Initial Commit

AGPLv3 Veröffentlichung gemäß Dienstanweisung vom 15. August 2018.

.gitignore

+# dot files
+.*
+!/.git*
+
+# extracted libraries
+/libs/**
+!/libs/*.zip
+
+# the build dir
+/public
+
+# screen logs
+screenlog.*

.gitlab-ci.yml

+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+#
+stages:
+    - setup
+    - linting
+    - test
+
+#######
+# setup
+#######
+
+# install pylint
+setup:install-pylint:
+    stage: setup
+    script:
+        - pip3 install pylint --user
+
+#########
+# linting
+#########
+
+# pylint everything
+linting:pylint:python3:
+    stage: linting
+    script:
+        - make pylint
+
+######
+# test
+######
+
+# run qunit tests
+test:qunit:
+    stage: test
+    artifacts:
+        paths:
+            - qunit.log
+            - screenlog.*
+    script:
+        - make run-qunit

README.md

+# Welcome
+
+This is the **CaosDB WebUI** repository and a part of the CaosDB project.
+
+# Setup
+
+Please read the [README_SETUP.md](README_SETUP.md) for instructions on how to
+setup this code.
+
+
+# Further Reading
+
+Please refer to the [official gitlab repository of the CaosDB
+project](https://gitlab.gwdg.de/bmp-caosdb/caosdb) for more information.
+
+# License
+
+Copyright (C) 2018 Research Group Biomedical Physics, Max Planck Institute for
+Dynamics and Self-Organization Göttingen.
+
+All files in this repository are licensed under a [GNU Affero General Public
+License](LICENCE.md) (version 3 or later).
+

README_SETUP.md

+# Structure
+
+* The `src` folder contains all source code for the webinterface.
+* The `libs` folder contains all necessary third-party libraries as zip files.
+* The `test` folder contains the unittests for the webinterface.
+* The `ext` folder contains extension for the webinterface. The make file will copy all javascript files from `ext/js/` into the public folder and links the javascript in the `public/xsl/main.xsl`.
+
+# Setup
+
+* run `make install` to compile/copy the webinterface to a newly created `public` folder.
+* run `make test` to compile/copy the webinterface and the tests to a newly created `public` folder and start a python http server. The test suite can be started with
+    `firefox http://localhost:8000/webinterface/`
+* run `make clean` to clean up everything.

ext/js/test.js

+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2018 Research Group Biomedical Physics,
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ *
+ * ** end header
+ */
+console.log("load test.js");

makefile

+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+#
+
+# Unzip all the external libraries and set up the links in the public folder
+
+SQ=\'
+ROOT_DIR = $(abspath .)
+MISC_DIR = $(abspath misc)
+PUBLIC_DIR = $(abspath public)
+SRC_DIR = $(abspath src)
+EXT_DIR = $(abspath ext)
+LIBS_DIR = $(abspath libs)
+TEST_DIR = $(abspath test)
+LIBS = fonts css/bootstrap.css js/bootstrap.js js/state-machine.js js/jquery.js js/showdown.js
+
+TEST_LIBS = $(LIBS) js/qunit.js css/qunit.css $(subst $(TEST_DIR)/,,$(shell find $(TEST_DIR)/))
+
+LIBS_ZIP = $(wildcard $(LIBS_DIR)/*.zip)
+LIBS_SUBDIRS = $(addprefix $(LIBS_DIR)/, js css fonts)
+
+ALL: test install
+
+install: clean cp-src cp-ext $(addprefix $(PUBLIC_DIR)/, $(LIBS))
+
+test: clean cp-src cp-ext $(addprefix $(PUBLIC_DIR)/, $(TEST_LIBS))
+	ln -s $(PUBLIC_DIR) $(PUBLIC_DIR)/webinterface
+
+PORT = 8000
+TIMEOUT = 200
+XVFB-RUN = xvfb-run -e /dev/stderr
+run-test-server: test
+	cd $(PUBLIC_DIR); $(MISC_DIR)/unit_test_http_server.py $(PORT) $(TIMEOUT); echo $$? > $(ROOT_DIR)/.server_done
+
+run-qunit:
+	# start server
+	screen -L -S caosdb-webui-test -t server -d -m -A make run-test-server
+	
+	# start firefox
+	screen -S caosdb-webui-test -X screen -t firefox $(XVFB-RUN) firefox "http://localhost:$(PORT)/webinterface/index.html?loggerPort=$(PORT)"
+
+	# wait until server stops
+	while [ 1 -eq 1 ]; do \
+		[ ! -e .server_done ] || break; \
+	done; \
+	true
+
+	# stop firefox
+	pkill -u caosdb firefox || true
+
+	# print stuff
+	cat screenlog.* || true
+	cat $(PUBLIC_DIR)/qunit.log || true
+	cat .server_done || true
+	[ $$(cat .server_done) -eq 0 ]
+
+cp-ext:
+	for f in $(wildcard $(EXT_DIR)/js/*) ; do \
+		cp -i -r $$f $(PUBLIC_DIR)/js/ ; \
+		sed -i "/EXTENSIONS/a \<xsl:element name=\"script\"><xsl:attribute name=\"src\"><xsl:value-of select=\"concat\(\$$basepath, 'webinterface$${f#$(EXT_DIR)}'\)\" /></xsl:attribute></xsl:element>" $(PUBLIC_DIR)/xsl/main.xsl ; \
+	done
+
+cp-src:
+	cp -r $(SRC_DIR) $(PUBLIC_DIR)
+
+$(PUBLIC_DIR)/%: $(LIBS_DIR)/%
+	ln -s $< $@
+
+$(PUBLIC_DIR)/%: $(TEST_DIR)/%
+	ln -s $< $@
+
+$(LIBS_DIR)/fonts: unzip
+	ln -s $(LIBS_DIR)/bootstrap-3.3.7-dist/fonts $@
+
+$(LIBS_DIR)/js/bootstrap.js: unzip $(LIBS_DIR)/js
+	ln -s $(LIBS_DIR)/bootstrap-3.3.7-dist/js/bootstrap.min.js $@
+
+$(LIBS_DIR)/css/bootstrap.css: unzip $(LIBS_DIR)/css
+	ln -s $(LIBS_DIR)/bootstrap-3.3.7-dist/css/bootstrap.min.css $@
+
+$(LIBS_DIR)/js/jquery.js: unzip $(LIBS_DIR)/js
+	ln -s $(LIBS_DIR)/jquery-3.3.1/jquery-3.3.1.min.js $@
+
+$(LIBS_DIR)/js/showdown.js: unzip $(LIBS_DIR)/js
+	ln -s $(LIBS_DIR)/showdown-1.8.6/dist/showdown.min.js $@
+
+$(LIBS_DIR)/js/state-machine.js: unzip $(LIBS_DIR)/js
+	ln -s $(LIBS_DIR)/javascript-state-machine-master/dist/state-machine.min.js $@
+
+$(LIBS_DIR)/css/qunit.css: unzip $(LIBS_DIR)/css
+	ln -s $(LIBS_DIR)/qunit-2.6.2/qunit-2.6.2.css $@
+
+$(LIBS_DIR)/js/qunit.js: unzip $(LIBS_DIR)/js
+	ln -s $(LIBS_DIR)/qunit-2.6.2/qunit-2.6.2.js $@
+
+$(addprefix $(LIBS_DIR)/, js css):
+	mkdir $@ || true
+
+.PHONY: clean
+clean:
+	$(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 $$f; done
+	$(RM) screenlog.*
+	$(RM) .server_done
+
+.PHONY: unzip
+unzip:
+	for f in $(LIBS_ZIP); do unzip -o -d libs $$f; done
+
+
+PYLINT = ~/.local/bin/pylint
+PYTHON_FILES = $(subst $(ROOT_DIR)/,,$(shell find $(ROOT_DIR)/ -iname "*.py"))
+pylint: $(PYTHON_FILES)
+	for f in $(PYTHON_FILES); do $(PYLINT) $$f || exit 1; done

misc/unit_test_http_server.py

+#!/usr/bin/env python3
+# -*- encoding: utf-8 -*-
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+#
+"""unit_test_http_server
+
+For running and logging the unit test suite of webcaosdb.
+"""
+import sys
+import os
+from http.server import SimpleHTTPRequestHandler, HTTPServer
+
+class UnitTestsHandler(SimpleHTTPRequestHandler):
+    """UnitTestsHandler
+
+    Handles GET requests and return the source files of webcaosdb or the test
+    suite and POST requests for the logger.
+    """
+
+    # do_POST is compliant with the BaseHTTPRequestHandler API
+    # pylint: disable=invalid-name
+    def do_POST(self):
+        """do_POST
+
+        Handle POST requests to the `log` and `done` resources.
+        """
+        path = self.path[1:]
+        if path in ["done", "log"]:
+            getattr(self, path)()
+            #return HTTP status: 204 No Content
+            self.send_response(204)
+        else:
+            #return HTTP status: 404 Not Found
+            self.send_response(404)
+
+    def done(self):
+        """done
+
+        Shut down the server with an exit code which depends on the success of
+        the unit test suite - If the tests succeeded the server exists with 0,
+        otherwise with 1.
+        """
+        #pylint: disable=protected-access
+        post_data = self.log()
+        if "SUCCESS" in post_data:
+            self.server._shutdown("[SUCCESS]", 0)
+        else:
+            self.server._shutdown("[ERROR]", 1)
+
+    def log(self):
+        """log
+
+        Print the body of a request.
+        """
+        content_length = int(self.headers['Content-Length'])
+        post_data = self.rfile.read(content_length).decode("utf-8")
+        with open("qunit.log", "a") as logfile:
+            logfile.write("[LOG] " + post_data + "\n")
+        return post_data
+
+
+class UnitTestHTTPServer(HTTPServer):
+    """UnitTestHTTPServer
+
+    A HTTP server which handles the request to the webcaosdb sources and the
+    tests and servers as a logger when POST request are send to the `log`
+    resource.
+    """
+
+    def __init__(self, server_address, timeout):
+        super(UnitTestHTTPServer, self).__init__(server_address,
+                                                 UnitTestsHandler)
+        self.timeout = timeout
+        self._keep_running = True
+        self._exit_message = None
+        self._exit_code = None
+
+    def handle_timeout(self):
+        """handle_timeout as defined in socketserver.BaseServer
+        """
+        self._shutdown("[TIMEOUT]", 2)
+
+    def _shutdown(self, message, code):
+        self._keep_running = False
+        self._exit_message = message
+        self._exit_code = code
+
+    def start(self):
+        """start
+
+        Start the server and handle request until the `done` resource is being
+        called or a timeout occurs.
+        """
+        print(("starting UnitTestHTTPServer on {address} with {t}s "
+               "timeout.").format(address=self.server_address, t=self.timeout))
+        self._keep_running = True
+        while self._keep_running:
+            self.handle_request()
+
+        print(self._exit_message)
+        os._exit(self._exit_code)#pylint: disable=protected-access
+
+
+UnitTestHTTPServer(server_address=('127.0.0.1', int(sys.argv[1])),
+                   timeout=float(sys.argv[2])).start()

src/css/webcaosdb.css

+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2018 Research Group Biomedical Physics,
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ *
+ * ** end header
+ */
+@CHARSET "UTF-8";
+
+.caosdb-comment-annotation-text h1 {
+    font-size: 24px;
+}
+
+.caosdb-comment-annotation-text h2 {
+    font-size: 20px;
+}
+
+.caosdb-comment-annotation-text h3 {
+    font-size: 18px;
+}
+
+.caosdb-comment-annotation-text h4 {
+    font-size: 16px;
+}
+
+
+.caosdb-show-preview-button, .caosdb-hide-preview-button {
+    position: absolute;
+    top: 5px;
+    left: -5px;
+}
+
+.caosdb-entity-heading-attr {
+    overflow-x: auto;
+}
+
+a.label.caosdb-id:hover {
+    background-color: #5E6762;
+}
+
+.caosdb-entity-preview .caosdb-entity-panel-body {
+    overflow-y: auto;
+    max-height: 250px;
+}
+
+.caosdb-preview-carousel-nav > .caosdb-value-list > .btn-group > .btn:first-child {
+    margin-left: 34px;
+}
+.caosdb-preview-carousel-nav > .caosdb-value-list > .btn-group > .btn:last-child {
+    margin-right: 34px;
+}
+
+.caosdb-preview-carousel-nav {
+    position: relative;
+}
+.caosdb-query-panel {
+	padding-top: 20px;
+	padding-bottom: 20px;
+}
+
+.navbar-default .btn-link:hover {
+	text-decoration: none;
+}
+
+.navbar-default .btn-link:focus {
+    text-decoration: none;
+}
+
+.caosdb-property-name {
+	font-weight: bold;
+	margin-left: 8px;
+}
+
+.caosdb-square {
+	position: relative;
+	overflow: hidden;
+}
+
+.caosdb-square::before {
+	content: "";
+	display: block;
+	padding-top: 100%;
+}
+
+.caosdb-square-content {
+	position: absolute;
+	top: 0px;
+	right: 0px;
+	bottom: 0px;
+	left: 0px;
+}
+
+.caosdb-parent-name {
+    font-weight: bold;
+    margin-right: 4px;	
+}
+
+/* lists of values */
+/* INLINE (with default scroll-bar) */
+.caosdb-value-list {	
+	overflow-x: auto;
+}
+
+.caosdb-value-list > .btn-group > .btn {
+    float: none;
+}
+.caosdb-value-list > .btn-group,
+.caosdb-value-list > ol {
+	display: inline-block;
+    float: none;
+    white-space: nowrap;
+    margin-bottom: 0px;
+    margin-left: 0px;
+}
+
+.caosdb-value-list > .list-inline > li {
+    border-left-width: 0px; 
+}
+
+.caosdb-value-list > .list-inline > li:first-child {
+	border-radius: 4px 0px 0px 4px;
+	border-left-width: 1px;
+}
+
+.caosdb-value-list > .list-inline > li:last-child {
+    border-radius: 0px 4px 4px 0px;
+}
+
+/* single boolean values */
+.caosdb-boolean-true {
+	font-weight: bold;
+	font-size: 90%;
+	border: 1px solid #bbb;
+	padding: 2px 8px;
+	border-radius: 8px;
+}
+
+.caosdb-boolean-false {
+    font-weight: bold;
+    font-size: 90%;
+    border: 1px solid #bbb;
+    padding: 2px 8px;
+    border-radius: 8px;
+}
+
+.caosdb-entity-panel-heading {
+    border-bottom-left-radius: 3px;
+    border-bottom-right-radius: 3px;  
+}
+
+.caosdb-entity-panel-body {
+    padding: 0px 15px;	
+}
+
+.caosdb-entity-panel-body > :first-child {
+	margin-top: 15px;
+}
+
+.caosdb-entity-heading-attr-name {
+	color: #6c6c6c;
+    font-size: 90%;
+    margin-right: 0.3em; 
+}
+
+.caosdb-subproperty-divider {
+    margin: 4px 0px;
+    border-top: 1px solid #dddddd
+}
+
+.caosdb-prop-label {
+    background-color: #f5f5f5;
+    font-weight: bold;
+    padding: 8px 15px;
+}
+
+.caosdb-prop-value {
+    background-color: #ffffff;
+    padding: 8px 15px;
+}
+
+.caosdb-prop-list-group .row {
+    margin-left: 0px;
+    margin-right: 0px;
+}
+
+.caosdb-prop-list-group>.list-group-item {
+    padding: 0px
+}
+
+.caosdb-prop-list-group>.list-group-item:first-child .caosdb-prop-label
+    {
+    border-top-left-radius: 4px;
+    border-top-right-radius: 4px;
+}
+
+.caosdb-prop-list-group>.list-group-item:first-child .caosdb-prop-value
+    {
+    border-top-right-radius: 4px;
+}
+
+.caosdb-prop-list-group>.list-group-item:last-child .caosdb-prop-label {
+    border-bottom-left-radius: 4px;
+}
+
+.caosdb-prop-list-group>.list-group-item:last-child .caosdb-prop-value {
+    border-bottom-left-radius: 4px;
+    border-bottom-right-radius: 4px;
+}
+
+.caosdb-label-record {
+    background-color: #F92108;
+    margin-right: 8px;
+}
+
+.caosdb-label-recordtype {
+    background-color: #00A32E;