Merge branch 'b_1_5_2' into 2284-bugfix

Signed-off-by: Mauro MSL <[email protected]>

.github/ISSUE_TEMPLATE/bug_report.md

@@ -4,7 +4,6 @@ about: Create a report to help us improve
 title: ''
 labels: bug
 assignees: ''
-
 ---
 
 **Describe the bug**

.github/ISSUE_TEMPLATE/documentation_update.md

@@ -0,0 +1,14 @@
+---
+name: Documentation update
+about: Suggest an update to Janeway Documentation
+title: ''
+labels: documentation
+assignees: ''
+
+---
+
+**Describe the area of the documentation you would like updated/added.**
+A clear and concise description of what the problem is. Ex. xyz is missing from the documentation
+
+**Additional context**
+Add any other context or screenshots about the request here.

.gitignore

@@ -70,10 +70,13 @@ src/core/settings.py
 /src/files/import_cache
 /src/files/data_backup
 /src/files/xsl
+/src/files/preprints
+/src/files/repos
 /src/media/django-summernote
 /src/media/*
 /src/collected-static
-
+/src/files/robots/**
+/src/files/sitemaps/**
 mydatabase
 node_modules/
 src/plugins/*
@@ -86,22 +89,15 @@ src/media/profile_images/*
 *.swp
 .vim/
 
-# gulp
-/src/static/OLH/*
-
 src/urls\.txt
 
 src/files/styling/
-src/static/OLH
 src/utils/management/commands/import_news\.py
 src/core/settings/
 src/utils/management/commands/redirects\.py
 .vscode/**
-src/static/mater
 ial/
 src/texture/**
-/src/static/material/**
-/src/static/admin/hypothesis/**
 
 *.ipynb
 
@@ -112,8 +108,8 @@ janeway\.sublime-workspace
 terminal\.glue
 
 src/core/management/commands
-
 src/core/management/__init__\.py
+src/utils/management/commands/test_command.py
 
 src/auth\.json
 
@@ -123,11 +119,29 @@ src/.DS_Store
 .DS_Store
 
 src/static/superhero/
-
-src/themes/clean
-
 src/themes/superhero
 
 # Lando
-dockerfiles/lando_local.env
+local.env
 .lando.local.yml
+dockerfiles/lando_local.env
+
+src/utils/management/commands/test_command.py
+
+# Emacs backup files
+*~
+
+# docker env
+\.env
+
+# Themes and subthemes
+/src/themes/*
+!/src/themes/clean/
+!/src/themes/material/
+!/src/themes/OLH/
+
+# Static files
+/src/static/*
+!/src/static/common/
+!/src/static/admin/
+/src/static/admin/hypothesis/**

.lando.yml

@@ -8,7 +8,7 @@ env_file:
 
 services:
   appserver:
-    type: python:3.5.9
+    type: python:3.6
     command: python /app/src/manage.py runserver 0.0.0.0:8000 -v 3
     build_as_root:
       - grep '^deb ' /etc/apt/sources.list | perl -pe 's/deb /deb-src /' >> /etc/apt/sources.list
@@ -36,9 +36,22 @@ tooling:
   python:
     service: appserver
     cmd: python
+    dir: /app/src
+  pip:
+    service: appserver
+    description: run pip commands to manage Python package installation in this environment
+    cmd: pip
+    dir: /app/src
   manage:
     service: appserver
-    cmd: cd /app/src && python manage.py
+    cmd: python manage.py
+    dir: /app/src
+  restart-runserver:
+    service: appserver
+    description: Quickly restarts the Django runserver process, follows logs, and enables interactive debugging
+    cmd: killall python || python /app/src/manage.py runserver 0.0.0.0:8000 -v 3
+    dir: /app/src
+    user: root
   psql:
     service: db
     cmd: psql -U postgres

.update.sh

@@ -1,11 +1,20 @@
 #!/usr/bin/env bash
+set -euo pipefail
 
 # This command will run an update on Janeway.
 
 pip3 install -r requirements.txt
-python3 src/manage.py backup
 python3 src/manage.py migrate
 python3 src/manage.py build_assets
 python3 src/manage.py collectstatic --no-input
+DJANGO_SETTINGS_MODULE=1 python3 src/manage.py compilemessages
 python3 src/manage.py load_default_settings
+python3 src/manage.py update_repository_settings
 python3 src/manage.py install_plugins
+python3 src/manage.py update_translation_fields
+python3 src/manage.py clear_cache
+python3 src/manage.py install_cron
+python3 src/manage.py populate_history cms.Page comms.NewsItem repository.Repository
+
+echo "REMINDER: don't forget to restart your webserver!"
+exit 0

Makefile

@@ -5,6 +5,7 @@ endif
 # Exposed ports
 JANEWAY_PORT ?= 8000
 PGADMIN_PORT ?= 8001
+SNAKEVIZ_PORT ?= 8002
 
 unexport NO_DEPS
 DB_NAME ?= janeway
@@ -45,6 +46,15 @@ ifdef VERBOSE
 	_VERBOSE=--verbose
 endif
 
+# Email
+ifdef DEBUG_SMTP
+	JANEWAY_EMAIL_BACKEND=django.core.mail.backends.smtp.EmailBackend
+	JANEWAY_EMAIL_HOST=janeway-debug-smtp
+	JANEWAY_EMAIL_PORT=1025
+	JANEWAY_EMAIL_USE_TLS=
+endif
+LOCALES_DIR = ./src/core/locales
+
 export DB_VENDOR
 export DB_HOST
 export DB_PORT
@@ -53,10 +63,17 @@ export DB_USER
 export DB_PASSWORD
 export JANEWAY_PORT
 export PGADMIN_PORT
+
+export JANEWAY_EMAIL_BACKEND
+export JANEWAY_EMAIL_HOST
+export JANEWAY_EMAIL_PORT
+export JANEWAY_EMAIL_USE_TLS
+
 SUFFIX ?= $(shell date +%s)
 SUFFIX := ${SUFFIX}
 DATE := `date +"%y-%m-%d"`
 
+.PHONY: janeway
 all: help
 run: janeway
 help:		## Show this help.
@@ -96,5 +113,26 @@ uninstall:	## Removes all janeway related docker containers, docker images and d
 	@echo " Janeway has been uninstalled"
 check:		## Runs janeway's test suit
 	bash -c "DB_VENDOR=sqlite make command CMD=test"
+migrate:		## Runs Django's migrate command
+	bash -c "make command CMD=migrate"
+makemigrations:		## Runs Django's makemigrations command
+	bash -c "make command CMD=makemigrations"
+makemessages:
+	#$(foreach file, $(wildcard $(LOCALES_DIR)/*), make command CMD="makemessages --locale=$(file) --ignore=src/plugins/*";)
+	#@for f in $(shell ls ${LOCALES_DIR}); make command CMD='makemessages --locale=$${f} --ignore=src/plugins/*';)
+	bash -c "make command CMD='makemessages \
+		--locale=de \
+		--locale=cy \
+		--locale=fr \
+		--locale=it \
+		--locale=nl \
+		--locale=en-us \
+		--ignore=src/plugins/* \
+	'"
+
+build_assets:		## Runs Janeway's build_assets command
+	bash -c "make command CMD=build_assets"
 basebuild:		## Builds the base docker image
-	bash -c "docker build --no-cache -t janeway:`git rev-parse --abbrev-ref HEAD` ."
+	bash -c "docker build --no-cache -t birkbeckctp/janeway-base:latest -f dockerfiles/Dockerfile.base ."
+snakeviz:
+	docker-compose run --publish $(SNAKEVIZ_PORT):$(SNAKEVIZ_PORT) $(NO_DEPS) --rm --entrypoint=snakeviz janeway-web $(FILE) --server -H 0.0.0.0 -p $(SNAKEVIZ_PORT)

README.md

@@ -1,13 +1,13 @@
 ![Janeway Logo](http://www.openlibhums.org/hosted_files/Janeway-Logo-05.png "Janeway")
 
-Janeway is a journal platform designed for publishing scholarly research material. It is developed and maintained by the Centre for Technology and Publishing at Birkbeck, University of London.
+Janeway is a web-based platform for publishing journals, preprints, conference proceedings, and books. It is developed and maintained by a team of developers at the Open Library of Humanities, part of Birkbeck, University of London.
 
 # Technology
-Janeway is written in Python (3.5+) and utilises the Django framework (1.11 LTS). 
+Janeway is written in Python (3.6+) and utilises the Django framework (3.2). 
 
 
 # Installation instructions
-Developer installation [instructions are available in our documentation site](https://janeway.readthedocs.io/en/feature-documentation/installation.html#installation-guide).
+Developer installation [instructions are available in our documentation site](https://janeway.readthedocs.io/en/latest/installation.html#installation-guide).
 
 A guide for installing on the live environment with [apache and mod_wsgi](https://github.com/BirkbeckCTP/janeway/wiki/Janeway%2C-Apache-and-WSGI) is also available.
 
@@ -33,6 +33,21 @@ Uninstalling Janeway is as simple as running ``make uninstall`` which will delet
 
 4. We will never accept commits of, or ourselves write, paywall features into Janeway.
 
+# Current development
+
+What are we working on right now? For a high-level view, check out our [public roadmap](https://github.com/orgs/BirkbeckCTP/projects/21).
+
+You can get more detail by viewing our [project boards here on GitHub](https://github.com/orgs/BirkbeckCTP/projects). Open a project to see which issues it includes and what their status is. The status should be one of these:
+
+- To Do -- we plan to do this and include it in this release
+- In Progress -- someone is working on it at this very moment!
+- PR Submitted -- this means one developer has come up with a solution and is waiting for feedback from others
+- Done -- this means at least one other developer has approved the solution and it has been merged into the main codebase in preparation for the release
+
+We aim to build releases in 8-week sprints, though some development cycles have taken quite a bit longer.
+
+[More on how we develop Janeway](https://github.com/orgs/BirkbeckCTP/projects/21/views/1?pane=issue&itemId=18253226).
+
 # Licensing
 Janeway is available under the terms of the GNU AFFERO GENERAL PUBLIC LICENSE (Version 3, 19 November 2007).
 
@@ -46,15 +61,18 @@ In order to more easily associate changes to their respective github issues, ple
 # Contacts
 If you wish to get in touch about Janeway, contact information is provided below.
 
-Project Lead - Martin Paul Eve, martin.eve@bbk.ac.uk
+Andy Byers, Senior Publishing Technologies Developer - a.byers@bbk.ac.uk
 
-Lead Developer - Andy Byers, [email protected]
+# Major Releases
+Major releases are listed below. Between v1.3 & v1.4 there were a large number of minor releases. You can find more information on the [releases](https://github.com/BirkbeckCTP/janeway/releases) page.
 
-# Releases
-- v1.0 Kathryn released 10/08/17
-- v1.1 Chakotay released 01/09/17
-- v1.2 Tuvok released 06/11/17
-- v1.3 Doctor released 10/08/18
+| Version | Released   | Code Name |
+|---------|------------|-----------|
+| v1.0    | 10/07/2017 | Kathryn   |
+| v1.1    | 01/09/2017 | Chakotay  |
+| v1.2    | 06/11/2017 | Tuvok     |
+| v1.3    | 10/08/2018 | Doctor    |
+| v1.4    | 25/10/2021 | Kes       |
 
 # Geolocation
 Janeway includes GeoLite2 data created by MaxMind, available from [https://www.maxmind.com](https://www.maxmind.com)

db/postgres-data/.gitignore

@@ -0,0 +1,3 @@
+*
+*/
+!.gitignore

dev-requirements.txt

@@ -3,3 +3,7 @@ coverage
 ipdb
 python-wordpress-xmlrpc
 Sphinx==1.8.2
+marshmallow
+freezegun
+snakeviz
+django-browser-reload

docker-compose.yml

@@ -59,6 +59,7 @@ services:
     image: dadarek/wait-for-dependencies
     depends_on:
      - "janeway-${DB_VENDOR}"
+     - janeway-debug-smtp
     command: "janeway-${DB_VENDOR}:${DB_PORT}"
 
   janeway-web:
@@ -82,8 +83,15 @@ services:
       - PYTHONDONTWRITEBYTECODE=yes
       - JANEWAY_SETTINGS_MODULE=core.dev_settings
       - NOSE_INCLUDE_EXE=1
+      - JANEWAY_EMAIL_BACKEND
+      - JANEWAY_EMAIL_HOST
+      - JANEWAY_EMAIL_PORT
+      - JANEWAY_EMAIL_USE_TLS
+
     depends_on:
       - "start_dependencies"
+    cap_add:
+      - SYS_PTRACE
 
   janeway-sqlite:
     build:
@@ -92,3 +100,7 @@ services:
     command: /bin/bash
     volumes:
       - ./db/janeway.sqlite:/var/lib/janeway.sqlite
+  janeway-debug-smtp:
+    # Use same python as janeway-web to reduce the number of images
+    image: python:3.8
+    entrypoint: python -u -m smtpd -c DebuggingServer -n 0.0.0.0:1025

dockerfiles/Dockerfile

@@ -3,6 +3,7 @@ ADD . /vol/janeway
 WORKDIR /vol/janeway
 RUN apt-get update
 RUN apt-get install -y pylint
+RUN apt-get install -y gettext
 RUN pip3 install -r requirements.txt --src /tmp/src
 RUN pip3 install -r dev-requirements.txt --src /tmp/src
 RUN if [ -n "$(ls -A ./lib)" ]; then pip3 install -e lib/*; fi

dockerfiles/Dockerfile.base

@@ -1,4 +1,4 @@
-FROM python:3.5
+FROM python:3.10
 ADD ./dockerfiles/janeway.sqlite3 /db/janeway.sqlite3
 RUN curl https://raw.githubusercontent.com/BirkbeckCTP/janeway/master/requirements.txt > /tmp/requirements.txt
 RUN pip3 install -r /tmp/requirements.txt

docs/Dockerfile

@@ -1,7 +1,11 @@
 FROM python:3.8
 
-ADD . /docs
-RUN apt-get update && apt-get install -y -q python-sphinx texlive texlive-latex-extra pandoc build-essential
+RUN mkdir /docs
+
+ADD ./Makefile /docs/Makefile
+ADD ./requirements.txt /docs/requirements.txt
+
+RUN apt-get update && apt-get install -y -q sphinx-doc sphinx-common texlive texlive-latex-extra pandoc build-essential
 RUN pip install -r /docs/requirements.txt
 
 WORKDIR /docs

docs/Makefile

@@ -17,7 +17,7 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-rebuild:
-	@docker build . -t sphinx
+docker-build:
+	@docker build . -t birkbeckctp/sphinx-rtd
 docker:
-	@docker run --rm -ti -v ${PWD}:/docs sphinx
+	@docker run --rm -ti -v ${PWD}:/docs birkbeckctp/sphinx-rtd

docs/README.md

@@ -3,7 +3,7 @@ Python Sphinx project for building the Janeway documentation
 
 ## How to build the documentation
 
-### Installing the depenencies
+### Installing the dependencies
 After installing the dependencies for Janeway, install the requirements described under `requirements.txt`
 `pip install -r requirements.txt`
 

docs/requirements.txt

@@ -1,3 +1,5 @@
 recommonmark
 Sphinx==1.8.2
 sphinx-rtd-theme
+jinja2==2.11.3
+markupsafe==2.0.1