Merge branch 'dev' into dev-bmpg

.gitignore

@@ -4,6 +4,9 @@
 .*
 !/.git*
 
+# backup files
+*~
+
 # extracted libraries
 /libs/**
 !/libs/*.zip
@@ -26,3 +29,4 @@ xerr.log
 conf/ext
 test/ext
 src/ext
+*~

.gitlab-ci.yml

@@ -23,9 +23,7 @@
 
 variables:
   DEPLOY_REF: dev
-  CI_REGISTRY_IMAGE: $CI_REGISTRY/caosdb/caosdb-webui/testenv
-  # When using dind, it's wise to use the overlayfs driver for
-  # improved performance.
+  CI_REGISTRY_IMAGE: $CI_REGISTRY/caosdb/src/caosdb-webui/testenv
 
 image: $CI_REGISTRY_IMAGE:latest
 
@@ -73,9 +71,8 @@ trigger_build:
   tags: [ docker ]
   stage: deploy
   script:
-    - echo $TOKEN
     - /usr/bin/curl -X POST
-       -F token=$DEPLOY_TRIGGER_TOKEN
+       -F token=$CI_JOB_TOKEN
        -F "variables[F_BRANCH]=$CI_COMMIT_REF_NAME"
        -F "variables[WEBUI]=$CI_COMMIT_REF_NAME"
        -F "variables[TriggerdBy]=WEBUI"
@@ -88,6 +85,9 @@ build-testenv:
   image: docker:19.03
   stage: setup
   timeout: 3 h
+  only:
+    - web
+    - schedules
   script: 
     - cd test/docker
     - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
@@ -102,13 +102,13 @@ build-testenv:
 #   stage: deploy
 
 # Special job for serving a static website. See https://docs.gitlab.com/ee/ci/yaml/README.html#pages
-pages:
-  tags: [ docker ]
+pages_prepare: &pages_prepare
+  tags: [ cached-dind ]
   stage: deploy
   only:
-    - dev
+    refs:
+      - /^release-.*$/i
   script:
-      # TODO is this a good location here?
     - npm install jsdoc
     - npm install jsdoc-sphinx
     - echo "Deploying"
@@ -117,3 +117,8 @@ pages:
   artifacts:
     paths:
       - public
+pages:
+  <<: *pages_prepare
+  only:
+    refs:
+      - main

.gitlab/issue_templates/default.md

+## Summary
+
+*Please give a short summary of what the issue is.*
+
+## Expected Behavior
+
+*What did you expect how the software should behave?*
+
+## Actual Behavior
+
+*What did the software actually do?*
+
+## Steps to Reproduce the Problem
+
+*Please describe, step by step, how others can reproduce the problem.  Please try these steps for yourself on a clean system.*
+
+1.
+2.
+3.
+
+## Specifications
+
+- Version: *Which version of this software?*
+- Platform: *Which operating system, which other relevant software versions?*
+
+## Possible fixes
+
+*Do you have ideas how the issue can be resolved?*

CHANGELOG.md

 # Changelog
 All notable changes to this project will be documented in this file.
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [Unpublished]
+
+### Added (for new features, dependecies etc.)
+
+### Changed (for changes in existing functionality)
+
+### Deprecated (for soon-to-be removed features)
+
+### Removed (for now removed features)
+
+### Fixed (for any bug fixes)
+
+### Security (in case of vulnerabilities)
+
+### Documentation (for notable additions or changes of the documentation)
+
+## [0.4.2] - 2021-12-06
+
+### Added (for new features, dependecies etc.)
+
+* Documentation link in standard footer
+* Build properties for footer elements:
+  * `BUILD_FOOTER_CONTACT_HREF`
+  * `BUILD_FOOTER_IMPRINT_HREF`
+  * `BUILD_FOOTER_DOCS_HREF`
+  * `BUILD_FOOTER_SOURCES_HREF`
+  * `BUILD_FOOTER_LICENCE_HREF`
+  See `build.properties.d/00_default.properties` for more information
+* Start editing an entity/creating a new record directly by adding an `#edit` or
+  `#new_record` URI fragment, respectively.
+* Optional WYSIWYG editor with markdown output for text properties. Controled by
+  the `BUILD_MODULE_EXT_EDITMODE_WYSIWYG_TEXT` build variable which is set do
+  `DISABLED` by default.
+  - Added button to version history panel that allows restoring old versions
+
+### Changed (for changes in existing functionality)
+
+* Default footer elements contain invalid links for imprint, contact, and data-policy now
+
+### Deprecated (for soon-to-be removed features)
+
+### Removed (for now removed features)
+
+* Build property `BUILD_CUSTOM_IMPRINT`. Please use BUILD_FOOTER_IMPRINT_HREF
+  and link a document instead. You can always put a html page to
+  `src/ext/html/` and link to that.
+
+### Fixed (for any bug fixes)
+- #156
+- #251
+
+### Security (in case of vulnerabilities)
+
+### Documentation (for notable additions or changes of the documentation)
+
+
+## [0.4.1] - 2021-11-04
+
+### Added (for new features, dependecies etc.)
+
+* `form_panel` module for conveniently creating a panel for web forms.
+* `restore_old_version` function to base functionality (caosdb.js)
+* buttons to the version history modal that allow restoring older versions
+
+### Changed (for changes in existing functionality)
+
+* Default footer elements contain invalid links for imprint, contact, and data-policy now
+
+### Deprecated (for soon-to-be removed features)
+
+### Removed (for now removed features)
+
+* Build property `BUILD_CUSTOM_IMPRINT`. Please use BUILD_FOOTER_IMPRINT_HREF
+  and link a document instead. You can always put a html page to
+  `src/ext/html/` and link to that.
+
+### Fixed (for any bug fixes)
+
+* Auto-completion and edit_mode can handle entity names with empty spaces better now
+* [#251](https://gitlab.indiscale.com/caosdb/src/caosdb-webui/-/issues/251) - Data loss when editing Entities with URL-like properties
+
+### Security (in case of vulnerabilities)
+
+### Documentation (for notable additions or changes of the documentation)
+
+## [0.4.0] - 2021-10-28
+
+### Added (for new features, dependecies etc.)
+
+* Module `ext_qrcode` which generates a QR Code for an entity (pointing to the
+  the head or the exact version).
+* Optional functionality to bookmark all query results. Note that too many
+  bookmarks will result in the URI being too lang and bookmarks will have to be
+  cleared manually.
+
+### Changed (for changes in existing functionality)
+
+### Deprecated (for soon-to-be removed features)
+
+### Removed (for now removed features)
+
+* `getEntityId`, a former duplicate of `getEntityID` which must be used instead.
+
+### Fixed (for any bug fixes)
+
+### Security (in case of vulnerabilities)
+
+### Documentation (for notable additions or changes of the documentation)
+
+## [v0.4.0-rc1] - 2021-06-16
+
+### Added (for new features, dependecies etc.)
+
+- `ext_applicable` module for building fancy features which append
+  functionality to entities (EXPERIMENTAL).
+- `ext_cosmetics` module which converts http(s) uris in property values into
+  clickable links (with tests)
+- Added a menu/toc for the tour
+- Added a previous and next buttons for pages in the tour
+- Added warnings to inform about minimum width when accessing tour and
+  edit mode on small screens.
+- Added a tutorial for the edit mode to the documentation
+- Documentation on how to customize reference resolving
+
+### Changed (for changes in existing functionality)
+
+- Updated from bootstrap 3 to bootstrap 5. This is a major change which will
+  possibly break existing custom implementations (e.g. a custom welcome page)
+  since a lot of classes where renamed by bootstrap an other classes have been
+  dropped entirely (e.g. "jumbotron"). Please have a look at
+    * https://getbootstrap.com/docs/5.0/migration/
+    * https://getbootstrap.com/docs/4.6/migration/
+- Moved the resolving of references to Person Records to separate
+  example which can be disabled
+
+### Deprecated (for soon-to-be removed features)
+
+- css-class `.caosdb-property-text-value`. Please use
+  `.caosdb-f-property-text-value` or `.caosdb-v-property-text-value` instead.
+
+### Removed (for now removed features)
+
+* `#subnav` element from navbar which was previously used for spacing
+* `caosdb.form.ready` event
+
+### Fixed
+
+- #212 - form_elements: Drop-down menu shows wrong value after clicking "None"
+- #202 - Make filter fields in edit mode toolbox visible
+- #117 - Reload data model after adding an RT or a Property
+- #214 - Paging panel is hidden.
+- Displaying issues with long lists in property values
+- An issue whereby a grey container would appear above the map when
+  changing the map view.
+- #200 - Re-enabled the file-upload button
+
+### Security (in case of vulnerabilities)
+
+## [v0.3.1] - 2021-06-15
+
+This is the last Bootstrap-3 compatible release.
+
+### Added (for new features, dependecies etc.)
+
+* Displaying and interacting with the entity state.
+* Change password functionality for users of the internal user source. Disable
+  with `BUILD_MODULE_USER_MANAGEMENT=DISABLED` and set the user realm with
+  `BUILD_MODULE_USER_MANAGEMENT_CHANGE_OWN_PASSWORD_REALM=CaosDB`.
+* Visually highlighted drop zones for properties and parents in the edit_mode.
+* two new field types for the form_elements module, `file` and `select`. See
+  the module documentation for more information.
+
+### Changed (for changes in existing functionality)
+- The heading attributes datatype, path, checksum and size are now placed
+  in a `details` html element.
+
+### Deprecated (for soon-to-be removed features)
+
+* Any bootstrap-3 dependencies. Please prepare upgrading to bootstrap-5 with the next release.
+
+### Removed (for now removed features)
+
+* `ext_revisions` module. This module was only a work-around which had been
+  used for versioning functionality before the native versioning was
+  implemented. Also, the `BUILD_MODULE_EXT_REVISIONS` is no longer used and can
+  be removed from the config files in `build.properties.d/`
+
+### Fixed
+
+* #156 - Edit mode for Safari 11
+* #160 - Entity preview for Safari 11
+* Several minor cosmetic flaws
+* Fixed edit mode for Safari 11.
+
+### Security (in case of vulnerabilities)
+
+## [v0.3.0] - 2021-02-10
 
 ### Added (for new features, dependecies etc.)
 
@@ -40,11 +236,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- #144 (Select with ANY VERSION OF).
 - #136 (adding reference properties to entities in edit mode)
 - exclude configuration files when reading files from build.properties.d
 - summaries when opening preview
 - #125 special characters like "\t", \"n", "#" are replaced in table
   download
+- #158 show preview if the entity is too large for the viewport if
+  bottom line is in view.
 
 ### Security (in case of vulnerabilities)
 

DEPENDENCIES.md

+* CaosDB Server 0.5.x
+* Make 4.2.0
+
+# Java Script Libraries (included in this repository)
+* bootstrap-5.0.1
+* bootstrap-autocomplete-2.3.5
+* bootstrap-icons-1.4.1
+* bootstrap-select-1.14.0-beta2
+* dropzone-5.5.0
+* javascript-state-machine-master
+* jquery-3.6.0.min.js
+* loglevel-1.6.4
+* qrcode-1.4.4
+* showdown-1.8.6
+* plotly.js-1.52.2
+* UTIF-8205c1f
+
+## For the map
+
+* leaflet-1.5.1
+* Leaflet.Coordinates-0.1.5
+* leaflet.latlng-graticule-20191007
+* L.Graticule.js https://github.com/turban/Leaflet.Graticule/blob/e9146fbea59ce1b0ada4ea2a012087f9a1a12473/L.Graticule.js
+* proj4js-2.5.0
+* Proj4Leaflet-1.0.1
+
+## For CKEditor (WYSIWYG editor in edit mode)
+
+* we're using a custom-built ckeditor 31.0.0 from
+  https://ckeditor.com/ckeditor-5/online-builder/ with a customized set of
+  editor plugins. Please refer to the `package.json` within
+  `libs/ckeditor...zip` for a full list of said plugins.
+
+## For testing
+* qunit-2.9.2

Makefile

@@ -43,7 +43,8 @@ LIBS_DIR = $(abspath libs)
 TEST_CORE_DIR = $(abspath test/core/)
 TEST_EXT_DIR = $(abspath test/ext)
 TEST_SSS_DIR =$(abspath test/server_side_scripting)
-LIBS = fonts css/bootstrap.css js/bootstrap.js js/state-machine.js js/jquery.js js/showdown.js js/dropzone.js css/dropzone.css js/loglevel.js js/leaflet.js css/leaflet.css css/images js/leaflet-latlng-graticule.js js/proj4.js js/proj4leaflet.js js/leaflet-coordinates.js css/leaflet-coordinates.css js/leaflet-graticule.js js/bootstrap-select.js css/bootstrap-select.css js/bootstrap-autocomplete.min.js js/plotly.js js/pako.js js/utif.js
+LIBS = fonts css/fonts css/bootstrap.css css/bootstrap-icons.css js/state-machine.js js/jquery.js js/showdown.js js/dropzone.js css/dropzone.css js/loglevel.js js/leaflet.js css/leaflet.css css/images js/leaflet-latlng-graticule.js js/proj4.js js/proj4leaflet.js js/leaflet-coordinates.js css/leaflet-coordinates.css js/leaflet-graticule.js js/bootstrap-select.js css/bootstrap-select.css js/bootstrap-autocomplete.min.js js/plotly.js js/pako.js js/utif.js js/bootstrap.js js/qrcode.js js/ckeditor.js
+
 
 TEST_LIBS = $(LIBS) js/qunit.js css/qunit.css $(subst $(TEST_CORE_DIR)/,,$(shell find $(TEST_CORE_DIR)/))
 
@@ -52,9 +53,9 @@ LIBS_SUBDIRS = $(addprefix $(LIBS_DIR)/, js css fonts)
 
 ALL: install
 
-install: clean install-sss cp-src cp-ext cp-conf $(addprefix $(PUBLIC_DIR)/, $(LIBS)) build_properties merge_xsl
+install: clean-ignore-zips install-sss cp-src cp-ext cp-conf $(addprefix $(PUBLIC_DIR)/, $(LIBS)) merge_js build_properties merge_xsl
 
-test: clean install-sss cp-src cp-ext cp-ext-test cp-conf $(addprefix $(PUBLIC_DIR)/, $(TEST_LIBS)) build_properties merge_xsl
+test: clean-ignore-zips install-sss cp-src cp-ext cp-ext-test cp-conf $(addprefix $(PUBLIC_DIR)/, $(TEST_LIBS)) merge_js build_properties merge_xsl
 	@for f in $(shell find $(TEST_EXT_DIR) -type f -iname *.js) ; do \
 		sed -i "/EXTENSIONS/a \<script src=\"$${f#$(TEST_EXT_DIR)/}\" ></script>" $(PUBLIC_DIR)/index.html ; \
 		echo include $$f; \
@@ -67,8 +68,12 @@ test: clean install-sss cp-src cp-ext cp-ext-test cp-conf $(addprefix $(PUBLIC_D
 merge_xsl:
 	misc/merge_xsl.sh
 
+merge_js:
+	for f in ${BUILDFILELIST} ; do source "$$f" ; done ; \
+	JS_DIST_BUNDLE=$${JS_DIST_BUNDLE} AUTO_DISCOVER_MODULES=$$AUTO_DISCOVER_MODULES misc/merge_js.sh $${MODULE_DEPENDENCIES[*]}
+
 EXCLUDE_EXPR = %~ %.backup
-BUILDFILELIST = $(filter-out $(EXCLUDE_EXPR),$(wildcard build.properties.d/*))
+BUILDFILELIST = $(sort $(filter-out $(EXCLUDE_EXPR),$(wildcard build.properties.d/*)))
 build_properties:
 	@set -a -e ; \
 	pushd build.properties.files ; \
@@ -91,24 +96,24 @@ build_properties:
 	@ln -s $(PUBLIC_DIR) $(PUBLIC_DIR)/$(BUILD_NUMBER)
 	@ln -s $(PUBLIC_DIR) $(PUBLIC_DIR)/webinterface
 
-PORT = 8000
+TEST_PORT ?= 8000
 TIMEOUT = 60
 run-test-server: test
-	$(MISC_DIR)/unit_test_http_server.py $(PORT) $(TIMEOUT) False $(PUBLIC_DIR)
+	$(MISC_DIR)/unit_test_http_server.py $(TEST_PORT) $(TIMEOUT) False $(PUBLIC_DIR)
 
 keep-test-server: test
-	$(MISC_DIR)/unit_test_http_server.py $(PORT) -1 True $(PUBLIC_DIR)
+	$(MISC_DIR)/unit_test_http_server.py $(TEST_PORT) -1 True $(PUBLIC_DIR)
 
 run-qunit: test
 	$(foreach exec, firefox Xvfb xwd,\
 	    $(if $(shell which $(exec)),echo "found $(exec)",$(error "No $(exec) in PATH")))
 
 	# start server in background
-	$(MISC_DIR)/unit_test_http_server.py $(PORT) $(TIMEOUT) False $(PUBLIC_DIR) &
+	$(MISC_DIR)/unit_test_http_server.py $(TEST_PORT) $(TIMEOUT) False $(PUBLIC_DIR) &
 
 	# start firefox with virtual xserver
 	Xvfb :1 -screen 0 1024x768x24 &
-	DISPLAY=:1 firefox "http://localhost:$(PORT)/?hidepassed" &
+	DISPLAY=:1 firefox "http://localhost:$(TEST_PORT)/?hidepassed" &
 
 	while [ 1 -eq 1 ]; do \
 		sleep 5 ; \
@@ -171,6 +176,9 @@ cp-ext:
 	for f in $(wildcard $(SRC_EXT_DIR)/xsl/*) ; do \
 		echo "y" | $(CMD_COPY_EXT_FILES) "$$(realpath "$$f")" $(PUBLIC_DIR)/xsl/ ; \
 	done
+	for f in $(wildcard $(SRC_EXT_DIR)/include/*) ; do \
+		echo "y" | $(CMD_COPY_EXT_FILES) "$$(realpath "$$f")" "$(PUBLIC_DIR)/$$(basename "$$f")" ; \
+	done
 
 cp-ext-test:
 	for f in $(wildcard $(TEST_EXT_DIR)/js/*) ; do \
@@ -211,22 +219,25 @@ $(PUBLIC_DIR)/%: $(TEST_EXT_DIR)/%
 	cp -r $< $@
 
 $(LIBS_DIR)/fonts: unzip
-	ln -s $(LIBS_DIR)/bootstrap-3.4.1-dist/fonts $@
+	ln -s $(LIBS_DIR)/bootstrap-icons-1.4.1/fonts/ $@
 
 $(LIBS_DIR)/js/bootstrap.js: unzip $(LIBS_DIR)/js
-	ln -s $(LIBS_DIR)/bootstrap-3.4.1-dist/js/bootstrap.min.js $@
+	ln -s $(LIBS_DIR)/bootstrap-5.0.1-dist/js/bootstrap.bundle.min.js $@
 
 $(LIBS_DIR)/css/bootstrap.css: unzip $(LIBS_DIR)/css
-	ln -s $(LIBS_DIR)/bootstrap-3.4.1-dist/css/bootstrap.min.css $@
+	ln -s $(LIBS_DIR)/bootstrap-5.0.1-dist/css/bootstrap.min.css $@
+
+$(LIBS_DIR)/css/bootstrap-icons.css: unzip $(LIBS_DIR)/css
+	ln -s $(LIBS_DIR)/bootstrap-icons-1.4.1/bootstrap-icons.css $@
 
 $(LIBS_DIR)/js/bootstrap-select.js: unzip $(LIBS_DIR)/js
-	ln -s $(LIBS_DIR)/bootstrap-select-1.13.9/dist/js/bootstrap-select.min.js $@
+	ln -s $(LIBS_DIR)/bootstrap-select-1.14.0-beta2/js/bootstrap-select.min.js $@
 
 $(LIBS_DIR)/css/bootstrap-select.css: unzip $(LIBS_DIR)/css
-	ln -s $(LIBS_DIR)/bootstrap-select-1.13.9/dist/css/bootstrap-select.min.css $@
+	ln -s $(LIBS_DIR)/bootstrap-select-1.14.0-beta2/css/bootstrap-select.min.css $@
 
 $(LIBS_DIR)/js/jquery.js: unzip $(LIBS_DIR)/js
-	ln -s $(LIBS_DIR)/jquery-3.5.1/jquery-3.5.1.min.js $@
+	ln -s $(LIBS_DIR)/jquery-3.6.0.min.js $@
 
 $(LIBS_DIR)/js/showdown.js: unzip $(LIBS_DIR)/js
 	ln -s $(LIBS_DIR)/showdown-1.8.6/dist/showdown.min.js $@
@@ -261,6 +272,9 @@ $(LIBS_DIR)/css/images: unzip $(LIBS_DIR)/css
 $(LIBS_DIR)/js/leaflet-graticule.js: unzip $(LIBS_DIR)/js
 	ln -s $(LIBS_DIR)/L.Graticule.js $@
 
+$(LIBS_DIR)/js/bootstrap.bundle.min.js: unzip $(LIBS_DIR)/js
+	ln -s $(LIBS_DIR)/bootstrap.bundle.min.js $@
+
 $(LIBS_DIR)/js/leaflet-latlng-graticule.js: unzip $(LIBS_DIR)/js
 	ln -s $(LIBS_DIR)/leaflet.latlng-graticule-20191007/leaflet.latlng-graticule.js $@
 
@@ -288,21 +302,33 @@ $(LIBS_DIR)/js/pako.js: unzip $(LIBS_DIR)/js
 $(LIBS_DIR)/js/utif.js: unzip $(LIBS_DIR)/js
 	ln -s $(LIBS_DIR)/UTIF-8205c1f/UTIF.js $@
 
+$(LIBS_DIR)/js/qrcode.js: unzip $(LIBS_DIR)/js
+	ln -s $(LIBS_DIR)/qrcode-1.4.4/qrcode.min.js $@
+
+$(LIBS_DIR)/js/ckeditor.js: unzip $(LIBS_DIR)/js
+	ln -s $(LIBS_DIR)/ckeditor5-31.0.0-k356w86hp13l/build/ckeditor.js $@
+
 
 $(addprefix $(LIBS_DIR)/, js css):
 	mkdir $@ || true
 
-.PHONY: clean
-clean:
+$(LIBS_DIR)/css/fonts: $(LIBS_DIR)/css
+	ln -s $(LIBS_DIR)/fonts/ $(LIBS_DIR)/css/fonts
+
+.PHONY: clean-ignore-zips
+clean-ignore-zips:
 	$(RM) -r $(SSS_BIN_DIR)
 	$(RM) -r $(PUBLIC_DIR)
 	for f in $(LIBS_SUBDIRS); do unlink $$f || $(RM) -r $$f || true; done
-	for f in $(patsubst %.zip,%/,$(LIBS_ZIP)); do $(RM) -r $$f; done
 	$(RM) .server_done
 
+.PHONY: clean
+clean: clean-ignore-zips
+	for f in $(patsubst %.zip,%/,$(LIBS_ZIP)); do $(RM) -r $$f; done
+
 .PHONY: unzip
 unzip:
-	for f in $(LIBS_ZIP); do unzip -q -o -d libs $$f; done
+	for f in $(LIBS_ZIP); do echo "unzip $$f" ; unzip -u -q -o -d libs $$f; done
 
 
 PYLINT ?= pylint

README.md

-<!--THIS FILE HAS BEEN GENERATED BY A SCRIPT. PLEASE DON'T CHANGE IT MANUALLY.-->
 
-Project migrated to https://gitlab.com/caosdb
+# README
 
-# Welcome
+## Welcome
 
-This is the **CaosDB WebUI** repository and a part of the CaosDB project.
+This is the **CaosDB Web User Interface** repository and a part of the
+CaosDB project.
 
-# Setup
+## Setup
 
 Please read the [README_SETUP.md](README_SETUP.md) for instructions on how to
 setup this code.
 
 
-# Further Reading
+## Further Reading
 
-Please refer to the [official gitlab repository of the CaosDB
-project](https://gitlab.com/caosdb/caosdb) for more information.
+Please refer to the [official documentation](https://docs.indiscale.com/caosdb-webui/) for more information.
 
-# License
+## Contributing
 
-Copyright (C) 2018 Research Group Biomedical Physics, Max Planck Institute for
-Dynamics and Self-Organization Göttingen.
+Thank you very much to all contributers—[past, present](https://gitlab.com/caosdb/caosdb/-/blob/dev/HUMANS.md), and prospective ones.
+
+### Code of Conduct
+
+By participating, you are expected to uphold our [Code of Conduct](https://gitlab.com/caosdb/caosdb/-/blob/dev/CODE_OF_CONDUCT.md).
+
+### How to Contribute
+
+* You found a bug, have a question, or want to request a feature? Please
+[create an issue](https://gitlab.com/caosdb/caosdb-webui/-/issues).
+* You want to contribute code? Please fork the repository and create a merge
+request in GitLab and choose this repository as target. Make sure to select
+"Allow commits from members who can merge the target branch" under Contribution
+when creating the merge request. This allows our team to work with you on your request.
+- If you have a suggestion for the [documentation](https://docs.indiscale.com/caosdb-webui/),
+the preferred way is also a merge request as describe above (the documentation resides in `src/doc`).
+However, you can also create an issue for it.
+- You can also contact us at **info (AT) caosdb.de**  and join the
+  CaosDB community on
+  [#caosdb:matrix.org](https://matrix.to/#/!unwwlTfOznjEnMMXxf:matrix.org).
+
+## License
+
+* Copyright (C) 2018 Research Group Biomedical Physics, Max Planck Institute
+  for Dynamics and Self-Organization Göttingen.
+* Copyright (C) 2020-2021 Indiscale GmbH <info@indiscale.com>
 
 All files in this repository are licensed under a [GNU Affero General Public
 License](LICENCE.md) (version 3 or later).
-

RELEASE_GUIDELINES.md

-# Release Guidelines for the CaosDB MySQL Backend
+# Release Guidelines for the CaosDB Web Interface
 
 This document specifies release guidelines in addition to the generel release
 guidelines of the CaosDB Project
@@ -8,7 +8,7 @@ guidelines of the CaosDB Project
 
 * All tests are passing.
 * FEATURES.md is up-to-date and a public API is being declared in that document.
-* CHANGELOG.md is up-to-date.
+* CHANGELOG.md is up-to-date (insert version number and remove unpublished)
 * DEPENDENCIES.md is up-to-date.
 
 ## Steps
@@ -18,10 +18,12 @@ guidelines of the CaosDB Project
 
 2. Check all general prerequisites.
 
-3. Merge the release branch into the master branch.
+3. Merge the release branch into the main branch.
 
-4. Tag the latest commit of the master branch with `v<VERSION>`.
+4. Tag the latest commit of the main branch with `v<VERSION>`.
 
 5. Delete the release branch.
 
-6. Merge the master branch back into the dev branch.
+6. Merge the main branch back into the dev branch.
+
+7. Prepare CHANGELOG for next release cycle.

build.properties.d/00_default.properties

@@ -42,7 +42,6 @@
 # Modules enabled/disabled by default
 ##############################################################################
 BUILD_MODULE_EXT_PREVIEW=ENABLED
-BUILD_MODULE_EXT_RESOLVE_REFERENCES=ENABLED
 BUILD_MODULE_EXT_SSS_MARKDOWN=DISABLED
 BUILD_MODULE_EXT_TRIGGER_CRAWLER_FORM=DISABLED
 BUILD_MODULE_EXT_AUTOCOMPLETE=ENABLED
@@ -50,6 +49,18 @@ BUILD_MODULE_EXT_BOTTOM_LINE=ENABLED
 BUILD_MODULE_EXT_BOTTOM_LINE_TABLE_PREVIEW=DISABLED
 BUILD_MODULE_EXT_BOTTOM_LINE_TIFF_PREVIEW=DISABLED
 BUILD_MODULE_EXT_BOOKMARKS=ENABLED
+BUILD_MODULE_EXT_ADD_QUERY_TO_BOOKMARKS=DISABLED
+BUILD_MODULE_EXT_ANNOTATION=ENABLED
+BUILD_MODULE_EXT_COSMETICS_LINKIFY=DISABLED
+BUILD_MODULE_EXT_QRCODE=ENABLED
+
+BUILD_MODULE_USER_MANAGEMENT=ENABLED
+BUILD_MODULE_USER_MANAGEMENT_CHANGE_OWN_PASSWORD_REALM=CaosDB
+
+BUILD_MODULE_EXT_RESOLVE_REFERENCES=ENABLED
+BUILD_EXT_REFERENCES_CUSTOM_RESOLVER=person_reference
+
+BUILD_MODULE_EXT_EDITMODE_WYSIWYG_TEXT=DISABLED
 
 ##############################################################################
 # Navbar properties
@@ -68,7 +79,24 @@ BUILD_FAVICON=pics/caosdb_logo_42.png
 ##############################################################################
 
 # Link to the data policy statement document.
-BUILD_FOOTER_DATA_POLICY_HREF=https://missing-domain.com/missing-page
+BUILD_FOOTER_DATA_POLICY_HREF="Please configure me!"
+
+# Contact mail or link to contact information for the responsible administrator of this caosdb server instance.
+BUILD_FOOTER_CONTACT_HREF="Please configure me!"
+#BUILD_FOOTER_CONTACT_HREF=mailto:info@indiscale.com
+
+# Link to imprint for this caosdb server instance.
+BUILD_FOOTER_IMPRINT_HREF="Please configure me!"
+#BUILD_FOOTER_IMPRINT_HREF=https://www.indiscale.com/imprint/
+
+# Link to docs (should rarely be changed (maybe for additional docs))
+BUILD_FOOTER_DOCS_HREF="https://docs.indiscale.com"
+
+# Link to sources (should almost never be changed (maybe for additional sources))
+BUILD_FOOTER_SOURCES_HREF="https://gitlab.com/caosdb"
+
+# Link to license (should almost never be changed (maybe for other languages))
+BUILD_FOOTER_LICENCE_HREF="https://www.gnu.org/licenses/agpl-3.0.en.html"
 
 # Custom footer elements can be placed here (will be placed inside a <div>
 # element).
@@ -81,9 +109,72 @@ BUILD_FOOTER_CUSTOM_ELEMENT_ONE=
 # ${BUILD_NUMBER}.
 BUILD_FOOTER_CUSTOM_ELEMENT_TWO=
 # BUILD_FOOTER_CUSTOM_ELEMENT_TWO=$(cat footer_element_2.html)
-BUILD_CUSTOM_IMPRINT='<p> Put an imprint note here </p>'
 
 ##############################################################################
 # ext_trigger_crawler_form properties
 ##############################################################################
 BUILD_MODULE_EXT_TRIGGER_CRAWLER_FORM_TOOLBOX="Tools"
+
+##############################################################################
+# Build a dist file containing all JS code from the files in the
+# MODULE_DEPENDENCIES array.
+##############################################################################
+JS_DIST_BUNDLE=TRUE
+##############################################################################
+# TRUE means that all javascript sources which are no mentioned in the
+# MODULE_DEPENDENCIES array will be added in no particular order into the
+# build. If you need to guarantee a specific order (in which the are loaded or
+# appear in the dit file) you need to add them to the MODULE_DEPENDENCIES.
+##############################################################################
+AUTO_DISCOVER_MODULES=TRUE
+##############################################################################
+# Module dependencies
+# Override or extend to specify the order of js files in the resulting
+# bundled js file
+##############################################################################
+MODULE_DEPENDENCIES=(
+    jquery.js
+    bootstrap.js
+    bootstrap-autocomplete.min.js
+    bootstrap-select.js
+    state-machine.js
+    showdown.js
+    dropzone.js
+    loglevel.js
+    plotly.js
+    webcaosdb.js
+    pako.js
+    utif.js
+    caosdb.js
+    form_elements.js
+    ext_autocomplete.js
+    preview.js
+    ext_references.js
+    ext_applicable.js
+    ext_table_preview.js
+    ext_xls_download.js
+    query_shortcuts.js
+    ext_jupyterdrag.js
+    annotation.js
+    edit_mode.js
+    ext_entity_state.js
+    ext_file_download.js
+    leaflet.js
+    leaflet-graticule.js
+    leaflet-latlng-graticule.js
+    leaflet-coordinates.js
+    proj4.js
+    proj4leaflet.js
+    ext_map.js
+    tour.js
+    ext_bottom_line.js
+    ext_sss_markdown.js
+    ext_trigger_crawler_form.js
+    ext_bookmarks.js
+    ext_cosmetics.js
+    qrcode.js
+    ext_qrcode.js
+    form_panel.js
+    ckeditor.js
+    ext_editmode_wysiwyg_text.js
+)

doc/QueryShortcuts/doc.tex

-\documentclass{article}
-% General document formatting
-\usepackage[margin=0.7in]{geometry}
-\usepackage[parfill]{parskip}
-\usepackage[utf8]{inputenc}
-\usepackage{graphicx}
-
-% Related to math
-\usepackage{amsmath,amssymb,amsfonts,amsthm}
-\title{Documentation Query Shortcuts}
-
-\begin{document}
-\maketitle
-\section{Introduction}\label{introduction}
-
-The WebUI supports the creation of query shortcuts which appear below
-the normal query input field. These shortcuts facilitate looking for
-data as query strings which are used frequently. They can be stored and
-reused.
-
-\begin{figure}[h]
-\centering
-\includegraphics[width=.8\textwidth]{shortcut_toolbox.png}
-\caption{The Shortcuts in the Query Panel; Note the Toolbox for in the top
-right}
-\end{figure}
-
-There are two ways to integrate query templates into the WebUI:
-
-\begin{itemize}
-\item
-  Global shortcuts are integrated by the webmaster only. They are
-  defined and stored in a\\
-  \texttt{./conf/ext/json/globale\_query\_shortcuts.json} in the root
-  directory of the webui.
-\item
-  User-defined templates can be defined by users and are only visible
-  for the user who created them. In this sense, user-defined shortcuts
-  are also private, whereas global shortcuts are always publicly
-  visible.
-\end{itemize}
-
-\section{User-defined Query Shortcuts}\label{user-defined-query-shortcuts}
-
-\subsection{Create a New Shortcut}\label{create-a-new-shortcut}
-
-New Query Shortcuts can be generated by any authenticated user with
-sufficient write permissions.
-
-In the web interface, click \texttt{Query}. In the \texttt{Shortcuts}
-section, click the wrench (on the right side).
-
-In the drop-down menu, click \texttt{Create}.
-
-It now opens a form with two input fields, \texttt{Description} and
-\texttt{Query}.
-\begin{figure}[h]
-\centering
-\includegraphics[width=.6\textwidth]{create_shortcut.png}
-\caption{The view to create a new shortcut}
-\end{figure}
-
-See \ref{basic-shortcut} and
-\ref{advanced-shortcut} for further
-explanation of the components of a Query Shortcut.
-
-Edit the fields and click \texttt{Submit} for the creation of the new
-shortcut or click \texttt{Cancel} to cancel the process.
-
-The new shortcut is shown in the shortcuts section.
-\begin{figure}[h]
-\centering
-\includegraphics[width=.6\textwidth]{create_success.png}
-\caption{The view when creation was successful}
-\end{figure}
-
-\subsection{Change an Existing Shortcut}\label{change-an-existing-shortcut}
-
-Existing Query Shortcuts which are visible in your shortcuts section can
-be edited directly in the shortcuts section.
-
-In the web interface, click \texttt{Query}. In the \texttt{Shortcuts}
-section, click the wrench (on the right side).
-
-In the drop-down menu, click \texttt{Edit}.
-
-\begin{figure}[h]
-\centering
-\includegraphics[width=.6\textwidth]{choose_edit.png}
-\caption{Choosing which shortcut to edit}
-\end{figure}
-Every editable shortcut (note: global shortcuts are not editable in the
-webinterface at all) will receive a new button \texttt{Edit}
-
-Click \texttt{Edit} of the shortcut that is to be changed.
-
-It now opens a form with two input fields, \texttt{Description} and
-\texttt{Query}, pre-filled.
-
-See \ref{basic-shortcut} and
-\ref{advanced-shortcut} for further
-explanation of the components of a Query Shortcut.
-
-Edit the fields and click \texttt{Submit} for the creation of the new
-shortcut or click \texttt{Cancel} to cancel the process.
-
-The updated shortcut is shown in the shortcuts section.
-
-See the
-
-\subsection{Delete an Existing Shortcut}\label{delete-an-existing-shortcut}
-
-Existing Query Shortcut which are visible in your shortcuts section can
-be edited directly in the shortcuts section.
-
-In the web interface, click \texttt{Query}. In the \texttt{Shortcuts}
-section, click the wrench (on the right side).
-
-In the drop-down menu, click \texttt{Delete}.
-\begin{figure}[h]
-\centering
-\includegraphics[width=.6\textwidth]{delete_shortcuts.png}
-\caption{Choosing which shortcuts to delete}
-\end{figure}
-
-Every user-defined shortcut (note: global shortcuts are not deletable in
-the webinterface at all) will receive checkbox and \texttt{Delete} and
-\texttt{Cancel} buttons appear at the bottom of the shortcuts section.
-
-Check all shortcuts which are to be deleted and click \texttt{Delete} or
-click \texttt{Cancel} to cancel the deletion.
-
-All deleted shortcuts are marked as deleted afterwards and will not
-appear again in the shortcuts section after reload.
-
-\subsection{Basic Shortcut}\label{basic-shortcut}
-
-The \texttt{Description} is a verbose definition of the query,
-e.g.~``Search for experiments and return a table.''. It will be the text
-that is visible in the shortcuts section.
-
-The \texttt{Query} is the query that will be executed with the shortcut.
-It adheres to the definition of the CaosDB Query Language (CQL).
-
-The corresponding query of our example is
-\texttt{SELECT\ date,\ name\ FROM\ Experiment}.
-
-\subsection{Advanced Shortcut}\label{advanced-shortcut}
-
-The basic shortcut does not allow for any parameterization. It is just a
-plain string or like a bookmark.
-
-Advanced shortcuts use a special syntax, where text placeholders are
-used to define parameters of the shortcut. The parameters can be set by
-the user at the time of the execution. An example can best illustrate
-what that means:
-
-Suppose you want to search for experiments by their year. The query for
-that would be
-\texttt{SELECT\ date,\ name\ FROM\ Experiment\ WITH\ date\ IN\ 2018}.
-
-Now, the actual year in the query can be made editable by replacing the
-year \texttt{2018} with \texttt{\{year\}}.
-
-The \texttt{Description} now must also contain this placeholder
-\texttt{\{year\}}, e.g.~``Search for experiements conducted in year
-\{year\}''. When the shortcut is displayed in the shortcuts section
-below the query input field, the placeholder is replaced by a text input
-field and the user can insert a year and execute the shortcut with the
-year being inserted into the query.
-
-\subsubsection{Placeholders}\label{placeholders}
-
-The placeholders have simple rules. A placeholder always starts and ends
-with curly brackets, like in the example \texttt{\{year\}}. The text
-inside the brackets (the placeholder's \emph{id}) may contain any
-combination of alphanumeric signs (0-9,a-z,A-Z). The use of special
-characters like colons, commas or the like is discouraged. They are
-reserved for future extensions of the placeholders. Apart from that, you
-are free to choose any placeholder \emph{id} that seems suitable for
-you.
-
-Both components of the query shortcut (description and query) must
-contain the same set of placeholders, otherwise the query shortcuts
-might not work as intended. If there is a \texttt{\{year\}} in the
-query, there must be a \texttt{\{year\}} in the description.
-
-Each placeholder \emph{id} must occur only once in both components -- if
-you need to use two years in your shortcut you have to use
-\texttt{\{year1\}} and \texttt{\{year2\}} or any other combinations of
-placeholder \emph{ids}.
-\end{document}