": "GL-UNIQUE-C", - "fields": [ - "gl_username" - ], - "fillFactor": -1, - "indexTablespace": "", - "comment": "", - "isDeferrable": true, - "isDeferred": true, - "oldName": "GL-UNIQUE-C" - }, - { - "objectType": "Unique_PGSQL", - "name": "GL-cntrb-LOGIN-UNIQUE", - "fields": [ - "cntrb_login" - ], - "fillFactor": -1, - "indexTablespace": "", - "comment": "", - "isDeferrable": false, - "isDeferred": false, - "oldName": "GL-cntrb-LOGIN-UNIQUE" - } - ], - "checks": [], - "excludes": [], - 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"partitions": [] - }, - { - "objectType": "TableNormal_PGSQL", - "name": "issue_assignees", - "comment": "", - "tablespace": "", - "isUnlogged": false, - "owner": "augur", - "inheritFromTables": [], - "hasOIDs": false, - "fillFactor": -1, - "oldName": "issue_assignees", - "oid": 528435109, - "rows": 423268, - "isInheritTables": false, - "cluster": "", - "ACL": "{augur=arwdDxt/augur,cali=r/augur,austin=r/augur}", - "isPartition": false, - "partitioningStrategy": "None", - "partitionOfSchema": "", - "partitionOfTable": "", - "partitionListValues": [], - "partitionRangeFromValues": [], - "partitionRangeToValues": [], - "foreignServer": "", - "foreignOptionDisplay": "", - "fields": [ - { - "objectType": "TableField_PGSQL", - "name": "issue_assignee_id", - "type": "int8", - "length": 64, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": false, - "defaultType": "Others", - "defaultValue": "nextval('augur_data.issue_assignees_issue_assignee_id_seq'::regclass)", - "comment": "", - "oldName": "issue_assignee_id", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 1, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "issue_id", - "type": "int8", - "length": 64, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "issue_id", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 2, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "repo_id", - "type": "int8", - "length": 64, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "repo_id", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 3, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "issue_assignee_src_id", - "type": "int8", - "length": 64, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "This ID comes from the source. In the case of GitHub, it is the id that is the first field returned from the issue events API in the issue_assignees embedded JSON object. We may discover it is an ID for the person themselves; but my hypothesis is that its not.", - "oldName": "issue_assignee_src_id", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 5, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "issue_assignee_src_node", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "This character based identifier comes from the source. In the case of GitHub, it is the id that is the second field returned from the issue events API in the issue_assignees embedded JSON object. We may discover it is an ID for the person themselves; but my hypothesis is that its not.", - "oldName": "issue_assignee_src_node", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 6, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "tool_source", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "tool_source", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 7, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "tool_version", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "tool_version", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 8, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "data_source", - "type": "varchar", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "default", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "data_source", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "pg_catalog", - "ordinalPosition": 9, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - 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"identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - "geographyType": "", - "geographySRID": -1, - "geometryType": "", - "geometrySRID": -1 - }, - { - "objectType": "TableField_PGSQL", - "name": "cntrb_id", - "type": "uuid", - "length": 0, - "decimals": 0, - "dimensions": 0, - "collation": "", - "isNullable": true, - "defaultType": "None", - "defaultValue": "", - "comment": "", - "oldName": "cntrb_id", - "typeOID": 1, - "fieldObjectType": "", - "objectTypeSchema": "", - "isDomainType": false, - "collationSchema": "", - "ordinalPosition": 11, - "foreignOptions": [], - "isIdentity": false, - "identityGeneration": "None", - "oldIdentityGeneration": "None", - "identityStart": 0, - "identityIncrement": 0, - "identityMinimum": 0, - "hasNoIdentityMinValue": false, - "identityMaximum": 0, - "hasNoIdentityMaxValue": false, - "identityCache_inServer": 0, - "isIdentityCycle": false, - "generationExpression": "", - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/docs/macOS_SetUp.md b/docs/macOS_SetUp.md deleted file mode 100644 index 764c643908..0000000000 --- a/docs/macOS_SetUp.md +++ /dev/null @@ -1,17 +0,0 @@ -# Instructions for macOS SetUp: -#### While running Augur on macOS, we strongly recommend updating your shell’s initialization script as follows: - -1. Open a terminal: - - `nano .bash_profile` -2. Add the following line to the end of the file: - - `export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES` - - - -#### Issue Resolved - -Users faced this issues that in the installation page, it says: - -- If you’re running Augur on macOS, we strongly suggest adding the following line to your shell’s initialization script: -export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES - diff --git a/docs/macOS_Setup_instructions.md b/docs/macOS_Setup_instructions.md deleted file mode 100644 index 5b43097556..0000000000 --- a/docs/macOS_Setup_instructions.md +++ /dev/null @@ -1,17 +0,0 @@ -# Instructions for macOS SetUp: -#### While running Augur on macOS, we strongly recommend updating your shell’s initialization script as follows: - -1. Open a terminal: - - `nano .bash_profile` -2. Add the following line to the end of the file: - - `export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES` - - - -### Issue Resolved - -Users faced the issue that in the installation page, it says: - -- If you’re running Augur on macOS, we strongly suggest adding the following line to your shell’s initialization script: -export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES - diff --git a/docs/new-install-archive.md b/docs/new-install-archive.md deleted file mode 100644 index 370be06a23..0000000000 --- a/docs/new-install-archive.md +++ /dev/null @@ -1,185 +0,0 @@ -## Augur Setup - -# Ubuntu 20.04.x -We default to this version of Ubuntu for the moment because Augur does not yet support python3.10, which is the default version of python3.x distributed with Ubuntu 22.0x.x - -## Git Platform Requirements (Things to have setup prior to initiating installation.) -1. Obtain a GitHub Access Token: https://github.com/settings/tokens -2. Obtain a GitLab Access Token: https://gitlab.com/-/profile/personal_access_tokens - -### Fork and Clone Augur -1. Fork https://github.com/chaoss/augur -2. Clone your fork. We recommend creating a `github` directory in your user's base directory. - -## Pre-Requisite Operating System Level Packages -Here we ensure your system is up to date, install required python libraries, install postgresql, and install our queuing infrastrucutre, which is composed of redis-server and rabbitmq-server - -### Executable -```shell -sudo apt update && -sudo apt upgrade && -sudo apt install software-properties-common && -sudo apt install python3-dev && -sudo apt install python3.8-venv && -sudo apt install postgresql postgresql-contrib postgresql-client && -sudo apt install build-essential && -sudo apt install redis-server && -sudo apt install erlang && -sudo apt install rabbitmq-server && -sudo snap install go --classic && -sudo apt install nginx && -sudo apt install firefox-geckodriver -``` - -### Annotated -```shell -sudo apt update && -sudo apt upgrade && -sudo apt install software-properties-common && -sudo apt install python3-dev && -sudo apt install python3.8-venv && -sudo apt install postgresql postgresql-contrib postgresql-client && -sudo apt install build-essential && -sudo apt install redis-server && # required -sudo apt install erlang && # required -sudo apt install rabbitmq-server && #required -sudo snap install go --classic && #required: Go Needs to be version 1.19.x or higher. Snap is the package manager that gets you to the right version. Classic enables it to actually be installed at the correct version. -sudo apt install nginx && # required for hosting -sudo apt install firefox-geckodriver # required for visualization API -``` - -## Git Configuration -There are some Git configuration parameters that help when you are cloning repos over time, and a platform prompts you for credentials when it finds a repo is deleted: -```shell - git config --global diff.renames true - git config --global diff.renameLimit 200000 - git config --global credential.helper cache - git config --global credential.helper 'cache --timeout=9999999999999' -``` - - -## Postgresql Configuration -Create a PostgreSQL database for Augur to use -```shell -sudo su - -su - postgres -psql -``` - -Then, from within the resulting postgresql shell: -```sql -CREATE DATABASE augur; -CREATE USER augur WITH ENCRYPTED PASSWORD 'password'; -GRANT ALL PRIVILEGES ON DATABASE augur TO augur; -``` - -Once you are successfully logged out, return to your user by exiting `psql`, then typing `exit` to exit the postgres user, and `exit` a SECOND time to exit the root user. -``` -postgres=# \quit -``` - -```shell -exit -exit -``` - -## Rabbitmq Broker Configuration -You have to setup a specific user, and broker host for your augur instance. You can accomplish this by running the below commands: -```shell -sudo rabbitmqctl add_user augur password123 || -sudo rabbitmqctl add_vhost augur_vhost && -sudo rabbitmqctl set_user_tags augur augurTag && -sudo rabbitmqctl set_permissions -p augur_vhost augur ".*" ".*" ".*" -``` - -NOTE: it is important to have a static hostname when using rabbitmq as it uses hostname to communicate with nodes. - -If your setup of rabbitmq is successful your broker url should look like this: - -**broker_url = `amqp://augur:password123@localhost:5672/augur_vhost`** - -**During Augur installation, you will be prompted for this broker_url** - -## Proxying Augur through Nginx -Assumes nginx is installed. - -Then you create a file for the server you want Augur to run under in the location of your `sites-enabled` directory for nginx (In this example, Augur is running on port 5038: - -``` -server { - listen 80; - server_name zoo.chaoss.tv; - - location /api/unstable/ { - proxy_pass http://zoo.chaoss.tv:5038; - proxy_set_header Host $host; - } - - location / { - proxy_pass http://127.0.0.1:5038; - } - - error_log /var/log/nginx/augurview.osshealth.error.log; - access_log /var/log/nginx/augurview.osshealth.access.log; - -} -``` - -## Installing and Configuring Augur! -Create a Python Virtual Environment `python3 -m venv ~/virtual-env-directory` - -Activate your Python Virtual Environment `source ~/virtual-env-directory/bin/activate` - -From the root of the Augur Directory, type `make install` - -You will be prompted to provide your GitHub username and password, your GitLab username and password, and the postgresql database where you want to have the Augur Schema built. You will also be prompted to provide a directory where repositories will be clone into. - -## Post Installation of Augur - -### Redis Broker Configuration -If applications other than Augur are running on the same server, and using `redis-server` it is important to ensure that Augur and these other applications (or additional instances of Augur) are using distinct "cache_group". You can change from the default value of zero by editing the `augur_operations.config` table directly, looking for the "Redis" section_name, and the "cache_group" setting_name. This SQL is also a template: -```sql -UPDATE augur_operations.config -SET value = 2 -WHERE -section_name='Redis' -AND -setting_name='cache_group'; -``` - -## Augur Commands - -To access command line options, use `augur --help`. To load repos from GitHub organizations prior to collection, or in other ways, the direct route is `augur db --help`. - -Start a Flower Dashboard, which you can use to monitor progress, and report any failed processes as issues on the Augur GitHub site. The error rate for tasks is currently 0.04%, and most errors involve unhandled platform API timeouts. We continue to identify and add fixes to handle these errors through additional retries. Starting Flower: `(nohup celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)` NOTE: You can use any open port on your server, and access the dashboard in a browser with http://servername-or-ip:8400 in the example above (assuming you have access to that port, and its open on your network.) - -## Starting your Augur Instance -Start Augur: `(nohup augur backend start &)` - -When data collection is complete you will see only a single task running in your flower Dashboard. - -## Accessing Repo Addition and Visualization Front End -Your Augur intance will now be available at http://hostname.io:port_number - -For example: http://chaoss.tv:5038 - -Note: Augur will run on port 5000 by default (you probably need to change that in augur_operations.config for OSX) - -## Stopping your Augur Instance -You can stop augur with `augur backend stop`, followed by `augur backend kill`. We recommend waiting 5 minutes between commands so Augur can shutdown more gently. There is no issue with data integrity if you issue them seconds apart, its just that stopping is nicer than killing. - -### Docker -1. Make sure docker, and docker-compose are both installed -2. Modify the `environment.txt` file in the root of the repository to include your GitHub and GitLab API keys. -3. If you are already running postgresql on your server you have two choices: - - Change the port mappings in the `docker-compose.yml` file to match ports for Postgresql not currently in use. - - Change to variables in `environment.txt` to include the correct values for your local, non-docker-container database. -4. `sudo docker build -t augur-new -f docker/backend/Dockerfile .` -5. `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to run the database in a Docker Container or - `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to connect to an already running database. - -### Errata (Old Frontend) - -14. If you have frontend configuration issues that result in a *failure* to complete steps with npm, we recommend you install and use `nvm`: https://tecadmin.net/how-to-install-nvm-on-ubuntu-20-04/ to set your nodejs release to the latest LTS of 12.x or 16.x. For example: `nvm ls-remote | grep -i 'latest'` and `nvm alias default 16.??` (whatever the latest version of 16 is.) -15. Also, please explore our new frontend, being developed at https://github.com/augurlabs/augur_view. The `dev` branch is the most current. - diff --git a/docs/new-install-ubuntu-20.x.md b/docs/new-install-ubuntu-20.x.md deleted file mode 100644 index b0eaf3b562..0000000000 --- a/docs/new-install-ubuntu-20.x.md +++ /dev/null @@ -1,185 +0,0 @@ -## Augur Setup - -# Ubuntu 20.04.x -We default to this version of Ubuntu for the moment because Augur does not yet support python3.10, which is the default version of python3.x distributed with Ubuntu 22.0x.x - -## Git Platform Requirements (Things to have setup prior to initiating installation.) -1. Obtain a GitHub Access Token: https://github.com/settings/tokens -2. Obtain a GitLab Access Token: https://gitlab.com/-/profile/personal_access_tokens - -### Fork and Clone Augur -1. Fork https://github.com/chaoss/augur -2. Clone your fork. We recommend creating a `github` directory in your user's base directory. - -## Pre-Requisite Operating System Level Packages -Here we ensure your system is up to date, install required python libraries, install postgresql, and install our queuing infrastrucutre, which is composed of redis-server and rabbitmq-server - -### Executable -```shell -sudo apt update && -sudo apt upgrade && -sudo apt install software-properties-common && -sudo apt install python3-dev && -sudo apt install python3.8-venv && -sudo apt install postgresql postgresql-contrib postgresql-client && -sudo apt install build-essential && -sudo apt install redis-server && -sudo apt install erlang && -sudo apt install rabbitmq-server && -sudo snap install go --classic && -sudo apt install nginx && -sudo apt install firefox-geckodriver -``` - -### Annotated -```shell -sudo apt update && -sudo apt upgrade && -sudo apt install software-properties-common && -sudo apt install python3-dev && -sudo apt install python3.8-venv && -sudo apt install postgresql postgresql-contrib postgresql-client && -sudo apt install build-essential && -sudo apt install redis-server && # required -sudo apt install erlang && # required -sudo apt install rabbitmq-server && #required -sudo snap install go --classic && #required: Go Needs to be version 1.19.x or higher. Snap is the package manager that gets you to the right version. Classic enables it to actually be installed at the correct version. -sudo apt install nginx && # required for hosting -sudo apt install firefox-geckodriver # required for visualization API -``` - -## Git Configuration -There are some Git configuration parameters that help when you are cloning repos over time, and a platform prompts you for credentials when it finds a repo is deleted: -```shell - git config --global diff.renames true - git config --global diff.renameLimit 200000 - git config --global credential.helper cache - git config --global credential.helper 'cache --timeout=9999999999999' -``` - - -## Postgresql Configuration -Create a PostgreSQL database for Augur to use -```shell -sudo su - -su - postgres -psql -``` - -Then, from within the resulting postgresql shell: -```sql -CREATE DATABASE augur; -CREATE USER augur WITH ENCRYPTED PASSWORD 'password'; -GRANT ALL PRIVILEGES ON DATABASE augur TO augur; -``` - -Once you are successfully logged out, return to your user by exiting `psql`, then typing `exit` to exit the postgres user, and `exit` a SECOND time to exit the root user. -``` -postgres=# \quit -``` - -```shell -exit -exit -``` - -## Rabbitmq Broker Configuration -You have to setup a specific user, and broker host for your augur instance. You can accomplish this by running the below commands: -```shell -sudo rabbitmqctl add_user augur password123 || -sudo rabbitmqctl add_vhost augur_vhost && -sudo rabbitmqctl set_user_tags augur augurTag && -sudo rabbitmqctl set_permissions -p augur_vhost augur ".*" ".*" ".*" -``` - -NOTE: it is important to have a static hostname when using rabbitmq as it uses hostname to communicate with nodes. - -If your setup of rabbitmq is successful your broker url should look like this: - -**broker_url = `amqp://augur:password123@localhost:5672/augur_vhost`** - -**During Augur installation, you will be prompted for this broker_url** - -## Proxying Augur through Nginx -Assumes nginx is installed. - -Then you create a file for the server you want Augur to run under in the location of your `sites-enabled` directory for nginx (In this example, Augur is running on port 5038: - -``` -server { - listen 80; - server_name zoo.chaoss.tv; - - location /api/unstable/ { - proxy_pass http://zoo.chaoss.tv:5038; - proxy_set_header Host $host; - } - - location / { - proxy_pass http://127.0.0.1:5038; - } - - error_log /var/log/nginx/augurview.osshealth.error.log; - access_log /var/log/nginx/augurview.osshealth.access.log; - -} -``` - -## Installing and Configuring Augur! -Create a Python Virtual Environment `python3 -m venv ~/virtual-env-directory` - -Activate your Python Virtual Environment `source ~/virtual-env-directory/bin/activate` - -From the root of the Augur Directory, type `make install` - -You will be prompted to provide your GitHub username and password, your GitLab username and password, and the postgresql database where you want to have the Augur Schema built. You will also be prompted to provide a directory where repositories will be clone into. - -## Post Installation of Augur - -### Redis Broker Configuration -If applications other than Augur are running on the same server, and using `redis-server` it is important to ensure that Augur and these other applications (or additional instances of Augur) are using distinct "cache_group". You can change from the default value of zero by editing the `augur_operations.config` table directly, looking for the "Redis" section_name, and the "cache_group" setting_name. This SQL is also a template: -```sql -UPDATE augur_operations.config -SET value = 2 -WHERE -section_name='Redis' -AND -setting_name='cache_group'; -``` - -## Augur Commands - -To access command line options, use `augur --help`. To load repos from GitHub organizations prior to collection, or in other ways, the direct route is `augur db --help`. - -Start a Flower Dashboard, which you can use to monitor progress, and report any failed processes as issues on the Augur GitHub site. The error rate for tasks is currently 0.04%, and most errors involve unhandled platform API timeouts. We continue to identify and add fixes to handle these errors through additional retries. Starting Flower: `(nohup celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)` NOTE: You can use any open port on your server, and access the dashboard in a browser with http://servername-or-ip:8400 in the example above (assuming you have access to that port, and its open on your network.) - -## Starting your Augur Instance -Start Augur: `(nohup augur backend start &)` - -When data collection is complete you will see only a single task running in your flower Dashboard. - -## Accessing Repo Addition and Visualization Front End -Your Augur intance will now be available at http://hostname.io:port_number - -For example: http://chaoss.tv:5038 - -Note: Augur will run on port 5000 by default (you probably need to change that in augur_operations.config for OSX) - -## Stopping your Augur Instance -You can stop augur with `augur backend stop`, followed by `augur backend kill`. We recommend waiting 5 minutes between commands so Augur can shutdown more gently. There is no issue with data integrity if you issue them seconds apart, its just that stopping is nicer than killing. - -### Docker -1. Make sure docker, and docker-compose are both installed -2. Modify the `environment.txt` file in the root of the repository to include your GitHub and GitLab API keys. -3. If you are already running postgresql on your server you have two choices: - - Change the port mappings in the `docker-compose.yml` file to match ports for Postgresql not currently in use. - - Change to variables in `environment.txt` to include the correct values for your local, non-docker-container database. -4. `sudo docker build -t augur-new -f docker/backend/Dockerfile .` -5. `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to run the database in a Docker Container or - `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to connect to an already running database. - -### Errata (Old Frontend) - -14. If you have frontend configuration issues that result in a *failure* to complete steps with npm, we recommend you install and use `nvm`: https://tecadmin.net/how-to-install-nvm-on-ubuntu-20-04/ to set your nodejs release to the latest LTS of 12.x or 16.x. For example: `nvm ls-remote | grep -i 'latest'` and `nvm alias default 16.??` (whatever the latest version of 16 is.) -15. Also, please explore our new frontend, being developed at https://github.com/augurlabs/augur_view. The `dev` branch is the most current. - diff --git a/docs/new-install-ubuntu-python-3.10.md b/docs/new-install-ubuntu-python-3.10.md new file mode 100644 index 0000000000..d9216672bc --- /dev/null +++ b/docs/new-install-ubuntu-python-3.10.md @@ -0,0 +1,378 @@ +## Augur Setup + +# Ubuntu 22.x +We default to this version of Ubuntu for the moment because Augur does not yet support python3.10, which is the default version of python3.x distributed with Ubuntu 22.0x.x + +## Git Platform Requirements (Things to have setup prior to initiating installation.) +1. Obtain a GitHub Access Token: https://github.com/settings/tokens +2. Obtain a GitLab Access Token: https://gitlab.com/-/profile/personal_access_tokens + +### Fork and Clone Augur +1. Fork https://github.com/chaoss/augur +2. Clone your fork. We recommend creating a `github` directory in your user's base directory. + +## Pre-Requisite Operating System Level Packages +Here we ensure your system is up to date, install required python libraries, install postgresql, and install our queuing infrastrucutre, which is composed of redis-server and rabbitmq-server + +### Executable +```shell +sudo apt update && +sudo apt upgrade && +sudo apt install software-properties-common && +sudo apt install python3.10 && +sudo apt install python3-dev && +sudo apt install python3.10-venv && +sudo apt install postgresql postgresql-contrib postgresql-client && +sudo apt install build-essential && +sudo apt install redis-server && # required +sudo apt install erlang && # required +sudo apt install rabbitmq-server && #required +sudo snap install go --classic && #required: Go Needs to be version 1.19.x or higher. Snap is the package manager that gets you to the right version. Classic enables it to actually be installed at the correct version. +sudo apt install nginx && # required for hosting +sudo add-apt-repository ppa:mozillateam/firefox-next && +sudo apt install firefox=111.0~b8+build1-0ubuntu0.22.04.1 && +sudo apt install firefox=115.0~b9+build1-0ubuntu0.22.04.1 +sudo apt install firefox-geckodriver + +# You will almost certainly need to reboot after this. +``` + +### RabbitMQ Configuration +The default timeout for RabbitMQ needs to be set on Ubuntu 22.x. +```shell +sudo vi /etc/rabbitmq/advanced.config +``` + +Add this one line to that file (the period at the end matters): +```shell +[ {rabbit, [ {consumer_timeout, undefined} ]} ]. +``` + +## Git Configuration +There are some Git configuration parameters that help when you are cloning repos over time, and a platform prompts you for credentials when it finds a repo is deleted: +```shell + git config --global diff.renames true && + git config --global diff.renameLimit 200000 && + git config --global credential.helper cache && + git config --global credential.helper 'cache --timeout=9999999999999' +``` + + +## Postgresql Configuration +Create a PostgreSQL database for Augur to use +```shell +sudo su - && +su - postgres && +psql +``` + +Then, from within the resulting postgresql shell: +```sql +CREATE DATABASE augur; +CREATE USER augur WITH ENCRYPTED PASSWORD 'password'; +GRANT ALL PRIVILEGES ON DATABASE augur TO augur; +``` + +**If you're using PostgreSQL 15 or later**, default database permissions will prevent Augur's installer from configuring the database. Add one last line after the above to fix this: +```sql +GRANT ALL ON SCHEMA public TO augur; +``` + +After that, return to your user by exiting `psql` +``` +postgres=# \quit +``` + +Here we want to start an SSL connection to the `augur` database on port 5432: +```shell +psql -h localhost -U postgres -p 5432 +``` + +Now type `exit` to log off the postgres user, and `exit` a SECOND time to log off the root user. +```shell +exit +exit +``` + +## Rabbitmq Broker Configuration +You have to setup a specific user, and broker host for your augur instance. You can accomplish this by running the below commands: +```shell +sudo rabbitmq-plugins enable rabbitmq_management && +sudo rabbitmqctl add_user augur password123 && +sudo rabbitmqctl add_vhost augur_vhost && +sudo rabbitmqctl set_user_tags augur augurTag administrator && +sudo rabbitmqctl set_permissions -p augur_vhost augur ".*" ".*" ".*" +``` + +- We need rabbitmq_management so we can purge our own queues with an API call +- We need a user +- We need a vhost +- We then set permissions + +NOTE: it is important to have a static hostname when using rabbitmq as it uses hostname to communicate with nodes. + +RabbitMQ's server can then be started from systemd: +```shell +sudo systemctl start rabbitmq-server +``` + +If your setup of rabbitmq is successful your broker url should look like this: + +**broker_url = ` `** + +### RabbitMQ Developer Note: +These are the queues we create: +- celery (the main queue) +- secondary +- scheduling + +The endpoints to hit to purge queues on exit are: +``` +curl -i -u augur:password123 -XDELETE http://localhost:15672/api/queues/augur_vhost/celery + +curl -i -u augur:password123 -XDELETE http://localhost:15672/api/queues/augur_vhost/secondary + +curl -i -u augur:password123 -XDELETE http://localhost:15672/api/queues/augur_vhost/scheduling +``` + +We provide this functionality to limit, as far as possible, the need for sudo privileges on the Augur operating system user. With sudo, you can accomplish the same thing with (Given a vhost named AugurB [case sensitive]): + +1. To list the queues +``` + sudo rabbitmqctl list_queues -p AugurB name messages consumers +``` + +2. To empty the queues, simply execute the command for your queues. Below are the 3 queues that Augur creates for you: +``` + sudo rabbitmqctl purge_queue celery -p augur_vhost + sudo rabbitmqctl purge_queue secondary -p augur_vhost + sudo rabbitmqctl purge_queue scheduling -p augur_vhost +``` + + +Where augur_vhost is the vhost. The management API at port 15672 will only exist if you have already installed the rabbitmq_management plugin. + +**During Augur installation, you will be prompted for this broker_url** + +## Proxying Augur through Nginx +Assumes nginx is installed. + +Then you create a file for the server you want Augur to run under in the location of your `sites-enabled` directory for nginx. In this example, Augur is running on port 5038: (the long timeouts on the settings page is for when a user adds a large number of repos or orgs in a single session to prevent timeouts from nginx) + +``` +server { + server_name ai.chaoss.io; + + location /api/unstable/ { + proxy_pass http://ai.chaoss.io:5038; + proxy_set_header Host $host; + } + + location / { + proxy_pass http://127.0.0.1:5038; + } + + location /settings { + + proxy_read_timeout 800; + proxy_connect_timeout 800; + proxy_send_timeout 800; + } + + error_log /var/log/nginx/augurview.osshealth.error.log; + access_log /var/log/nginx/augurview.osshealth.access.log; + +} + +``` + +### Setting up SSL (https) +Install Certbot: +``` +sudo apt update && +sudo apt upgrade && +sudo apt install certbot && +sudo apt-get install python3-certbot-nginx +``` + +Generate a certificate for the specific domain for which you have a file already in the sites-enabled directory for nginx (located at `/etc/nginx/sites-enabled` on Ubuntu): +``` + sudo certbot -v --nginx -d ai.chaoss.io +``` + +In the example file above. Your resulting nginx sites-enabled file will look like this: + +``` +server { + server_name ai.chaoss.io; + + location /api/unstable/ { + proxy_pass http://ai.chaoss.io:5038; + proxy_set_header Host $host; + } + + location / { + proxy_pass http://127.0.0.1:5038; + } + + location /settings { + + proxy_read_timeout 800; + proxy_connect_timeout 800; + proxy_send_timeout 800; + } + + error_log /var/log/nginx/augurview.osshealth.error.log; + access_log /var/log/nginx/augurview.osshealth.access.log; + + listen 443 ssl; # managed by Certbot + ssl_certificate /etc/letsencrypt/live/ai.chaoss.io/fullchain.pem; # managed by Certbot + ssl_certificate_key /etc/letsencrypt/live/ai.chaoss.io/privkey.pem; # managed by Certbot + include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot + ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot + +} + +server { + if ($host = ai.chaoss.io) { + return 301 https://$host$request_uri; + } # managed by Certbot + + + listen 80; + server_name ai.chaoss.io; + return 404; # managed by Certbot + + +} +``` + +## Installing and Configuring Augur! +Create a Python Virtual Environment `python3 -m venv ~/virtual-env-directory` + +Activate your Python Virtual Environment `source ~/virtual-env-directory/bin/activate` + +From the root of the Augur Directory, type `make install`. You will be prompted to provide: + +- "User" is the PSQL database user, which is `augur` if you followed instructions exactly +- "Password" is the above user's password +- "Host" is the domain used with nginx, e.g. `ai.chaoss.io` +- "Port" is 5432 unless you reconfigured something +- "Database" is the name of the Augur database, which is `augur` if you followed instructions exactly +- The GitHub token created earlier +- Then the username associated with it +- Then the same for GitLab +- and finally a directory to clone repositories to + +## Post Installation of Augur + +### Redis Broker Configuration +If applications other than Augur are running on the same server, and using `redis-server` it is important to ensure that Augur and these other applications (or additional instances of Augur) are using distinct "cache_group". You can change from the default value of zero by editing the `augur_operations.config` table directly, looking for the "Redis" section_name, and the "cache_group" setting_name. This SQL is also a template: +```sql +UPDATE augur_operations.config +SET value = 2 +WHERE +section_name='Redis' +AND +setting_name='cache_group'; +``` + +#### What does Redis Do? +Redis is used to make the state of data collection jobs visible on an external dashboard, like Flower. Internally, Augur relies on Redis to cache GitHub API Keys, and for OAuth Authentication. Redis is used to maintain awareness of Augur's internal state. + +#### What does RabbitMQ Do? +Augur is a distributed system. Even on one server, there are many collection processes happening simultaneously. Each job to collect data is put on the RabbitMQ Queue by Augur's "Main Brain". Then independent workers pop messages off the RabbitMQ Queue and go collect the data. These tasks then become standalone processes that report their completion or failure states back to the Redis server. + + +**Edit** the `/etc/redis/redis.conf` file to ensure these parameters are configured in this way: +```shell +supervised systemd +databases 900 +maxmemory-samples 10 +maxmemory 20GB +``` + +**NOTE**: You may be able to have fewer databases and lower maxmemory settings. This is a function of how many repositories you are collecting data for at a given time. The more repositories you are managing data for, the close to these settings you will need to be. + +**Consequences** : If the settings are too low for Redis, Augur's maintainer team has observed cases where collection appears to stall. (TEAM: This is a working theory as of 3/10/2023 for Ubuntu 22.x, based on EC2 experiments.) + + +#### Possible EC2 Configuration Requirements + +With virtualization there may be issues associated with redis-server connections exceeding available memory. In these cases, the following workarounds help to resolve issues. + +Specifically, you may find this error in your augur logs: +```shell +redis.exceptions.ConnectionError: Error 111 connecting to 127.0.0.1:6379. Connection refused. +``` + +**INSTALL** `sudo apt install libhugetlbfs-bin` + +**COMMAND**: +``` +sudo && +sudo echo never > /sys/kernel/mm/transparent_hugepage/enabled +``` + + +```shell +sudo vi /etc/rc.local +``` + +**paste** into `/etc/rc.local` +```shell +if test -f /sys/kernel/mm/transparent_hugepage/enabled; then + echo never > /sys/kernel/mm/transparent_hugepage/enabled +fi +``` + + +**EDIT** : `/etc/default/grub` add the following line: +```shell +GRUB_DISABLE_OS_PROBER=true +``` + + +## Postgresql Configuration +Your postgresql instance should optimally allow 1,000 connections: + +```shell +max_connections = 1000 # (change requires restart) +shared_buffers = 8GB # min 128kB +work_mem = 2GB # min 64kB +``` + +Augur will generally hold up to 150 simultaneous connections while collecting data. The 1,000 number is recommended to accommodate both collection and analysis on the same database. Use of PGBouncer or other utility may change these characteristics. + +## Augur Commands + +To access command line options, use `augur --help`. To load repos from GitHub organizations prior to collection, or in other ways, the direct route is `augur db --help`. + +Start a Flower Dashboard, which you can use to monitor progress, and report any failed processes as issues on the Augur GitHub site. The error rate for tasks is currently 0.04%, and most errors involve unhandled platform API timeouts. We continue to identify and add fixes to handle these errors through additional retries. Starting Flower: `(nohup celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)` NOTE: You can use any open port on your server, and access the dashboard in a browser with http://servername-or-ip:8400 in the example above (assuming you have access to that port, and its open on your network.) + +If you're using a virtual machine within Windows and you get an error about missing AVX instructions, you should kill Hyper-V. Even if it doesn't *appear* to be active, it might still be affecting your VM. Follow [these instructions](https://stackoverflow.com/a/68214280) to disable Hyper-V, and afterward AVX should pass to the VM. + +## Starting your Augur Instance +Start Augur: `(nohup augur backend start &)` + +When data collection is complete you will see only a single task running in your flower Dashboard. + +## Accessing Repo Addition and Visualization Front End +Your Augur instance will now be available at http://hostname.io:port_number + +For example: http://chaoss.tv:5038 + +Note: Augur will run on port 5000 by default (you probably need to change that in augur_operations.config for OSX) + +## Stopping your Augur Instance +You can stop augur with `augur backend stop`, followed by `augur backend kill`. We recommend waiting 5 minutes between commands so Augur can shutdown more gently. There is no issue with data integrity if you issue them seconds apart, its just that stopping is nicer than killing. + +### Docker +1. Make sure docker, and docker-compose are both installed +2. Modify the `environment.txt` file in the root of the repository to include your GitHub and GitLab API keys. +3. If you are already running postgresql on your server you have two choices: + - Change the port mappings in the `docker-compose.yml` file to match ports for Postgresql not currently in use. + - Change to variables in `environment.txt` to include the correct values for your local, non-docker-container database. +4. `sudo docker build -t augur-new -f docker/backend/Dockerfile .` +5. `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to run the database in a Docker Container or + `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to connect to an already running database. diff --git a/docs/source/login.rst b/docs/source/login.rst index 92ab6914a8..f549751186 100644 --- a/docs/source/login.rst +++ b/docs/source/login.rst @@ -6,6 +6,10 @@ Augur implements the Oauth 2.0 specification, and each Augur instance is capable Prerequisites -------------- +If your Augur instance is running behind Nginx or Apache, make sure this parameter (or its Apache equivalent) is set in your ``sites-enabled`` configuration:: + + proxy_set_header X-Forwarded-Proto $scheme; + Registering a user account on the desired Augur instance is a requirement for creating a Client Application. The developer of the application must follow the below steps: 1. Navigate to the home page of the desired Augur instance. @@ -18,10 +22,10 @@ Once you have registered an account, follow the below steps to create a new Clie 2. Click "Profile". 3. Click "Applications" 4. In the create application form, fill out the application name and redirect URL - - The redirect URL is relative to the user-agent (IE: the user's browser), and **must** be accessible to the user-agent. - - If you are testing an application locally, you may use ``http://127.0.0.1/`` as the host for the redirect URL. The authorization server will *not* prevent redirection if the redirect url is unreachable. + - The redirect URL is relative to the user-agent (i.e. the user's browser), and **must** be accessible to the user-agent. + - If you are testing an application locally, you may use ``http://127.0.0.1/`` or ``http://localho.st`` as the host for the redirect URL. The authorization server will *not* prevent redirection if the redirect url is unreachable. -Once the application has been created, note the Client ID and API Key, as you will need them for application authentication requests. +Once the application has been created, note the Application ID and Client Secret, as you will need them for application authentication requests. Authorization Flow -------------------- @@ -34,7 +38,7 @@ Initial Request The authorization flow is initiated when a user clicks a link or button which redirects the user-agent (browser) to the authorization server. This request URL must be of the following format:: https://augur.example.com/user/authorize? - client_id=[your app client ID] + client_id=[your application ID] &response_type="code" &state=[optional value that you define] @@ -63,9 +67,9 @@ The Client Application must make the following request in order to facilitate th URL: https://augur.example.com/api/unstable/user/session/generate arguments: code: [the temporary authorization code] - grand_type: "code" + grant_type: "code" headers: - Authorization: Client [your app API Key] + Authorization: Client [your client secret] The authorization server will respond with the following on success: @@ -97,9 +101,9 @@ The application may also attempt automatic reauthorization using the previously URL: https://augur.example.com/api/unstable/user/session/refresh arguments: refresh_token: [the previously provided refresh token] - grand_type: "refresh_token" + grant_type: "refresh_token" headers: - Authorization: Client [your app API Key] + Authorization: Client [your client secret] The authorization server will respond with the following on success: @@ -120,8 +124,8 @@ See the rest API documentation for more specific details about these login endpo Making Authenticated Requests ------------------------------ -Once the User Session Token has been aqcuired, authenticated requests must be made using both the Client Application API Key and the Bearer Token. Authentication credentials must be provided in the ``Authorization`` header as such:: +Once the User Session Token has been acquired, authenticated requests must be made using both the Client Secret and the Bearer Token. Authentication credentials must be provided in the ``Authorization`` header as such:: - Authorization: Client [API Key], Bearer [User Session Token] + Authorization: Client [Client Secret], Bearer [User Session Token] -**Please note that both the Client API Key and the User Sesson Token must be included in the Authorization header for authenticated requests** \ No newline at end of file +**Please note that both the Client Secret and the User Sesson Token must be included in the Authorization header for authenticated requests** diff --git a/metadata.py b/metadata.py index 3ab4ed8bba..0d41a3e5e3 100644 --- a/metadata.py +++ b/metadata.py @@ -5,8 +5,8 @@ __short_description__ = "Python 3 package for free/libre and open-source software community metrics, models & data collection" -__version__ = "0.51.0" -__release__ = "v0.51.0 (Free Taylor Swift Tickets)" +__version__ = "0.51.1" +__release__ = "v0.51.1 (Free Taylor Swift Tickets)" __license__ = "MIT" __copyright__ = "University of Missouri, University of Nebraska-Omaha, CHAOSS, Brian Warner & Augurlabs 2023"