diff --git a/.gitignore b/.gitignore
index cc9336b6256771f79eb104a8b1325a55352657e1..ef0861267fc42504b306d158ecfd332a44b3f6ce 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
+# -*- mode:conf; -*-
+
# dot files
.*
!/.git*
@@ -8,6 +10,9 @@
# the build dir
/public
+/sss_bin
+/node_modules/
+/build
# screen logs
screenlog.*
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 548f86457c3216f5eed7b75b4b81d7f048351248..6caa815dba6c984cc36720866cf863bdd11e1512 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,6 +6,7 @@
# Copyright (C) 2019 Henrik tom Wörden
# Copyright (C) 2020 Timm Fitschen (t.fitschen@indiscale.com)
# Copyright (C) 2020 IndiScale GmbH (info@indiscale.com)
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -58,6 +59,14 @@ test:
script:
- make run-qunit
+test-server-side-scripting:
+ timeout: 10 minutes
+ tags: [ docker ]
+ stage: test
+ script:
+ - whereis pytest pytest3 py.test pytest-3 py.test-3
+ - make test-sss
+
# Trigger building of server image and integration tests
trigger_build:
timeout: 15 minutes
@@ -78,13 +87,30 @@ build-testenv:
tags: [ cached-dind ]
image: docker:19.03
stage: setup
+ timeout: 3 h
script:
- cd test/docker
- docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
# use here general latest or specific branch latest...
- - docker pull $CI_REGISTRY_IMAGE:latest || true
- docker build
--pull
- --cache-from $CI_REGISTRY_IMAGE:latest
-t $CI_REGISTRY_IMAGE:latest .
- docker push $CI_REGISTRY_IMAGE:latest
+
+# Build the sphinx documentation and make it ready for deployment by Gitlab Pages
+# documentation:
+# stage: deploy
+
+# Special job for serving a static website. See https://docs.gitlab.com/ee/ci/yaml/README.html#pages
+pages:
+ tags: [ docker ]
+ stage: deploy
+ only:
+ - dev
+ script:
+ - echo "Deploying"
+ - make doc
+ - rm -r public || true ; cp -r build/doc/html public
+ artifacts:
+ paths:
+ - public
diff --git a/CHANGELOG.md b/CHANGELOG.md
index cdc0bbfb39e53824ff52ea968b8926f4eeb413b3..f2c54f430fd5e7f3ccd11294c8fe0daf5c7a23f1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added (for new features, dependecies etc.)
+- The versioning model has a new styling and can show and tsv-export the full
+ version history now.
+- Module `ext_bookmarks` which allows users to bookmark entities, store them in
+ a link or export them to TSV.
+- table previews in the bottom line module
+- added preview for tif images
+* new function `form_elements.make_alert` which generates a proceed/cancel
+ dialog which intercepts a function call and asks the user for confirmation.
+* Deleting entities prompts for user confirmation after hitting the "Delete"
+ button (edit_mode).
+* Plotly preview has an additional parameter for a config object,
+ e.g., for disabling the plotly logo
+* After a SELECT statement now also all referenced files can be downloaded.
+* Automated documentation builds: `make doc`
+
### Changed (for changes in existing functionality)
+- enabled and enhanced autocompletion
+
+* Login form is hidden behind another button.
### Deprecated (for soon-to-be removed features)
@@ -16,6 +34,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed
+- #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
+
### Security (in case of vulnerabilities)
## [v0.2.1] - 2020-09-07
diff --git a/makefile b/Makefile
similarity index 81%
rename from makefile
rename to Makefile
index 50dd72b500724bbe40801292ab39c3c5cf7ce70f..92f69dfb6234826b752a1c3355e1e812e5b2df61 100644
--- a/makefile
+++ b/Makefile
@@ -33,14 +33,17 @@ SQ=\'
ROOT_DIR = $(abspath .)
MISC_DIR = $(abspath misc)
PUBLIC_DIR = $(abspath public)
+SSS_BIN_DIR = $(abspath sss_bin)
CONF_CORE_DIR = $(abspath conf/core)
CONF_EXT_DIR = $(abspath conf/ext)
SRC_CORE_DIR = $(abspath src/core)
SRC_EXT_DIR = $(abspath src/ext)
+SRC_SSS_DIR = $(abspath src/server_side_scripting)
LIBS_DIR = $(abspath libs)
TEST_CORE_DIR = $(abspath test/core/)
TEST_EXT_DIR = $(abspath test/ext)
-LIBS = fonts css/bootstrap.css js/bootstrap.js js/state-machine.js js/jquery.js js/showdown.js js/dropzone.js css/dropzone.css js/loglevel.js js/leaflet.js css/leaflet.css css/images js/leaflet-latlng-graticule.js js/proj4.js js/proj4leaflet.js js/leaflet-coordinates.js css/leaflet-coordinates.css js/leaflet-graticule.js js/bootstrap-select.js css/bootstrap-select.css js/bootstrap-autocomplete.min.js js/plotly.js
+TEST_SSS_DIR =$(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
TEST_LIBS = $(LIBS) js/qunit.js css/qunit.css $(subst $(TEST_CORE_DIR)/,,$(shell find $(TEST_CORE_DIR)/))
@@ -49,9 +52,9 @@ LIBS_SUBDIRS = $(addprefix $(LIBS_DIR)/, js css fonts)
ALL: install
-install: clean cp-src cp-ext cp-conf $(addprefix $(PUBLIC_DIR)/, $(LIBS)) build_properties merge_xsl
+install: clean install-sss cp-src cp-ext cp-conf $(addprefix $(PUBLIC_DIR)/, $(LIBS)) build_properties merge_xsl
-test: clean cp-src cp-ext cp-ext-test cp-conf $(addprefix $(PUBLIC_DIR)/, $(TEST_LIBS)) 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
@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; \
@@ -64,10 +67,12 @@ test: clean cp-src cp-ext cp-ext-test cp-conf $(addprefix $(PUBLIC_DIR)/, $(TEST
merge_xsl:
misc/merge_xsl.sh
+EXCLUDE_EXPR = %~ %.backup
+BUILDFILELIST = $(filter-out $(EXCLUDE_EXPR),$(wildcard build.properties.d/*))
build_properties:
@set -a -e ; \
pushd build.properties.files ; \
- for f in ../build.properties.d/* ; do source "$$f" ; done ; \
+ for f in ${BUILDFILELIST} ; do echo "processing ../$$f" && source "../$$f" ; done ; \
popd ; \
BUILD_NUMBER=$(BUILD_NUMBER) ; \
PROPS=$$(printenv | grep -e "^BUILD_") ; \
@@ -127,18 +132,31 @@ run-qunit: test
exit 1; \
fi
+install-sss:
+ @set -a -e ; \
+ pushd build.properties.files ; \
+ for f in ../build.properties.d/* ; do source "$$f" ; done ; \
+ popd ; \
+ ./install-sss.sh $(SRC_SSS_DIR) $(SSS_BIN_DIR)
+
+PYTEST ?= pytest-3
+test-sss: install-sss
+ $(PYTEST) -vv $(TEST_SSS_DIR)
+
+
+CMD_COPY_EXT_FILES = cp -i -r -L
cp-ext:
# TODO FIXME Base path for not-XSL-expanded files
mkdir -p $(PUBLIC_DIR)/html
for f in $(wildcard $(SRC_EXT_DIR)/html/*) ; do \
- echo "y" | cp -i -r "$$(realpath "$$f")" $(PUBLIC_DIR)/html/ ; \
+ echo "y" | $(CMD_COPY_EXT_FILES) "$$(realpath "$$f")" $(PUBLIC_DIR)/html/ ; \
done
for f in $(wildcard $(SRC_EXT_DIR)/js/*) ; do \
- echo "y" | cp -i -r "$$f" $(PUBLIC_DIR)/js/ ; \
+ echo "y" | $(CMD_COPY_EXT_FILES) "$$f" $(PUBLIC_DIR)/js/ ; \
sed -i "/JS_EXTENSIONS/a \<xsl:element name=\"script\"><xsl:attribute name=\"src\"><xsl:value-of select=\"concat\(\$$basepath, 'webinterface/${BUILD_NUMBER}$${f#$(SRC_EXT_DIR)}'\)\" /></xsl:attribute></xsl:element>" $(PUBLIC_DIR)/xsl/main.xsl ; \
done
for f in $(wildcard $(SRC_EXT_DIR)/css/*) ; do \
- echo "y" | cp -i -r "$$f" $(PUBLIC_DIR)/css/ ; \
+ echo "y" | $(CMD_COPY_EXT_FILES) "$$f" $(PUBLIC_DIR)/css/ ; \
sed -i "/CSS_EXTENSIONS/a \<xsl:element name=\"link\"><xsl:attribute name=\"rel\">stylesheet</xsl:attribute><xsl:attribute name=\"href\"><xsl:value-of select=\"concat\(\$$basepath, 'webinterface/${BUILD_NUMBER}$${f#$(SRC_EXT_DIR)}'\)\" /></xsl:attribute></xsl:element>" $(PUBLIC_DIR)/xsl/main.xsl ; \
for html in $(PUBLIC_DIR)/html/* ; do \
echo "$$html"; \
@@ -146,26 +164,26 @@ cp-ext:
done \
done
for f in $(wildcard $(SRC_EXT_DIR)/pics/*) ; do \
- echo "y" | cp -i -r "$$(realpath "$$f")" $(PUBLIC_DIR)/pics/ ; \
+ echo "y" | $(CMD_COPY_EXT_FILES) "$$(realpath "$$f")" $(PUBLIC_DIR)/pics/ ; \
done
for f in $(wildcard $(SRC_EXT_DIR)/xsl/*) ; do \
- echo "y" | cp -i -r "$$(realpath "$$f")" $(PUBLIC_DIR)/xsl/ ; \
+ echo "y" | $(CMD_COPY_EXT_FILES) "$$(realpath "$$f")" $(PUBLIC_DIR)/xsl/ ; \
done
cp-ext-test:
for f in $(wildcard $(TEST_EXT_DIR)/js/*) ; do \
- echo "y" | cp -i -r "$$f" $(PUBLIC_DIR)/js/ ; \
+ echo "y" | $(CMD_COPY_EXT_FILES) "$$f" $(PUBLIC_DIR)/js/ ; \
sed -i "/JS_EXTENSIONS/a \<xsl:element name=\"script\"><xsl:attribute name=\"src\"><xsl:value-of select=\"concat\(\$$basepath, 'webinterface/${BUILD_NUMBER}$${f#$(SRC_EXT_DIR)}'\)\" /></xsl:attribute></xsl:element>" $(PUBLIC_DIR)/xsl/main.xsl ; \
done
mkdir -p $(PUBLIC_DIR)/html
for f in $(wildcard $(TEST_EXT_DIR)/html/*) ; do \
- echo "y" | cp -i -r "$$(realpath "$$f")" $(PUBLIC_DIR)/html/ ; \
+ echo "y" | $(CMD_COPY_EXT_FILES) "$$(realpath "$$f")" $(PUBLIC_DIR)/html/ ; \
done
for f in $(wildcard $(TEST_EXT_DIR)/pics/*) ; do \
- echo "y" | cp -i -r "$$(realpath "$$f")" $(PUBLIC_DIR)/pics/ ; \
+ echo "y" | $(CMD_COPY_EXT_FILES) "$$(realpath "$$f")" $(PUBLIC_DIR)/pics/ ; \
done
for f in $(wildcard $(TEST_EXT_DIR)/xsl/*) ; do \
- echo "y" | cp -i -r "$$(realpath "$$f")" $(PUBLIC_DIR)/xsl/ ; \
+ echo "y" | $(CMD_COPY_EXT_FILES) "$$(realpath "$$f")" $(PUBLIC_DIR)/xsl/ ; \
done
cp-conf: convert-yaml
@@ -191,13 +209,13 @@ $(PUBLIC_DIR)/%: $(TEST_EXT_DIR)/%
cp -r $< $@
$(LIBS_DIR)/fonts: unzip
- ln -s $(LIBS_DIR)/bootstrap-3.3.7-dist/fonts $@
+ ln -s $(LIBS_DIR)/bootstrap-3.4.1-dist/fonts $@
$(LIBS_DIR)/js/bootstrap.js: unzip $(LIBS_DIR)/js
- ln -s $(LIBS_DIR)/bootstrap-3.3.7-dist/js/bootstrap.min.js $@
+ ln -s $(LIBS_DIR)/bootstrap-3.4.1-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 $@
+ ln -s $(LIBS_DIR)/bootstrap-3.4.1-dist/css/bootstrap.min.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 $@
@@ -206,7 +224,7 @@ $(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 $@
$(LIBS_DIR)/js/jquery.js: unzip $(LIBS_DIR)/js
- ln -s $(LIBS_DIR)/jquery-3.3.1/jquery-3.3.1.min.js $@
+ ln -s $(LIBS_DIR)/jquery-3.5.1/jquery-3.5.1.min.js $@
$(LIBS_DIR)/js/showdown.js: unzip $(LIBS_DIR)/js
ln -s $(LIBS_DIR)/showdown-1.8.6/dist/showdown.min.js $@
@@ -257,17 +275,24 @@ $(LIBS_DIR)/css/leaflet-coordinates.css: unzip $(LIBS_DIR)/css
ln -s $(LIBS_DIR)/Leaflet.Coordinates-0.1.5/dist/Leaflet.Coordinates-0.1.5.css $@
$(LIBS_DIR)/js/bootstrap-autocomplete.min.js: unzip $(LIBS_DIR)/js
- ln -s $(LIBS_DIR)/bootstrap-autocomplete-2.3.0/dist/latest/bootstrap-autocomplete.min.js $@
+ ln -s $(LIBS_DIR)/bootstrap-autocomplete-2.3.5/dist/latest/bootstrap-autocomplete.min.js $@
$(LIBS_DIR)/js/plotly.js: unzip $(LIBS_DIR)/js
ln -s $(LIBS_DIR)/plotly.js-1.52.2/dist/plotly.min.js $@
+$(LIBS_DIR)/js/pako.js: unzip $(LIBS_DIR)/js
+ ln -s $(LIBS_DIR)/pako-dummy/pako.js $@
+
+$(LIBS_DIR)/js/utif.js: unzip $(LIBS_DIR)/js
+ ln -s $(LIBS_DIR)/UTIF-8205c1f/UTIF.js $@
+
$(addprefix $(LIBS_DIR)/, js css):
mkdir $@ || true
.PHONY: clean
clean:
+ $(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 $$f; done
@@ -278,11 +303,13 @@ unzip:
for f in $(LIBS_ZIP); do unzip -q -o -d libs $$f; done
-PYLINT = pylint3 -d all -e E,F
+PYLINT ?= pylint3
PYTHON_FILES = $(subst $(ROOT_DIR)/,,$(shell find $(ROOT_DIR)/ -iname "*.py"))
pylint: $(PYTHON_FILES)
- for f in $(PYTHON_FILES); do $(PYLINT) $$f || exit 1; done
+ for f in $(PYTHON_FILES); do $(PYLINT) -d all -e E,F $$f || exit 1; done
+
-PYLINT_LOCAL = /usr/bin/pylint3 -d all -e E,F
-pylint-local: $(PYTHON_FILES)
- for f in $(PYTHON_FILES); do $(PYLINT_LOCAL) $$f || exit 1; done
+# Compile the standalone documentation
+.PHONY: doc
+doc:
+ $(MAKE) -C src/doc html
diff --git a/README_SETUP.md b/README_SETUP.md
index c027fd7d9af49c33492122fc575254b8d6b00845..8a2cd006f4e6963b9eb591268d0826b802229ae8 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -21,12 +21,14 @@
* ** end header
-->
-# Folder Structure
+# Getting Started with the Web Interface
-* The `src` folder contains all source code for the webinterface.
+## Folder Structure
+
+* The `src` folder contains all source code for the web interface.
* 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
+* The `test` folder contains the unittests for the web interface.
+* The `ext` folder contains extension for the web interface. 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`.
* The `misc` folder contains a simple http server which is used for running the
@@ -34,13 +36,13 @@
* The `build.properties.d/` folder contains configuration files for the build.
-# Build Configuration
+## Build Configuration
The default configuration is defined in
`build.properties.d/00_default.properties`.
-This file defines default variables which will be replaced in the source files
-during the build.
+This file defines default variables which can be used in source files and
+will be replaced with the defined values during the build.
All files in that directory will be sourced during `make install` and `make test`.
Thus any customized configuration can also be added to that folder by just placing
@@ -49,18 +51,34 @@ files in there which override the default values from `00_default.properties`.
See `build.properties.d/00_default.properties` for more
information.
-# Setup
+## Setup
-* Run `make install` to compile/copy the webinterface to a newly created
+* Run `make install` to compile/copy the web interface to a newly created
`public` folder.
+* Also, `make install` will copy the scripts from `src/server_side_scripting/`
+ to `sss_bin/`. If you want to make the server-side scripts callable for the
+ server as server-side scripts you need to include the `sss_bin/` directory
+ into the server property `SERVER_SIDE_SCRIPTING_BIN_DIRS`.
-# Test
+## Test
-* Run `make test` to compile/copy the webinterface and the tests to a newly
+* Run `make test` to compile/copy the web interface and the tests to a newly
created `public` folder.
* Run `make run-test-server` to start a python http server.
* The test suite can be started with `firefox http://localhost:8000/`.
-# Clean
+## Clean
* Run `make clean` to clean up everything.
+
+## Documentation #
+
+Build documentation in `build/` with `make doc`.
+
+### Requirements ##
+
+- sphinx
+- sphinx-autoapi
+- jsdoc (`npm install jsdoc`)
+- sphinx-js
+- recommonmark
diff --git a/build.properties.d/00_default.properties b/build.properties.d/00_default.properties
index 23b1e9ff929b030750f6cab0014f22cd0d6b7cf4..cb0a89ce6d5cf991de67b9063caaf4349e34b59d 100644
--- a/build.properties.d/00_default.properties
+++ b/build.properties.d/00_default.properties
@@ -45,6 +45,11 @@ 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
+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
##############################################################################
# Navbar properties
@@ -63,7 +68,7 @@ BUILD_FAVICON=pics/caosdb_logo_42.png
##############################################################################
# Link to the data policy statement document.
-BUILD_FOOTER_DATA_POLICY_HREF=https://indiscale.com/?page_id=156
+BUILD_FOOTER_DATA_POLICY_HREF=https://missing-domain.com/missing-page
# Custom footer elements can be placed here (will be placed inside a <div>
# element).
diff --git a/install-sss.sh b/install-sss.sh
new file mode 100755
index 0000000000000000000000000000000000000000..bb2db57649000ba1e701786f56dba575753110eb
--- /dev/null
+++ b/install-sss.sh
@@ -0,0 +1,17 @@
+SRC_DIR=$1
+INSTALL_DIR=$2
+
+mkdir -p $INSTALL_DIR
+
+# from here on do your module-wise installing
+
+# ext_table_preview
+if [ "${BUILD_MODULE_EXT_BOTTOM_LINE_TABLE_PREVIEW}" == "ENABLED" ]; then
+ mkdir -p $INSTALL_DIR/ext_table_preview
+ cp $SRC_DIR/ext_table_preview/*.py $INSTALL_DIR/ext_table_preview/
+ echo "installed all server-side scripts for ext_table_preview"
+fi
+# ext_file_download; should always be installed - No build variable
+mkdir -p $INSTALL_DIR/ext_file_download
+cp $SRC_DIR/ext_file_download/*.py $INSTALL_DIR/ext_file_download/
+echo "installed all server-side scripts for ext_file_download"
diff --git a/libs/UTIF-8205c1f.zip b/libs/UTIF-8205c1f.zip
new file mode 100644
index 0000000000000000000000000000000000000000..7069cd288d5d629a7fc3a03d8d92415e78aeb728
Binary files /dev/null and b/libs/UTIF-8205c1f.zip differ
diff --git a/libs/bootstrap-3.3.7-dist.zip b/libs/bootstrap-3.3.7-dist.zip
deleted file mode 100644
index 6fbb95ebaa3867ce196ef3b54951a732107d94d2..0000000000000000000000000000000000000000
Binary files a/libs/bootstrap-3.3.7-dist.zip and /dev/null differ
diff --git a/libs/bootstrap-3.4.1-dist.zip b/libs/bootstrap-3.4.1-dist.zip
new file mode 100644
index 0000000000000000000000000000000000000000..9002b8521706bc582546f41635da3437edf20c3c
Binary files /dev/null and b/libs/bootstrap-3.4.1-dist.zip differ
diff --git a/libs/bootstrap-autocomplete-2.3.0.zip b/libs/bootstrap-autocomplete-2.3.0.zip
deleted file mode 100644
index 206c00f49c87794e996c46da2f086d0a1d118071..0000000000000000000000000000000000000000
Binary files a/libs/bootstrap-autocomplete-2.3.0.zip and /dev/null differ
diff --git a/libs/bootstrap-autocomplete-2.3.5.zip b/libs/bootstrap-autocomplete-2.3.5.zip
new file mode 100644
index 0000000000000000000000000000000000000000..8cc2e03067955193bb89af2972a35ee9e0260b35
Binary files /dev/null and b/libs/bootstrap-autocomplete-2.3.5.zip differ
diff --git a/libs/jquery-3.3.1.zip b/libs/jquery-3.3.1.zip
deleted file mode 100644
index 404fac0639caf20bd4cf55419aa9a5f5bb768029..0000000000000000000000000000000000000000
Binary files a/libs/jquery-3.3.1.zip and /dev/null differ
diff --git a/libs/jquery-3.5.1.zip b/libs/jquery-3.5.1.zip
new file mode 100644
index 0000000000000000000000000000000000000000..c554bbf416786da9c18bef62061cba932646f996
Binary files /dev/null and b/libs/jquery-3.5.1.zip differ
diff --git a/libs/pako-dummy.zip b/libs/pako-dummy.zip
new file mode 100644
index 0000000000000000000000000000000000000000..e493ee9d673c81a523ad8e488c509c392765da52
Binary files /dev/null and b/libs/pako-dummy.zip differ
diff --git a/misc/versioning_test_data.py b/misc/versioning_test_data.py
index eaa83e46f61ea2f20263b487e4bb42c37678c94f..5ec7073aeaffc894916ee8a6c4cfdc82bc25a4f1 100755
--- a/misc/versioning_test_data.py
+++ b/misc/versioning_test_data.py
@@ -91,3 +91,8 @@ else:
str(rec1.id),
str(rec1.id)])
rec4.insert()
+
+for i in range(4,11):
+ rec1.name = f"TestRecord1-{i}thVersion"
+ rec1.description = f"This is the {i}th version."
+ rec1.update()
diff --git a/src/core/css/webcaosdb.css b/src/core/css/webcaosdb.css
index 05e36429b7dfe6144915b522de2fa6c36375c484..69a700376423a44bcb28a9920f1f3d15ef9a3b90 100644
--- a/src/core/css/webcaosdb.css
+++ b/src/core/css/webcaosdb.css
@@ -27,6 +27,55 @@ body {
flex-direction: column;
}
+
+div.export-data {
+ display: none;
+}
+
+tr:not(:hover) .caosdb-v-entity-version-hint-cur {
+ color: #DDD;
+}
+
+tr:hover .caosdb-v-entity-version-hint {
+ color: unset;
+}
+
+.caosdb-v-entity-version-hint {
+ color: #DDD;
+}
+
+tbody:not(:hover) tr .caosdb-v-entity-version-hint-cur {
+ color: unset;
+}
+
+.caosdb-v-entity-version-no-related {
+ color: #DDD;
+}
+
+.caosdb-v-entity-version-no-related:hover {
+ color: unset;
+}
+
+#top-navbar>ul>li>a {
+ margin: 8px 0px;
+ padding: 6px 12px;
+ display: inline-block;
+}
+
+.caosdb-v-bookmark-button,
+.caosdb-v-bookmark-button:focus,
+.caosdb-v-bookmark-button:hover {
+ color: #333;
+ position: relative;
+ top: 3px;
+}
+
+.caosdb-v-bookmark-button:active,
+.caosdb-v-bookmark-button.active {
+ color: red;
+}
+
+
.caosdb-v-navbar-toolbox li a:hover,
.caosdb-v-navbar-toolbox li input:hover,
.caosdb-v-navbar-toolbox li button:hover {
diff --git a/src/core/js/autocomplete.js b/src/core/js/autocomplete.js
deleted file mode 100644
index 345d06b37bc6456645ef02947c70b3f2f5d6c44f..0000000000000000000000000000000000000000
--- a/src/core/js/autocomplete.js
+++ /dev/null
@@ -1,109 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2019 IndiScale GmbH
- *
- * 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
- */
-
-'use strict';
-
-var autocomplete = new function() {
- this.version = "0.1";
-
- /**
- * @type {Promise} promise for a list of entity names.
- */
- this.candidates = undefined;
- var logger = log.getLogger("autocomplete");
- this.init = function() {
- this.candidates = undefined;
- this.toggle_completion();
- logger.setLevel("trace");
- };
-
- this.retrieve_names = async function () {
- var response = $(await connection.get(transaction.generateEntitiesUri(
- ["names"]))).find("Response [name]")
-
- return response.toArray().map(x=> $(x).attr("name"));
- };
-
- /**
- * @return {Promise} promise for a list of entity names.
- */
- this.get_candidates = function () {
-
- if (typeof this.candidates === "undefined"){
-
- this.candidates = this.retrieve_names();
- };
- return this.candidates;
- };
-
- this.filter = function (x, qry){
- return x.toLowerCase().startsWith(qry.toLowerCase())
- };
-
- this.search = async function (qry, callback, origJQElement) {
- const names = await autocomplete.get_candidates();
- callback(names.filter(x => autocomplete.filter(x, qry)));
- };
-
- this.typed = function (newValue, origJQElement) {
- var cursorpos = origJQElement[0].selectionEnd;
- var beginning_of_word = newValue.slice(0, cursorpos).lastIndexOf(" ");
- var word = newValue.slice(beginning_of_word+1, cursorpos);
- return word;
- };
-
- this.searchPost = function (resultsFromServer, origJQElement) {
- var cursorpos = origJQElement[0].selectionEnd;
- var newValue = origJQElement[0].value
- var beginning_of_word = newValue.slice(0, cursorpos).lastIndexOf(
- " ");
- var start = newValue.slice(0, beginning_of_word+1);
- var end = origJQElement[0].value.slice(cursorpos);
- var result = resultsFromServer.map( x => {
- return {
- text: start + x + end,
- html: x
- }});
- return result;
- };
-
- this.toggle_completion = function () {
- var field = $("#caosdb-query-textarea");
- field.toggleClass("basicAutoComplete", true);
- field.autoComplete({
- events: {
- search: this.search,
- typed: this.typed,
- searchPost: this.searchPost,
- }
- }
- );
- return field;
- };
-};
-
-// this will be replaced by require.js in the future.
-$(document).ready(function() {
- if ("${BUILD_MODULE_EXT_AUTOCOMPLETE}" === "ENABLED") {
- caosdb_modules.register(autocomplete);
- }
-});
diff --git a/src/core/js/caosdb.js b/src/core/js/caosdb.js
index 2bbc16407ea883a0f6cd37306da3c3a8875fdf25..031c6da4bd8c57d3dda652b7aef62376e2a97b7d 100644
--- a/src/core/js/caosdb.js
+++ b/src/core/js/caosdb.js
@@ -337,6 +337,32 @@ function input2caosdbDate(date, time) {
return date + "T" + time;
}
+/**
+ * Return true if the current user has the given permission for the given
+ * entity.
+ *
+ * @param {HTMLElement} entity
+ * @return {boolean}
+ */
+var hasEntityPermission = function (entity, permission) {
+ if (userHasRole("administration")) {
+ // administration is a special role. It has * permissions.
+ return true;
+ }
+ const permissions = getAllEntityPermissions(entity);
+ return permissions.indexOf(permission.toUpperCase()) > -1;
+}
+
+/**
+ * Get all permissions the current user has for this entity.
+ * @param {HTMLElement} entity
+ * @return {string[]} array of permissions.
+ */
+var getAllEntityPermissions = function (entity) {
+ const permissions = $(entity).find("[data-permission]").toArray().map(x => x.getAttribute("data-permission"));
+ return permissions;
+}
+
/**
* Take a datetime from caosdb and return a date and a time
* suitable for html inputs.
diff --git a/src/core/js/edit_mode.js b/src/core/js/edit_mode.js
index a4773b247181c841a63ee0107fe75012fb4eed18..9df7505f1e81fd0234aaa4461444535846921885 100644
--- a/src/core/js/edit_mode.js
+++ b/src/core/js/edit_mode.js
@@ -42,6 +42,11 @@ var edit_mode = new function() {
*/
this.start_edit = new Event("caosdb.edit_mode.start_edit")
+ /**
+ * Fired by the entity element after editing (canceled or saved).
+ */
+ this.end_edit = new Event("caosdb.edit_mode.end_edit")
+
/**
* Fired by a list-property when an (input) element is added to the list during editing.
*/
@@ -1203,7 +1208,7 @@ var edit_mode = new function() {
*/
this.delete_action = async function(entity) {
var app = edit_mode.app;
- // this is the callback of the delete button
+
// show waiting notification
edit_mode.smooth_replace(entity, app.waiting);
// send delete request
@@ -1548,6 +1553,7 @@ var edit_mode = new function() {
}
hintMessages.hintMessages(app.entity);
edit_mode.unfreeze();
+ app.entity.dispatchEvent(edit_mode.end_edit);
resolve_references.init();
preview.init();
}
@@ -1795,7 +1801,24 @@ var edit_mode = new function() {
$(entity).find(".caosdb-f-edit-mode-entity-actions-panel").append(button);
$(button).click(() => {
- edit_mode.delete_action(entity);
+ // hide other elements
+ const _alert = form_elements.make_alert({
+ title: "Warning",
+ message: "You are going to delete this entity permanently. This cannot be undone.",
+ proceed_callback: () => {
+ edit_mode.delete_action(entity)
+ },
+ cancel_callback: () => {
+ $(_alert).remove();
+ $(entity).find(".caosdb-f-edit-mode-entity-actions-panel").show();
+ },
+ proceed_text: "Yes, delete!",
+ remember_my_decision_id : "delete_entity",
+ });
+ $(_alert).addClass("text-right");
+
+ $(entity).find(".caosdb-f-edit-mode-entity-actions-panel").after(_alert).hide();
+
});
}
diff --git a/src/core/js/ext_autocomplete.js b/src/core/js/ext_autocomplete.js
new file mode 100644
index 0000000000000000000000000000000000000000..9d99241485245ca6232a7626c04f7998579174e8
--- /dev/null
+++ b/src/core/js/ext_autocomplete.js
@@ -0,0 +1,161 @@
+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2019 IndiScale GmbH, Henrik tom Wörden
+ *
+ * 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
+ */
+
+/*
+ * This module uses and extends bootstrap-autocomplete to provide
+ * autocompletion to the query field.
+ * Currently, completion exists for names that are stored in CaosDB
+ */
+'use strict';
+
+var ext_autocomplete = new function () {
+ this.CQL_WORDS = [
+ "FIND",
+ "FILE",
+ "ENTITY",
+ "SELECT",
+ "COUNT",
+ "RECORD",
+ "PROPERTY",
+ "RECORDTYPE",
+ "REFERENCES",
+ "REFERENCED BY",
+ "WHICH",
+ "WITH",
+ "CREATED BY",
+ "CREATED ON",
+ "SOMEONE",
+ "STORED AT",
+ "HAS A PROPERTY",
+ "HAS BEEN",
+ "ANY VERSION OF",
+ ];
+ this.version = "0.1";
+
+
+ /**
+ * configure logging
+ */
+ var logger = log.getLogger("ext_autocomplete");
+
+ /**
+ * Initialize this module.
+ *
+ * Fetch candidates and prepare bootstrap-autocomplete.
+ */
+ this.init = async function () {
+ this.candidates = await this.retrieve_names();
+ this.switch_on_completion();
+ };
+
+
+ /**
+ * creates a list of names from the server resource Entity/names
+ */
+ this.retrieve_names = async function () {
+ var response = $(await connection.get(transaction.generateEntitiesUri(
+ ["names"]))).find("Property[name],RecordType[name],Record[name]")
+
+ response = response.toArray().map(x => $(x).attr("name"));
+ response = response.concat(ext_autocomplete.CQL_WORDS);
+
+ return response
+ };
+
+ /**
+ * case insensitive filter that returns elements that start with qry
+ */
+ this.starts_with_filter = function (x, qry) {
+ return x.toLowerCase().startsWith(qry.toLowerCase())
+ };
+
+ /**
+ * Overwrites the default search function of bootstrap-autocomplete
+ * uses candidates and filters the list using filter
+ */
+ this.search = async function (qry, callback, origJQElement) {
+ callback(ext_autocomplete.candidates.filter(
+ x => ext_autocomplete.starts_with_filter(x, qry)));
+ };
+
+ /**
+ * Overwrites the default typed function of bootstrap-autocomplete
+ * This assures that only the word before the cursor is used for completion
+ */
+ this.typed = function (newValue, origJQElement) {
+ var cursorpos = origJQElement[0].selectionEnd;
+ var beginning_of_word = newValue.slice(0, cursorpos).lastIndexOf(" ");
+ var word = newValue.slice(beginning_of_word + 1, cursorpos);
+ return word;
+ };
+
+ /**
+ * Overwrites the default searchPost function of bootstrap-autocomplete
+ * This assures that only the word before the cursor is replaced.
+ * It is achieved by returning not a simple list, but an object where each
+ * element has "text" and "html" fields, where "html" is what is visible
+ * in the dropdown and "text" will be inserted.
+ */
+ this.searchPost = function (resultsFromServer, origJQElement) {
+ var cursorpos = origJQElement[0].selectionEnd;
+ var newValue = origJQElement[0].value
+ var beginning_of_word = newValue.slice(0, cursorpos).lastIndexOf(
+ " ");
+ var start = newValue.slice(0, beginning_of_word + 1);
+ var end = origJQElement[0].value.slice(cursorpos);
+ var result = resultsFromServer.map(x => {
+ return {
+ text: start + x + end,
+ html: x
+ }
+ });
+ return result;
+ };
+
+ /**
+ * enables autocompletion in the query field
+ */
+ this.switch_on_completion = function () {
+ var field = $("#caosdb-query-textarea");
+ field.attr("autocomplete", "off");
+ field.toggleClass("basicAutoComplete", true);
+ field.autoComplete({
+ events: {
+ search: this.search,
+ typed: this.typed,
+ searchPost: this.searchPost,
+ },
+ noResultsText: 'No autocompletion suggestions',
+ bootstrapVersion: "3",
+
+ });
+
+ return field;
+ };
+};
+
+// this will be replaced by require.js in the future.
+$(document).ready(function () {
+ if ("${BUILD_MODULE_EXT_AUTOCOMPLETE}" == "ENABLED") {
+ caosdb_modules.register(ext_autocomplete);
+ }
+});
diff --git a/src/core/js/ext_bookmarks.js b/src/core/js/ext_bookmarks.js
new file mode 100644
index 0000000000000000000000000000000000000000..d99ff362d8a26ee4818a76a624c80f55f757c419
--- /dev/null
+++ b/src/core/js/ext_bookmarks.js
@@ -0,0 +1,730 @@
+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ *
+ * 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
+ */
+
+'use strict';
+
+
+/**
+ * Keep track of bookmarked entities and provide functions for export, viewing
+ * all entities and resetting the bookmarks.
+ *
+ * @module ext_bookmarks
+ * @version 0.2
+ *
+ * @param jQuery - well-known library.
+ * @param log - singleton from loglevel library or javascript console.
+ * @param {ext_bookmarks_config} config
+ *
+ * @type ext_bookmarks_config
+ * @property {function} [get_context_root] - param-less function which returns the
+ * uri of the collection resource which returns the bookmarked entities.
+ * @property {string} [data_attribute=data-bmval] - name of the data-attribute
+ * which contains the bookmark key.
+ * @property {Storage} [bookmark_storage=localStorage] - the Storage
+ * implementation which is used for storing bookmarks.
+ * @property {function} [set_collection_link] - a function which sets the
+ * collection link.
+ * @property {function} [set_counter] - a function which sets the counter
+ * @property {function} [getPaging] - a function which returns the paging string
+ * @property {function} [set_export_button_click] - a function which sets the click
+ * event handler of the export button.
+ * @property {function} [set_clear_button_click] - a function which sets the click
+ * event handler of the clear button.
+ * @property {string[]} [tsv_columns=["URI"]]
+ * @property {function} [get_export_table_row] - function which receives the
+ * bookmarked id and must return an array of columns.
+ * @property {object} [data_getters={}] - a dictionary of functions which
+ * retrieve bookmark data for a given bookmark id and a data_key.
+ * @property {string[]} [data_no_cache] - an array of data_keys which are not
+ * to be cached.
+ */
+var ext_bookmarks = function ($, logger, config) {
+
+ config = config || {};
+
+ /**
+ * This counter is used as a cache for the number of current bookmarks. It
+ * is used to quickly change the counter in the bookmarks menu and lazily
+ * updated.
+ */
+ var counter = 0;
+
+ /**
+ * Currently this is mainly usefull for testing, but in the future it might
+ * be desirable to have multiple bookmark collection at the same time. It
+ * would be easy to extent this class for this because the collection_id is
+ * used in the generated links and as part of the storage key in the
+ * bookmark_storage.
+ */
+ var collection_id = config["collection_id"] || 0;
+
+ const data_getters = config["data_getters"] || {
+ "URI": (id) => get_context_root() + id
+ };
+ const data_no_cache = config["data_no_cache"] || ["URI"];
+
+ const data_attribute = config["data_attribute"] || "data-bmval";
+
+ /**
+ * Return all bookmark buttons on this page or which are children of scope.
+ *
+ * @param {HTMLElement|string} [scope='body']
+ * @return {HTMLElement[]} array of bookmark buttons.
+ */
+ const get_bookmark_buttons = function (scope) {
+ return $(scope || "body").find(`[${data_attribute}]`).toArray();
+ }
+
+ /**
+ * Sets the click event handler of the clear button.
+ *
+ * @param {function} cb - event handler.
+ */
+ const set_clear_button_click = config["set_clear_button_click"] || function (cb) {
+ $("#caosdb-f-bookmarks-clear")
+ .toggleClass("disabled", !cb)
+ .on("click", cb);
+ }
+
+ /**
+ * Sets the click event handler of the export button.
+ *
+ * @param {function} cb - event handler.
+ */
+ const set_export_button_click = config["set_export_button_click"] || function (cb) {
+ $("#caosdb-f-bookmarks-export-link")
+ .toggleClass("disabled", !cb)
+ .on("click", cb);
+ }
+
+ const getPaging = config["getPaging"] || (() => "?P=0L10");
+
+ /**
+ * The storage backend for the bookmarks.
+ */
+ const bookmark_storage = config["bookmark_storage"] || window.localStorage;
+
+ /**
+ * Set the href attribute of the bookmark collection link.
+ *
+ * @param {string} uri
+ */
+ const set_collection_link = config["set_collection_link"] || function (uri) {
+ const link = $("#caosdb-f-bookmarks-collection-link")
+ .toggleClass("disabled", !uri)
+ .find("a");
+ if (uri) {
+ link.attr("href", uri);
+ } else {
+ link.removeAttr("href");
+ }
+ }
+
+ /**
+ * Set the counter badge in the bookmark menu.
+ */
+ const update_counter = config["set_counter"] || function (counter) {
+ $("#caosdb-f-bookmarks-collection-counter").text(counter);
+ }
+
+ const get_context_root = config["get_context_root"] || (() => "");
+
+ /**
+ * This is used as a prefix of the key in the bookmark_storage.
+ */
+ const key_prefix = "_bm_";
+
+ /**
+ * This marker is used to identify uris which specify a bookmark collection
+ * which should be reloaded.
+ */
+ const uri_marker = "_bm_";
+
+ /**
+ * Extract the bookmark id from the bookmark button.
+ *
+ * @param {HTMLElement} button - the bookmark button.
+ * @return {string} the bookmark id.
+ */
+ const get_value = function (button) {
+ const result = $(button).attr(data_attribute);
+ return result;
+ }
+
+ /**
+ * Construct the prefix of the key for the bookmark_storage.
+ *
+ * This can be used to construct the item key and the data key
+ * to delete all storage keys which belong to the current bookmark
+ * collection.
+ *
+ * @param {string}
+ */
+ const get_collection_prefix = function () {
+ return key_prefix + collection_id;
+ }
+
+ /**
+ * Generate the key for the bookmark_storage.
+ *
+ * @param {string} val - the value which is used to generate the key.
+ */
+ const get_key = function (val) {
+ return get_collection_prefix() + '_it_' + val;
+ }
+
+
+ /**
+ * These will be the columns in the TSV file. For each column there should
+ * exist a data_getter.
+ */
+ const tsv_columns = config["tsv_columns"] || ["URI"];
+
+ /**
+ * Generate a single TSV row
+ *
+ * @return {string[]} array of row columns
+ */
+ const get_export_table_row = async function (id) {
+ const row = [];
+ for (var col of tsv_columns) {
+ row.push(await get_bookmark_data(id, col));
+ }
+ return row;
+ }
+
+ /**
+ * Generate the TSV data for the export callback with all current
+ * bookmarks.
+ *
+ * TODO merge with caosdb_utils.create_tsv_table.
+ *
+ * @param {string[]} bookmarks - array of ids.
+ * @param {string} [preamble="data:text/csv;charset=utf-8,"] - the preamble
+ * which is used for generating tables which can be downloaded by
+ * browsers.
+ * @param {string} [tab="%09"] - the tab string.
+ * @param {string} [newline="%0A"] - the newline string.
+ * @param {string[]} [leading_comments] - comment lines which are to be put
+ * even before the header line. They should be appropriately escaped (e.g.
+ * with "%23").
+ */
+ const get_export_table = async function (bookmarks, preamble, tab, newline, leading_comments) {
+ // TODO merge with related code in the module "caosdb_table_export".
+ preamble = ((typeof preamble == 'undefined') ? "data:text/csv;charset=utf-8,": preamble);
+ tab = tab || "%09";
+ newline = newline || "%0A";
+ leading_comments = (leading_comments ? leading_comments.join(newline) + newline : "");
+ const header = leading_comments + tsv_columns.join(tab) + newline;
+ const rows = [];
+ for (let i = 0; i < bookmarks.length; i++) {
+ rows.push((await get_export_table_row(bookmarks[i])).join(tab));
+ }
+ return `${preamble}${header}${rows.join(newline)}`;
+ }
+
+ /**
+ * Download the table with a given filename.
+ *
+ * This method adds a temporay <A> element to the dom tree and triggers
+ * "click" because otherwise the filename cannot be set.
+ *
+ * See also:
+ * https://stackoverflow.com/questions/21177078/javascript-download-csv-as-file
+ */
+ const download = function (table, filename) {
+ console.log("download");
+ const link = $(`<a style="display: none" download="${filename}" href="${table}"/>`);
+ $("body").append(link);
+ link[0].click();
+ link.remove();
+ }
+
+ /**
+ * Trigger the download of the TSV table with all current bookmarks.
+ *
+ * This is the call-back for the export button.
+ */
+ const export_bookmarks = async function () {
+ const ids = get_bookmarks();
+ const versioned_bookmarks = []
+ for (let id of ids) {
+ if (id.indexOf("@") > -1) {
+ versioned_bookmarks.push(id);
+ } else {
+ versioned_bookmarks.push(id + "@" + (await get_bookmark_data(id, "Version")));
+ }
+ }
+ const uri = get_collection_link(ids);
+ const leading_comments = [encodeURIComponent(`#Link to all entities: ${uri}`)];
+ const export_table = await get_export_table(ids, undefined, undefined, undefined, leading_comments);
+ download(export_table, "bookmarked_entities.tsv");
+ }
+
+ /**
+ * Return all current bookmarks.
+ *
+ * @return {string[]} array of bookmarked ids.
+ */
+ const get_bookmarks = function () {
+ const result = [];
+
+ const storage_key_prefix = get_key("");
+ for (let i = 0; i < bookmark_storage.length; i++) {
+ const key = bookmark_storage.key(i);
+ if (key.indexOf(storage_key_prefix) > -1) {
+ result.push(bookmark_storage[key]);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Update the clear button (i.e. add a click handler which resets the bookmarks.)
+ *
+ * @param {string[]} bookmarks - array of ids.
+ */
+ const update_clear_button = function (bookmarks) {
+ if (bookmarks.length > 0) {
+ set_clear_button_click(clear_bookmark_storage);
+ } else {
+ set_clear_button_click(false);
+ }
+ }
+
+ /**
+ * Update the export button (i.e. add a click handler which generates the
+ * tsv file.)
+ *
+ * @param {string[]} bookmarks - array of ids.
+ */
+ const update_export_link = function (bookmarks) {
+ if (bookmarks.length > 0) {
+ set_export_button_click(export_bookmarks);
+ } else {
+ set_export_button_click(false);
+ }
+ }
+
+ /**
+ * Generate the uri for the collection of all bookmarked entities.
+ *
+ * @param {string[]} bookmarks - array of ids.
+ * @return {string} uri
+ */
+ const get_collection_link = function (bookmarks) {
+ const uri_segment = bookmarks.join("&");
+ return get_context_root() + uri_segment + getPaging() +
+ "#" + uri_marker + collection_id;
+ }
+
+ /**
+ * Update the link of the collection of bookmarks in the bookmark drop down
+ * menu.
+ *
+ * @param {string[]} bookmarks - array of ids.
+ */
+ const update_collection_link = function (bookmarks) {
+ if (bookmarks.length > 0) {
+ const link = get_collection_link(bookmarks);
+ set_collection_link(link);
+ } else {
+ set_collection_link(false);
+ }
+ }
+
+ /**
+ * Syncronize the bookmark_storage and currently visible bookmark button and
+ * update all buttons and other visible elements and the bookmarks drop
+ * down menu.
+ *
+ * @param {string[]} [bookmarks] - array of ids. If omitted, the
+ * get_bookmarks function is being called.
+ */
+ const update_collection = function (bookmarks) {
+ bookmarks = bookmarks || get_bookmarks();
+ update_counter(bookmarks.length);
+ update_collection_link(bookmarks);
+ update_export_link(bookmarks);
+ update_clear_button(bookmarks);
+ }
+
+ /**
+ * Toggle the active class of the button and change the title of the button
+ * accordingly.
+ *
+ * @param {HTMLElement} button - bookmark button
+ * @param {boolean} is_active - whether the new state is active or not.
+ */
+ const set_button_state = function (button, is_active) {
+ $(button).toggleClass("active", is_active);
+ if (is_active) {
+ $(button).attr("title", "Remove bookmark");
+ } else {
+ $(button).attr("title", "Add bookmark");
+ }
+ }
+
+ /**
+ * Event handler for the click event of the bookmark buttons.
+ *
+ * Toggles the buttons state and adds or removes the bookmark.
+ *
+ * @param {Event} e - the click event;
+ */
+ const toggle_bookmark_active = function (e) {
+ const button = $(this);
+
+ const new_is_active = !button.is(".active");
+ set_button_state(button, new_is_active);
+
+ const value = get_value(button[0]);
+ const key = get_key(value);
+ if (new_is_active) {
+ bookmark_storage.setItem(key, value);
+ update_counter(++counter);
+
+ // fill the cache immediately. This is a good idea, because many
+ // data_getters can work on the DOM tree when the bookmark is being
+ // selected. Later, when the user has left the current page, the
+ // getters might need to request the database. We want to prevent
+ // that.
+ collect_bookmark_data(value);
+ } else {
+ bookmark_storage.removeItem(key);
+ update_counter(--counter);
+ remove_bookmark_data(value);
+ }
+ update_collection();
+ }
+
+ /**
+ * Fill the cache with data for the export for a bookmark.
+ *
+ * @param {string} id - bookmark id.
+ */
+ const collect_bookmark_data = function (id) {
+ for (let data_key in data_getters) {
+ if (data_no_cache.indexOf(data_key) == -1) {
+ // do nothing, only trigger the fetching
+ get_bookmark_data(id, data_key)
+ }
+ }
+ }
+
+ /**
+ * Remove all data item which belong to a bookmark.
+ *
+ * @param {string} id - bookmark id.
+ */
+ const remove_bookmark_data = function (id) {
+ const data_key_prefix = get_data_key(id, "");
+ remove_from_storage_by_prefix(data_key_prefix);
+ }
+
+ /**
+ * Initialize a single bookmark button.
+ *
+ * Fetch the state from the bookmark_storage and set the bookmark button to
+ * active or inactive. Also add the onclick handler which toggles the
+ * bookmark state.
+ *
+ * @param {HTMLElement} button - The bookmark button
+ */
+ const init_button = function (button) {
+ // load state
+ const key = get_key(get_value(button));
+ const is_bookmarked = !!key && !!bookmark_storage[key];
+ set_button_state(button, is_bookmarked);
+
+ // onlick handler
+ button.onclick = toggle_bookmark_active;
+ }
+
+ /**
+ * Remove all items in the bookmark_storage by a prefix.
+ *
+ * Useful for resetting the whole bookmark_storage or just deleting a
+ * single item along with its data items.
+ *
+ * @param {string} prefix
+ */
+ const remove_from_storage_by_prefix = function (prefix) {
+ const keys = [];
+ for (let i = 0; i < bookmark_storage.length; i++) {
+ const key = bookmark_storage.key(i);
+ if (key.indexOf(prefix) > -1) {
+ keys.push(key);
+ }
+ }
+ for (let i = 0; i < keys.length; i++) {
+ bookmark_storage.removeItem(keys[i]);
+ }
+ }
+
+ /**
+ * Remove all bookmarks, clear the counter and reset the buttons
+ */
+ const clear_bookmark_storage = function () {
+ counter = 0;
+ update_collection([]);
+
+ // reset all buttons
+ get_bookmark_buttons().forEach((x) => {
+ set_button_state(x, false);
+ });
+
+ const storage_key_prefix = get_collection_prefix()
+ remove_from_storage_by_prefix(storage_key_prefix);
+ }
+
+ /**
+ * Add all bookmarks to storage.
+ *
+ * @param {string[]} ids - an array of ids.
+ */
+ const add_all_bookmarks_to_storage = function (ids) {
+ counter = counter + ids.length;
+ for (let i = 0; i < ids.length; i++) {
+ const id = ids[i];
+ if (id) {
+ bookmark_storage[get_key(id)] = id
+ }
+ }
+ update_collection();
+ }
+
+ /**
+ * Parse a list of bookmarked entities and the collection_id from and URI.
+ *
+ * @param {string} uri
+ * @return {object} dict with two keys:
+ * {string[]} bookmarks
+ * {string} _collection_id
+ */
+ const parse_uri = function (uri) {
+ var cut_index = uri.indexOf("#" + uri_marker);
+ if (cut_index > -1) {
+ // get collection id
+ const _collection_id = uri
+ .substring(cut_index + uri_marker.length + 1)
+ // remove query
+ const query_marker = uri.indexOf("?");
+ if (query_marker > -1) {
+ cut_index = query_marker;
+ }
+ const uri_segments = uri.substring(0, cut_index).split("/")
+ const ids = uri_segments[uri_segments.length - 1].split("&");
+ logger.debug("found ids in uri", ids);
+ return {
+ bookmarks: ids,
+ collection_id: _collection_id
+ };
+ }
+ return undefined;
+ }
+
+
+ /**
+ * Initialize all bookmark buttons which are children of scope.
+ *
+ * @param {HTMLElement|string} [scope="body"] - element or jquery selector.
+ */
+ const init_bookmark_buttons = function (scope) {
+ logger.trace("enter init_bookmark_buttons", scope);
+ $(get_bookmark_buttons(scope)).each((idx, button) => {
+ init_button(button);
+ });
+ }
+
+ /**
+ * Setter for the collection_id.
+ *
+ * @param {string} id
+ */
+ const set_collection_id = function (id) {
+ collection_id = id;
+ }
+
+ /**
+ * Initialize this module.
+ */
+ const init = async function (scope) {
+ logger.info("init ext_bookmarks");
+ //add_bookmark_buttons();
+ counter = 0;
+ const parsed_uri = parse_uri(window.location.href);
+ if (typeof parsed_uri != "undefined") {
+ // this hack removes the "#_bm" marker from the uri without
+ // reloading the page.
+ window.location.href = "#";
+
+ clear_bookmark_storage();
+ collection_id = parsed_uri["collection_id"];
+ add_all_bookmarks_to_storage(parsed_uri["bookmarks"]);
+ }
+
+ init_bookmark_buttons(scope);
+ update_collection();
+ if (edit_mode) {
+ window.document.body.addEventListener(edit_mode.end_edit.type, (e) => {
+ init_bookmark_buttons(e.target);
+ }, true);
+ }
+ }
+
+ /**
+ * Construct the key for data items in the bookmark_storage.
+ */
+ const get_data_key = function (id, data_key) {
+ return get_collection_prefix() + '_da_' + id + "_" + data_key;
+ }
+
+ /**
+ * Get a specific data item which belongs to a bookmark.
+ *
+ * This is currently prominently used by the tsv-export.
+ *
+ * @param {string} id - the bookmarked id
+ * @param {string} data_key - an identifier for the data item to be
+ * retrieved.
+ * @returns {string} the `data_key` of bookmark `id`.
+ */
+ const get_bookmark_data = async function (id, data_key) {
+ // get full key (needed for the cache)
+ const full_data_key = get_data_key(id, data_key);
+
+ // retrieve from cache
+ const cached = bookmark_storage[full_data_key];
+ if (typeof cached != "undefined") {
+ return cached;
+ }
+
+ // not in cache, try the data_getters
+ var uncached = undefined
+ if (data_getters[data_key]) {
+ uncached = (await data_getters[data_key](id))
+ }
+
+ // don't cache if getting the information is trivial or there are other
+ // reasons why this is in the data_no_cache array.
+ if (data_no_cache.indexOf(data_key) == -1) {
+ bookmark_storage[full_data_key] = uncached || "";
+ }
+ return uncached;
+ }
+
+ return {
+ init: init,
+ parse_uri: parse_uri,
+ get_bookmarks: get_bookmarks,
+ get_key: get_key,
+ get_value: get_value,
+ set_collection_id: set_collection_id,
+ bookmark_storage: bookmark_storage,
+ get_export_table: get_export_table,
+ clear_bookmark_storage,
+ clear_bookmark_storage,
+ update_clear_button: update_clear_button,
+ update_export_link: update_export_link,
+ update_collection_link: update_collection_link,
+ get_collection_link: get_collection_link,
+ get_bookmark_buttons: get_bookmark_buttons,
+ init_button: init_button,
+ get_bookmark_data: get_bookmark_data,
+ }
+};
+
+
+
+$(document).ready(function () {
+ if ("${BUILD_MODULE_EXT_BOOKMARKS}" == "ENABLED") {
+ // The following is the configuration for the CaosDB WebUI.
+ const get_context_root = (() => connection.getBasePath() + "Entity/");
+
+ // This getter retrieves a file's path from the page or, if necessary,
+ // from the server.
+ const get_path = async function (id) {
+ if (id.indexOf("@") > -1) {
+ const entity = $(`[data-bmval='${id}']`);
+ if (entity.length > 0) {
+ return getEntityPath(entity[0]) || "";
+ }
+ }
+ return $(await transaction.retrieveEntityById(id)).attr("path");
+ }
+
+ // This retrieves the head version id
+ const get_version = async function (id) {
+ return $(await transaction.retrieveEntityById(id)).find("Version").attr("id");
+ }
+
+ const get_name = async function (id) {
+ if (id.indexOf("@") > -1) {
+ const entity = $(`[data-bmval='${id}']`);
+ if (entity.length > 0) {
+ return getEntityName(entity[0]) || "";
+ }
+ }
+ return $(await transaction.retrieveEntityById(id)).attr("name");
+ }
+
+ const get_rt = async function (id) {
+ if (id.indexOf("@") > -1) {
+ const entity = $(`[data-bmval='${id}']`);
+ if (entity.length > 0) {
+ return getParents(entity[0]).join("/");
+ }
+ }
+ const parent_names = $(await transaction.retrieveEntityById(id))
+ .find("Parent").toArray().map(x => x.getAttribute("name"))
+ return parent_names.join("/");
+ }
+
+ // these columns will be in the export
+ const tsv_columns = ["ID", "Version", "URI", "Path", "Name", "RecordType"];
+ // functions for collecting the export data for a particular bookmarked id.
+ const data_getters = {
+ "ID": (id) => id.indexOf("@") > -1 ? id.split("@")[0] : id,
+ "Version": async (id) => id.indexOf("@") > -1 ? id.split("@")[1] : await get_version(id),
+ "Path": get_path,
+ "URI": async (id) => get_context_root() + id + (id.indexOf("@") > -1 ? "" : ("@" + await get_version(id))),
+ "Name": get_name,
+ "RecordType": get_rt,
+ };
+
+ // we cannot cache these because the the values might change unnoticed
+ // when the head moves to a newer version.
+ const data_no_cache = ["ID", "Version", "URI", "Path", "Name", "RecordType"];
+
+ const config = {
+ get_context_root: get_context_root,
+ tsv_columns: tsv_columns,
+ data_getters: data_getters,
+ data_no_cache: data_no_cache,
+ };
+
+ ext_bookmarks = ext_bookmarks($, log.getLogger("ext_bookmarks"), config);
+ caosdb_modules.register(ext_bookmarks);
+ }
+});
diff --git a/src/core/js/ext_bottom_line.js b/src/core/js/ext_bottom_line.js
index 1bcf73dea17889bda9858ed78a2f6848e1dc21ee..bd7ec6a9938ff80afbd7dafdf0a734cd443678bc 100644
--- a/src/core/js/ext_bottom_line.js
+++ b/src/core/js/ext_bottom_line.js
@@ -42,8 +42,10 @@
* @requires load_config (function from caosdb.js)
* @requires getEntityPath (function from caosdb.js)
* @requires connection (module from webcaosdb.js)
+ * @requires UTIF (from utif.js library)
+ * @requires ext_table_preview (module from ext_table_preview.js)
*/
-var ext_bottom_line = function($, logger, is_in_view_port, load_config, getEntityPath, connection) {
+var ext_bottom_line = function($, logger, is_in_view_port, load_config, getEntityPath, connection, UTIF, ext_table_preview) {
/**
* @property {string|function} create - a function with one parameter
@@ -103,7 +105,91 @@ var ext_bottom_line = function($, logger, is_in_view_port, load_config, getEntit
*/
const _create_video_preview = function(entity) {
var path = connection.getFileSystemPath() + getEntityPath(entity);
- return $(`<div class="caosdb-v-bottom-line-video-preview"><video controls="controls"><source src="${path}"/></video></div>`)[0];
+ return $(`<div class="caosdb-v-bottom-line-video-preview">
+ <video controls="controls"><source src="${path}"/></video></div>`)[0];
+ }
+
+ /**
+ * Error class which has the special to_html method.
+ *
+ * The to_html method creates a html representation of the error which is
+ * intended for displaying in the bottom_line container.
+ */
+ const BottomLineError = function(arg) {
+ this._is_bottom_line_error = true;
+
+ if (arg.message) {
+ // arg is an Error object
+ this.message = arg.message;
+ this.stack = arg.stack;
+ } else {
+ this.message = arg;
+ }
+
+ this.to_html = function() {
+ return $(`<div><p>An error occured while loading this preview.<p>${
+ this.message}<div>`)[0];
+ }
+ }
+
+ const BottomLineWarning = function (arg) {
+ this._is_bottom_line_error = true;
+
+ if (arg.message) {
+ // arg is an Error object
+ this.message = arg.message;
+ this.stack = arg.stack;
+ } else {
+ this.message = arg;
+ }
+
+ this.to_html = function() {
+ return $(`<div>${this.message}<div>`)[0];
+ }
+ }
+
+ /**
+ * Create a preview for tiff files.
+ *
+ * Tiff files are decompressed if necessary and converted into png by UTIF library.
+ *
+ * @param {HTMLElement} entity
+ * @return {Promise | HTMLElement} Promise for an IMG element.
+ */
+ const _create_tiff_preview = function(entity) {
+ const path = connection.getFileSystemPath() + getEntityPath(entity);
+ const result = $(`<div class="caosdb-v-bottom-line-image-preview"></div>`);
+ const img = $(`<img src="${path}"/>`)[0];
+ result.append(img);
+
+ /**
+ * Promise which retrieves the tiff file and calls the UTIF library for
+ * decompression and conversion into png.
+ */
+ return new Promise((resolve, reject) => {
+ const xhr = new XMLHttpRequest();
+ UTIF._xhrs.push(xhr);
+ UTIF._imgs.push(img);
+ xhr.open("GET", path);
+ xhr.responseType = "arraybuffer";
+ xhr.onload = (e) => {
+ try {
+ // decompress and convert tiff file
+ UTIF._imgLoaded(e);
+
+ // return the result if no error occured.
+ resolve(result);
+ } catch(err) {
+ // throw errors from UTIF to the awaiting caller.
+ reject(new BottomLineError(err));
+ }
+ }
+ // throw http errors to the awaiting caller.
+ xhr.onerror = reject;
+
+ // this finally triggers the retrieval
+ xhr.send();
+ });
}
/**
@@ -119,6 +205,8 @@ var ext_bottom_line = function($, logger, is_in_view_port, load_config, getEntit
var fallback_preview = undefined;
+ const _tiff_preview_enabled = "${BUILD_MODULE_EXT_BOTTOM_LINE_TIFF_PREVIEW}" == "ENABLED";
+
/**
* Default creators.
*
@@ -128,17 +216,26 @@ var ext_bottom_line = function($, logger, is_in_view_port, load_config, getEntit
id: "_default_creators.pictures",
is_applicable: (entity) => _path_has_file_extension(
entity, ["jpg", "png", "gif", "svg"]),
- create: _create_picture_preview
+ create: _create_picture_preview,
+ }, {
+ id: "_default_creators.tiff_images",
+ is_applicable: (entity) => _tiff_preview_enabled && _path_has_file_extension(
+ entity, ["tif", "tiff","dng","cr2","nef"]),
+ create: _create_tiff_preview,
}, { // videos
id: "_default_creators.videos",
is_applicable: (entity) => _path_has_file_extension(
entity, ["mp4", "mov", "webm"]),
create: _create_video_preview,
+ }, { // tables
+ id: "_default_creators.table_preview",
+ is_applicable: (e) => ext_table_preview.is_table(e),
+ create: (e) => ext_table_preview.get_preview(e),
}, { // fallback
id: "_default_creators.fallback",
is_applicable: (entity) => true,
create: (entity) => fallback_preview,
- },
+ }
];
@@ -231,8 +328,10 @@ var ext_bottom_line = function($, logger, is_in_view_port, load_config, getEntit
}
} catch (err) {
logger.error(err);
- const err_msg = "An error occured while loading this preview";
- set_preview_container(entity, err_msg);
+ if (!err._is_bottom_line_error) {
+ err = new BottomLineError(err);
+ }
+ set_preview_container(entity, err.to_html());
}
}
@@ -460,8 +559,12 @@ var ext_bottom_line = function($, logger, is_in_view_port, load_config, getEntit
_css_class_preview_container,
_css_class_preview_container_button,
_css_class_preview_container_resolvable,
+ BottomLineError: BottomLineError,
+ BottomLineWarning: BottomLineWarning,
}
-}($, log.getLogger("ext_bottom_line"), resolve_references.is_in_viewport_vertically, load_config, getEntityPath, connection);
+}($, log.getLogger("ext_bottom_line"),
+ resolve_references.is_in_viewport_vertically, load_config, getEntityPath,
+ connection, UTIF, ext_table_preview);
/**
@@ -484,20 +587,23 @@ var plotly_preview = function(logger, ext_bottom_line, plotly) {
* to be plotted.
* @param {object[]} layout - dictionary of settings defining the layout of
* the plot.
+ * @param {object[]} settings - object containing additional
+ * settings for the plot.
* @returns {HTMLElement} the element which contains the plot.
*/
const create_plot = function(data,
- layout = {
- margin: {
- t: 0
- },
- height: 400,
- widht: 400
- }) {
+ layout = {
+ margin: {
+ t: 0
+ },
+ height: 400,
+ widht: 400
+ },
+ settings = {
+ responsive: true
+ }) {
var div = $('<div/>')[0];
- plotly.newPlot(div, data, layout, {
- responsive: true
- });
+ plotly.newPlot(div, data, layout, settings);
return div;
}
@@ -525,7 +631,7 @@ var plotly_preview = function(logger, ext_bottom_line, plotly) {
// this will be replaced by require.js in the future.
$(document).ready(function() {
- if ("${BUILD_MODULE_EXT_BOTTOM_LINE}" === "ENABLED") {
+ if ("${BUILD_MODULE_EXT_BOTTOM_LINE}" == "ENABLED") {
caosdb_modules.register(plotly_preview);
caosdb_modules.register(ext_bottom_line);
}
diff --git a/src/core/js/ext_file_download.js b/src/core/js/ext_file_download.js
new file mode 100644
index 0000000000000000000000000000000000000000..477349b421e03d74aa28fddf6b4748f64ffa9f7b
--- /dev/null
+++ b/src/core/js/ext_file_download.js
@@ -0,0 +1,186 @@
+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+ *
+ * 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
+ */
+
+'use strict';
+
+/**
+ * The ext_file_download module provides a very basic preview for table files.
+ *
+ * The preview is generated using a server side script.
+ *
+ * @module ext_file_download
+ * @version 0.1
+ *
+ * @requires jQuery
+ * @requires log
+ */
+var ext_file_download = function ($, logger) {
+
+ /**
+ * collect the file ids that will be passed to the zip script
+ *
+ * @return {string[]} array of entity ids
+ */
+ const collect_ids = function(){
+ var properties = $(".caosdb-f-property-value").find(
+ ".caosdb-id.caosdb-f-property-single-raw-value");
+ var id_list = properties.toArray().map(x=>x.textContent);
+ var entities = $("tr[data-entity-id]")
+ id_list = id_list.concat(entities.toArray().map(
+ x=>x.attributes['data-entity-id'].value));
+ return id_list
+ };
+
+ /**
+ * chunk list to smaller pieces.
+ *
+ * @param {string[]} list - array of (usually) ids
+ * @param {Number} size - chunk size (use integer)
+ * @return {string[][]} array of array of string from the original list.
+ */
+ const chunk_list = function(list, size){
+ size = size || 20;
+ var pieces = [];
+ var index = 0;
+ while (index < list.length){
+ pieces.push(list.slice(index,index+size));
+ index+=size;
+ }
+
+ return pieces
+ };
+
+
+ /**
+ * create select statement to find files.
+ *
+ * @param {string[]} id_list - array of ids
+ * @return {string} a query string
+ */
+ const query_files_str = function(id_list){
+ var povs = id_list.map(x=>` id=${x} `);
+ const query_str="SELECT ID FROM FILE WITH " + povs.join("or");
+ return query_str;
+ };
+
+ /**
+ * Reduce id list to files. Throw away all ids which do not belong to a
+ * file entity.
+ *
+ * @param {string[]} id_list - array of ids
+ * @return {string[]} array of file ids.
+ */
+ const reduce_ids = async function(id_list){
+ var file_ids = []
+ for (var part of chunk_list(id_list)) {
+ // query for files
+ var result = await query(query_files_str(part));
+ file_ids=file_ids.concat(result.map(x => getEntityID(x)));
+ }
+ return file_ids;
+ };
+
+
+ /**
+ * Callback function for the download files link.
+ *
+ * Collects all the file entities and sends them to a server-side script
+ * which then puts the files into a zip.
+ *
+ * @param {HTMLElement} zip_link - the link element which triggered this
+ * call and which will be disabled during the execution of this
+ * function in order to prevent the user from triggering the process
+ * twice.
+ */
+ const download_files = async function (zip_link) {
+ const onClickValue = zip_link.getAttribute("onClick");
+ try {
+ // remove click event handler which called this function in the first place
+ zip_link.removeAttribute("onClick");
+
+ // add loading info. TODO make an animated one
+ $("#downloadModal").find(".caosdb-f-modal-footer-left").append(
+ createWaitingNotification("Collecting files...")
+ );
+
+ var ids = collect_ids();
+ ids = await reduce_ids(ids);
+ if (ids.length == 0){
+ alert ("There are no file entities in this table.");
+ return;
+ }
+
+ var table = await ext_bookmarks.get_export_table(ids, "", "\t", "\n");
+
+ const result = await connection.runScript(
+ "ext_file_download/zip_files.py",
+ {
+ "-p0": ids,
+ "-p1": table,
+ }
+ );
+ const code = result.getElementsByTagName("script")[0].getAttribute("code");
+ if (parseInt(code) > 0) {
+ throw ("An error occurred during execution of the server-side script:\n"
+ + result.getElementsByTagName("script")[0].outerHTML);
+ }
+ const filename = result.getElementsByTagName("stdout")[0].textContent;
+ if (filename.length == 0) {
+ throw("Server-side script produced no file or did not return the file name: \n"
+ + result.getElementsByTagName("script")[0].outerHTML);
+ }
+
+
+ // trigger download of generated file
+ caosdb_table_export.go_to_script_results(filename);
+
+ //close modal
+ $("#downloadModal").find(".modal-footer").find(".btn")[0].click();
+ } catch (e) {
+ globalError(e);
+ } finally {
+ removeAllWaitingNotifications($("#downloadModal")[0]);
+ // restore the old click handler - hence a new file is generated with each click.
+ zip_link.setAttribute("onClick", onClickValue);
+ }
+
+ };
+
+ const init = function () {
+ // only enable when init is being called
+ logger.info("init ext_file_download");
+ if (userIsAnonymous()) {
+ $("#caosdb-f-query-select-files").parent().hide();
+ }
+ };
+
+ return {
+ init: init,
+ download_files: download_files,
+ collect_ids: collect_ids,
+ chunk_list: chunk_list,
+ };
+
+}($, log.getLogger("ext_file_download"));
+
+// This module is registered by caosdb_table_export.
diff --git a/src/core/js/ext_references.js b/src/core/js/ext_references.js
index d9829cb9959c1249a4381bd45be9429f7dbef855..7cd597e128e8c09da9134f42f542898fb84a4e53 100644
--- a/src/core/js/ext_references.js
+++ b/src/core/js/ext_references.js
@@ -450,9 +450,11 @@ var resolve_references = new function () {
// Loop over all property values in the container element. Note: each property_value can be a single reference or a list of references.
for (const property_value of property_values) {
- const lists = $(property_value).find(
- ".caosdb-value-list").has(
- `.${_unresolved_class_name}`);
+ var lists = findElementByConditions(
+ property_value,
+ x => x.classList.contains("caosdb-value-list"),
+ x => x.classList.contains("caosdb-preview-container"))
+ lists = $(lists).has(`.${_unresolved_class_name}`);
if (lists.length > 0) {
logger.debug("processing list of references", lists);
@@ -525,8 +527,10 @@ var resolve_references = new function () {
// Load all remaining references. These are single reference values
// and those references from lists which are left for lazy loading.
- const rs = $(property_value).find(
- `.${_unresolved_class_name}`);
+ const rs = findElementByConditions(
+ property_value,
+ x => x.classList.contains(`${_unresolved_class_name}`),
+ x => x.classList.contains("caosdb-preview-container"));
for (var i = 0; i < rs.length; i++) {
if (resolve_references.is_in_viewport_vertically(
rs[i]) &&
diff --git a/src/core/js/ext_table_preview.js b/src/core/js/ext_table_preview.js
new file mode 100644
index 0000000000000000000000000000000000000000..1d9da6fa9334a52de5eb39a66b585c7eb67cd120
--- /dev/null
+++ b/src/core/js/ext_table_preview.js
@@ -0,0 +1,97 @@
+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+ *
+ * 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
+ */
+
+'use strict';
+
+/**
+ * The ext_table_preview module provides a very basic preview for table files.
+ *
+ * The preview is generated using a server side script.
+ *
+ * @module ext_table_preview
+ * @version 0.1
+ *
+ * @requires jQuery
+ * @requires log
+ * @requires getEntityPath
+ * @requires getEntityID
+ * @requires markdown
+ */
+var ext_table_preview = function ($, logger, connection, getEntityPath, getEntityID, markdown) {
+
+ const get_preview = async function (entity) {
+ try {
+ const script_result = await connection.runScript("ext_table_preview/pandas_table_preview.py",
+ {"-p0": getEntityID(entity)}
+ );
+
+ const code = script_result.getElementsByTagName("script")[0].getAttribute("code");
+ if (parseInt(code) > 1) {
+ return script_result.getElementsByTagName("stderr")[0]
+ } else if (parseInt(code) != 0) {
+ throw ("An error occurred during execution of the server-side "
+ + "script:\n"
+ + script_result.getElementsByTagName("stderr")[0]);
+ } else {
+ const tablecontent = script_result.getElementsByTagName("stdout")[0];
+ const unformatted = markdown.textToHtml(tablecontent.textContent)
+ const formatted = $('<div class="table-responsive"/>').append(unformatted);
+ formatted.find("table").addClass("table table-bordered table-condensed").removeAttr("border");
+ return formatted[0];
+ }
+ } catch (err) {
+ if (err.message && err.message.indexOf && err.message.indexOf("HTTP status 403") > -1) {
+ throw new ext_bottom_line.BottomLineWarning("You are not allowed to generate the table preview. Please log in.");
+ } else {
+ throw err;
+ }
+ }
+ };
+
+ const is_table = function (entity) {
+ const path = getEntityPath(entity);
+ return path && (path.toLowerCase().endsWith('.xls')
+ || path.toLowerCase().endsWith('.xlsx')
+ || path.toLowerCase().endsWith('.csv')
+ || path.toLowerCase().endsWith('.tsv'));
+ };
+
+ const init = function () {
+ // only enable when init is being called
+ ext_table_preview.is_table = is_table;
+ };
+
+ return {
+ init: init,
+ get_preview: get_preview,
+ is_table: () => false,
+ };
+
+}($, log.getLogger("ext_table_preview"), connection, getEntityPath, getEntityID, markdown);
+
+// this will be replaced by require.js in the future.
+$(document).ready(function () {
+ if ("${BUILD_MODULE_EXT_BOTTOM_LINE_TABLE_PREVIEW}" == "ENABLED") {
+ caosdb_modules.register(ext_table_preview);
+ }
+});
diff --git a/src/core/js/ext_xls_download.js b/src/core/js/ext_xls_download.js
index 0f607a459b8e502e1d4c451b1636d99ceb01657c..ebeb2ac94ca7bd84cc41ffef7bf3d1abc1982875 100644
--- a/src/core/js/ext_xls_download.js
+++ b/src/core/js/ext_xls_download.js
@@ -24,7 +24,7 @@
/**
* @module caosdb_table_export
- * @version 0.1
+ * @version 0.2
*
* Convert Entities for TSV and XLS export.
*
@@ -35,8 +35,6 @@
var caosdb_table_export = new function () {
var logger = log.getLogger("caosdb_table_export");
- var TAB = "%09";
- var NEWLINE = "%0A";
/**
* Hide "Download XLS File" link if the user is not authenticted (i.e.
@@ -44,11 +42,7 @@ var caosdb_table_export = new function () {
*/
this.init = function() {
logger.info("init caosdb_table_export");
- // TODO with AMD, use userIsAnonymous()
- if (Array.from(
- document.getElementsByClassName("caosdb-user-role")).map(
- el => el.innerText
- ).filter(el => el == "anonymous").length > 0) {
+ if (userIsAnonymous()) {
$(".caosdb-v-query-select-data-xsl").parent().hide();
}
}
@@ -62,19 +56,64 @@ var caosdb_table_export = new function () {
* @return {string}
*/
this.get_tsv_string = function(raw) {
+ const columns = this._get_column_header();
+ const entities = this._get_table_content();
+ return this._create_tsv_string(entities, columns, raw);
+ }
+
+ /**
+ * In order to create a valid tsv table, characters that have a special
+ * meaning (line break and tab) need to be removed.
+ *
+ * Both characters will be replaced by a single white space
+ *
+ * @param {string} raw - the cell content.
+ * @return {string} cleaned up content
+ */
+ this._clean_cell = function(raw) {
+ return raw.replaceAll("\t"," ").replaceAll("\n"," ").replaceAll("\r"," ").replaceAll("\x1E"," ").replaceAll("\x15"," ")
+ }
+
+ /**
+ * Finds the table in the DOM tree and returns the column names as array
+ *
+ * @return {string[]}
+ */
+ this._get_column_header = function() {
const table = $('.caosdb-select-table');
- const columns = table.find("th").toArray()
- .map(e => e.textContent)
+ return table.find("th").toArray()
+ .map(e => caosdb_table_export._clean_cell(e.textContent))
.filter(e => e.length > 0);
+ }
+
+ /**
+ * Finds the table in the DOM tree and returns the table content as array
+ *
+ * @return {HTMLElement[]}
+ */
+ this._get_table_content = function() {
+ const table = $('.caosdb-select-table');
// TODO use entity-panel class in table as well (change in query.xsl
// and then here)
- const entities = table.find("tbody tr").toArray();
- const csv_string = this._get_tsv_string(entities, columns, raw);
- return csv_string;
+ return table.find("tbody tr").toArray();
+ }
+
+ /**
+ * Encode tsv string
+ *
+ * @param {string} main - the tsv table string.
+ * @return {string} the same with prefix and URL encoded
+ */
+ this._encode_tsv_string = function(main) {
+ const preamble = "data:text/csv;charset=utf-8,";
+ main = encodeURIComponent(main);
+ return `${preamble}${main}`;
}
/**
- * Convert all entities to a tsv string with the given columns.
+ * Convert all entities to an encoded tsv string with the given columns.
+ *
+ * TODO merge with caosdb_utils.create_tsv_table.
*
* @param {HTMLElement[]} entities - entities which are converted to rows
* of the tsv string.
@@ -83,36 +122,56 @@ var caosdb_table_export = new function () {
* cells. Otherwise, the displayed data is used instead.
* @return {string}
*/
- this._get_tsv_string = function (entities, columns, raw) {
- logger.trace("enter get_tsv_string", entities, columns);
- var preamble = "data:text/csv;charset=utf-8,";
- var header = "ID" + TAB + columns.join(TAB) + NEWLINE
- var rows = caosdb_table_export._get_tsv_rows(entities, columns, raw).join(NEWLINE);
-
- const ret = `${preamble}${header}${rows}`;
- logger.trace("leave get_tsv_string", ret);
- return ret;
+ this._create_tsv_string = function (entities, columns, raw) {
+ logger.trace("enter _create_tsv_string ", entities, columns);
+ var header = "ID\t" + columns.join("\t") + "\n"
+ var rows = [];
+ for (const table_row of entities) {
+ rows.push(caosdb_table_export._get_entity_row(table_row, columns, raw).join("\t"));
+ }
+ var rows = rows.join("\n");
+ logger.trace("leave _create_tsv_string ", rows);
+ return `${header}${rows}`;
}
/**
- * Return an array of rows with the given columns of the tsv table, one per
- * entity.
+ * Return an array of cells, one per column, which contain a string
+ * representation of the value of the properties with the same name (as the
+ * column).
*
- * @param {HTMLElement[]} entities - entities which are converted to rows
- * of the tsv string.
+ * @param {HTMLElement} entity - entity from which the cells are extracted.
* @param {string[]} columns - array of property names.
* @param {boolean} raw - if true, the raw entity ids are put into the
* cells. Otherwise, the displayed data is used instead.
* @return {string[]}
*/
- this._get_tsv_rows = function (entities, columns, raw) {
- var rows = [];
- for (const entity of entities) {
- rows.push(this._get_entity_row(entity, columns, raw));
+ this._get_entity_row = function (entity, columns, raw) {
+ var cells = [getEntityID(entity)];
+ var properties = getProperties(entity);
+
+ for (const column of columns) {
+ var cell = "";
+ for (const property of properties) {
+ if(property.name.toLowerCase() === column.toLowerCase()) {
+ var value = caosdb_table_export
+ ._get_property_value(property.html);
+ if (raw) {
+ cell = value.raw;
+ } else if (value.summary) {
+ cell = value.summary;
+ } else if (value.pretty) {
+ cell = value.pretty;
+ } else {
+ cell = value.raw;
+ }
+ }
+ }
+ cells.push(caosdb_table_export._clean_cell(cell));
}
- return rows;
- }
+ logger.trace("leave _get_entity_row", cells);
+ return cells;
+ }
/**
* Return different string representations of the property's value.
@@ -187,73 +246,15 @@ var caosdb_table_export = new function () {
}
}
-
- /**
- * Return an array of cells, one per column, which contain a string
- * representation of the value of the properties with the same name (as the
- * column).
- *
- * @param {HTMLElement} entity - entity from which the cells are extracted.
- * @param {string[]} columns - array of property names.
- * @param {boolean} raw - if true, the raw entity ids are put into the
- * cells. Otherwise, the displayed data is used instead.
- * @return {string[]}
- */
- this._get_entity_row = function (entity, columns, raw) {
- var cells = [getEntityID(entity)];
- var properties = getProperties(entity);
-
- for (const column of columns) {
- var cell = "";
- for (const property of properties) {
- if(property.name.toLowerCase() === column.toLowerCase()) {
- var value = caosdb_table_export
- ._get_property_value(property.html);
- if (raw) {
- cell = value.raw;
- } else if (value.summary) {
- cell = value.summary;
- } else if (value.pretty) {
- cell = value.pretty;
- } else {
- cell = value.raw;
- }
- }
- }
- cells.push(cell);
- }
-
- logger.trace("leave _get_entity_row", cells);
- return cells.join(TAB);
- }
-
-
/**
* Open the resulting xls file by setting href to the location of the resulting
* file in the server's `Shared` resource and imitate a click.
*/
- this._go_to_script_results = function (xls_link, filename) {
- xls_link.setAttribute(
- "href",
- location.protocol + "//" +location.host + "/Shared/" + filename);
- xls_link.click();
- }
-
-
- this._get_csv_string = function (){
- const raw = $("input#caosdb-table-export-raw-flag-xls").is(":checked");
- const csv_string = caosdb_table_export.get_tsv_string(raw);
- //const csv_string = document.getElementById("caosdb-f-query-select-data-tsv").getAttribute(
- //"href");
- if (!csv_string) {
- return undefined;
- }
-
- return decodeURIComponent(csv_string.replace(/^data.*utf-8,/, ""));
+ this.go_to_script_results = function (filename) {
+ window.location.href = connection.getBasePath() + "Shared/" + filename;
}
}
-
/**
* This function is called on click by the link button which says "Download TSV
* File".
@@ -264,12 +265,12 @@ var caosdb_table_export = new function () {
*/
function downloadTSV(tsv_link) {
const raw = $("input#caosdb-table-export-raw-flag-tsv").is(":checked");
- const tsv_string = caosdb_table_export.get_tsv_string(raw);
+ var tsv_string = caosdb_table_export.get_tsv_string(raw);
+ tsv_string = caosdb_table_export._encode_tsv_string(tsv_string);
$(tsv_link).attr("href", tsv_string);
return true;
}
-
/**
* This function is called on click by the link button which says "Download XLS
* File".
@@ -279,15 +280,24 @@ function downloadTSV(tsv_link) {
* resulting file.
*/
async function downloadXLS(xls_link) {
- const csv_string = caosdb_table_export._get_csv_string();
-
- // remove click event handler which called this function in the first place
const onClickValue = xls_link.getAttribute("onClick");
- xls_link.removeAttribute("onClick");
-
try {
+ // remove click event handler which called this function in the first place
+ xls_link.removeAttribute("onClick");
+
+ // add loading info. TODO make an animated one
+ $("#downloadModal").find(".caosdb-f-modal-footer-left").append(
+ createWaitingNotification("Exporting table...")
+ );
+
+ const raw = $("input#caosdb-table-export-raw-flag-xls").is(":checked");
+ const tsv_string = caosdb_table_export.get_tsv_string(raw);
+ // TODO This existed previously. I do not know why.
+ if (!tsv_string) {
+ tsv_string = undefined;
+ }
const xls_result = await connection.runScript("xls_from_csv.py",
- {"-p0": {"filename": "selected.tsv", "blob": new Blob([csv_string], {type: "text/tab-separated-values;charset=utf-8"})}});
+ {"-p0": {"filename": "selected.tsv", "blob": new Blob([tsv_string], {type: "text/tab-separated-values;charset=utf-8"})}});
const code = xls_result.getElementsByTagName("script")[0].getAttribute("code");
if (parseInt(code) > 0) {
throw ("An error occurred during execution of the server-side script:\n"
@@ -299,11 +309,14 @@ async function downloadXLS(xls_link) {
+ xls_result.getElementsByTagName("script")[0].outerHTML);
}
- // set the href in order to download the file and simulate a click.
- caosdb_table_export._go_to_script_results(xls_link, filename);
+ // trigger download of generated file
+ caosdb_table_export.go_to_script_results(filename);
+
+
} catch (e) {
globalError(e);
} finally {
+ removeAllWaitingNotifications($("#downloadModal")[0]);
// restore the old click handler - hence a new file is generated with each click.
xls_link.setAttribute("onClick", onClickValue);
}
@@ -314,4 +327,5 @@ async function downloadXLS(xls_link) {
$(document).ready(function () {
caosdb_modules.register(caosdb_table_export);
+ caosdb_modules.register(ext_file_download);
});
diff --git a/src/core/js/footer.js b/src/core/js/footer.js
index 79f3ed0ecb382534d7c997ce0bc230178792f677..c48c5cf19c405aea326b36aba2868008466a8329 100644
--- a/src/core/js/footer.js
+++ b/src/core/js/footer.js
@@ -26,7 +26,7 @@
* Call initially.
*
* TODO refactor to async function for better readability.
- * @return
+ * @return something
*/
function footer_initOnDocumentReady() {
diff --git a/src/core/js/form_elements.js b/src/core/js/form_elements.js
index 0014f4db452a55839edaa860d7fa49f98529434e..47c8e0ce0cf0df2599c6ea1f2afee941edfab4cc 100644
--- a/src/core/js/form_elements.js
+++ b/src/core/js/form_elements.js
@@ -9,8 +9,7 @@
* 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
+ * 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.
*
@@ -164,6 +163,113 @@ var form_elements = new function () {
}
+ this._get_alert_decision = function (key) {
+ return localStorage["form_elements.alert_decision." + key];
+ }
+
+ this._set_alert_decision = function (key, val) {
+ localStorage["form_elements.alert_decision." + key] = val;
+ }
+
+ /**
+ * @type {AlertConfig}
+ * @property {string} [title] - an optional title for the alert.
+ * @property {string} [severity="danger"] - a bootstrap class suffix. Other
+ * examples: warning, info
+ * @property {string} message - informs the user what they are about to do.
+ * @property {function} proceed_callback - the function which is called
+ * then the user hits the "Proceed" button.
+ * @property {function} [cancel_callback] - a callback which is called then
+ * the cancel button is clicked. By default, only the alert is being
+ * closed an nothing happens.
+ * @property {string} [proceed_text="Proceed"] - the text on the proceed button.
+ * @property {string} [cancel_text="Cancel"] - the text on the cancel button.
+ * @property {string} [remember_my_decision_id] - if this parameter is
+ * present, a checkbox is appended to the alert ("Don't ask me
+ * again."). If the checkbox is checked the next time the make_alert
+ * function is called with the same remember_my_decision_id is created,
+ * the alert won't show up and the proceed_callback is called without
+ * any user interaction.
+ * @property {string} [remember_my_decision_text="Don't ask me again."] -
+ * label text for the checkbox.
+ * @property {HTMLElement} [proceed_button] - an optional custom proceed
+ * button.
+ * @property {HTMLElement] [cancel_button] - an optional custom cancel
+ * button.
+ */
+
+ /**
+ * Make an alert, that is a dialog which can intercept a function call and
+ * asks the user to proceed or cancel.
+ *
+ * @param {AlertConfig} config
+ * @return {HTMLElement}
+ */
+ this.make_alert = function (config) {
+ caosdb_utils.assert_string(config.message, "config param `message`");
+ caosdb_utils.assert_type(config.proceed_callback, "function",
+ "config param `proceed_callback`");
+
+ // define some defaults.
+ const title = config.title ? `<h4>${config.title}</h4>` : "";
+ const proceed_text = config.proceed_text || "Proceed";
+ const cancel_text = config.cancel_text || "Cancel";
+ const severity = config.severity || "danger";
+ const remember = !!config.remember_my_decision_id || false;
+
+ // check if alert should be created at all
+ if (remember) {
+ var result = this._get_alert_decision(config.remember_my_decision_id);
+ if (result == "proceed") {
+ // call callback asyncronously and return
+ (async function(){ config.proceed_callback(); })();
+ return undefined;
+ }
+ }
+
+ // create the alert
+ const _alert = $(`<div class="alert alert-${severity}
+ alert-dismissible fade in caosdb-f-form-elements-alert" role="alert">${title}
+ <p>${config.message}</p>
+ </div>`);
+
+ // create the "Don't ask me again" checkbox
+ var checkbox = undefined;
+ if (remember) {
+ const remember_my_decision_text = config.remember_my_decision_text
+ || "Don't ask me again.";
+ checkbox = $(`<p class="checkbox"><label>
+ <input type="checkbox"/> ${remember_my_decision_text}</label></p>`);
+ _alert.append(checkbox);
+ }
+
+
+ // create buttons ...
+ const cancel_button = config.cancel_button || $(`<button type="button" class="btn btn-default caosdb-f-btn-alert-cancel">${cancel_text}</button>`);
+ const proceed_button = config.proceed_button || $(`<button type="button" class="btn btn-${severity} caosdb-f-btn-alert-proceed">${proceed_text}</button>`);
+ _alert.append($("<p/>").append([proceed_button, cancel_button]));
+
+
+ // ... and bind callbacks to the buttons.
+ cancel_button.click(() => {
+ $(_alert).alert('close');
+ if (typeof config.cancel_callback == "function") {
+ config.cancel_callback();
+ }
+ });
+ proceed_button.click(() => {
+ if (remember && checkbox.find("input[type='checkbox']").is(":checked")) {
+ // store this decision.
+ form_elements._set_alert_decision(config.remember_my_decision_id,
+ "proceed");
+ }
+ $(_alert).alert('close');
+ config.proceed_callback();
+ });
+
+ return _alert[0];
+ }
+
/**
* (Re-)set this module's functions to standard implementation.
*/
diff --git a/src/core/js/preview.js b/src/core/js/preview.js
index f74fd13ffd2fe373543c025866e91cfe6b6fd9eb..b85f7b56dc13ff94aa2c3de90eb1b464d7f1e9d6 100644
--- a/src/core/js/preview.js
+++ b/src/core/js/preview.js
@@ -211,8 +211,8 @@ var preview = new function() {
/**
* Transform the raw xml response of the server into an array of entities for preview.
*
- * @param {Promise for XMLDocument} xml - A Promise for the servers xml response.
- * @return {Promise for HTMLElement[]} A Promise for an array of entities.
+ * @param {Promise | XMLDocument} xml - A Promise for the servers xml response.
+ * @return {Promise | HTMLElement[]} A Promise for an array of entities.
*/
this.processPreviewResponse = function(xml) {
let xsl = preview.getEntityXsl();
@@ -222,7 +222,7 @@ var preview = new function() {
/**
* Retrieve the XSL script for entities from the server.
*
- * @return {Promise for XMLDocument} A Promise for the XSL script.
+ * @return {Promise | XMLDocument} A Promise for the XSL script.
*/
this.getEntityXsl = async function _getEntityXsl() {
return transformation.retrieveEntityXsl();
@@ -679,7 +679,7 @@ var preview = new function() {
* Retrieve a list of entities from the server.
*
* @param {String[]} entityIds - The ids of the entities which are to be retrieved.
- * @return {Promise for HTMLElement[]} A Promise for an array of entities.
+ * @return {Promise | HTMLElement[]} A Promise for an array of entities.
*/
this.retrievePreviewEntities = async function _rPE(entityIds) {
try {
@@ -711,9 +711,9 @@ var preview = new function() {
/**
* Transform the xml to an array of entities.
*
- * @param {Promise XMLDocument} xml - The server response.
- * @param {Promise XMLDocument} xsl - The xsl script.
- * @return {Promise HTMLElement[]} A promise for an Array of HTMLElements.
+ * @param {Promise | XMLDocument} xml - The server response.
+ * @param {Promise | XMLDocument} xsl - The xsl script.
+ * @return {Promise | HTMLElement[]} A promise for an Array of HTMLElements.
*/
this.transformXmlToPreviews = async function _tXTP(xml, xsl) {
let html = await asyncXslt(xml, xsl);
diff --git a/src/core/js/webcaosdb.js b/src/core/js/webcaosdb.js
index df93703d83fafde15908efb40c3ae578824980d9..55337a36a97d6a7ad42aadfe673e429d6d942a0a 100644
--- a/src/core/js/webcaosdb.js
+++ b/src/core/js/webcaosdb.js
@@ -146,6 +146,64 @@ this.navbar = new function () {
.on("hidden.bs.collapse", function (e) {
logger.trace("navbar shrinks", e);
});
+ this.init_login_show_button();
+ }
+
+
+ /**
+ * Initialize the hiding/showing of the input form.
+ *
+ * If the viewport is xs (width <= 768px) the login form is hidden in the
+ * a menu anyways.
+ *
+ * If the viewport is greater then the folloging applies:
+ *
+ * When loading the page, the login form is hidden behind a "Login" button.
+ * When the user clicks the Login button the form appears and the other
+ * button disappears. After a timeout of 10 seconds of inactivity the form
+ * hides again. When the user starts typing, the timeout is canceled.
+ *
+ * If the user leaves the input fields ("blur" event) the timeout is
+ * reestablished and the form hides after 10 seconds.
+ */
+ this.init_login_show_button = function () {
+ const form = $("#caosdb-f-login-form");
+ const show_button = $("#caosdb-f-login-show-button");
+ var timeout = undefined;
+
+ // show form and hide the show_button
+ const _in = () => {
+ // xs means viewport <= 768px
+ form.removeClass("visible-xs-inline-block");
+ show_button.addClass("hidden");
+ }
+ // hide form and show the show_button
+ const _out = () => {
+ // xs means viewport <= 768px
+ form.addClass("visible-xs-inline-block");
+ show_button.removeClass("hidden");
+ }
+ show_button.on("click", () => {
+ // show form...
+ _in();
+
+ // and hide it after ten seconds if nothing happens
+ timeout = setTimeout(_out,10000)
+ });
+ form.find("input,button").on("blur", () => {
+ if (timeout) {
+ // cancel existing timeout (e.g. from showing)
+ clearTimeout(timeout);
+ }
+ // hide after 10 seconds if nothing happens
+ timeout = setTimeout(_out,10000)
+ });
+ form.find("input,button").on("change", () => {
+ // something happens!
+ if (timeout) {
+ clearTimeout(timeout);
+ }
+ });
}
@@ -269,6 +327,30 @@ this.caosdb_utils = new function () {
}
throw new TypeError(name + " is expected to be an array, was " + typeof obj);
}
+
+ /**
+ * Create a tsv table as string.
+ *
+ * The data must be appropriately encoded (e.g. urlencoded).
+ *
+ * With `tab=","` it is also possible to create csv tables.
+ *
+ * @param {string[][]} data - An array of rows which contain arrays of
+ * cells.
+ * @param {string} [preamble="data:text/csv;charset=utf-8,"] - a prefix for
+ * the the resulting string. The default is suitable for creating
+ * downloadable href attributes of links.
+ * @param {string} [tab="%09"] - the cell separator.
+ * @param {string} [newline="%0A"] - the row separator.
+ * @return {string} a tsv table as a string.
+ */
+ this.create_tsv_table = function(data, preamble, tab, newline) {
+ preamble = ((typeof preamble == 'undefined') ? "data:text/csv;charset=utf-8,": preamble);
+ tab = tab || "%09";
+ newline = newline || "%0A";
+ const rows = data.map(x => x.join(tab))
+ return `${preamble}${rows.join(newline)}`;
+ }
}
/**
@@ -592,7 +674,8 @@ this.transaction = new function () {
* @return {Element[]} array of xml elements.
*/
this.retrieveEntitiesById = async function _rEBIs(entityIds) {
- return $(await connection.get(this.generateEntitiesUri(entityIds))).find('Response [id]').toArray();
+ const response = await connection.get(this.generateEntitiesUri(entityIds));
+ return $(response).find('Response > [id]').toArray();
}
/** Sends a PUT request with an xml representation of entities and
@@ -905,6 +988,117 @@ this.transaction = new function () {
}
}
+/**
+ * This module provides the functionality to load the full version history (for
+ * privileged users) and export it to tsv.
+ */
+var version_history = new function () {
+
+ this._get = connection.get;
+ /**
+ * Retrieve the version history of an entity and return a table with the
+ * history.
+ *
+ * @param {string} entity - the entity id with or without version id.
+ * @return {HTMLElement} A table with the version history.
+ */
+ this.retrieve_history = async function(entity) {
+ const xml = this._get(transaction
+ .generateEntitiesUri([entity]) + "?H");
+ const html = (await transformation.transformEntities(xml))[0];
+ const history_table = $(html).find(".caosdb-f-entity-version-history");
+ return history_table[0];
+ }
+
+ /**
+ * Initalize the buttons for loading the version history.
+ *
+ * The buttons are visible when the entity has only the normal version info
+ * attached and the current user has the permissions to retrieve the
+ * version history.
+ *
+ * The buttons trigger the retrieval of the version history and append the
+ * version history to the version info modal.
+ */
+ this.init_load_history_buttons = function () {
+ for (let entity of $(".caosdb-entity-panel")) {
+ const is_permitted = hasEntityPermission(entity, "RETRIEVE:HISTORY");
+ if (!is_permitted) {
+ continue;
+ }
+ const entity_id_version = getEntityIdVersion(entity);
+ const version_info = $(entity)
+ .find(".caosdb-f-entity-version-info");
+ const button = $(version_info)
+ .find(".caosdb-f-entity-version-load-history-btn");
+ button.show();
+ button
+ .click(async () => {
+ button.prop("disabled", true);
+ const wait = createWaitingNotification("Retrieving full history. Please wait.");
+ const sparse = $(version_info)
+ .find(".caosdb-f-entity-version-history");
+ sparse.find(".modal-body *").replaceWith(wait);
+
+ const history_table = await version_history
+ .retrieve_history(entity_id_version);
+ sparse.replaceWith(history_table);
+ version_history.init_export_history_buttons(entity);
+ });
+ }
+ }
+
+ /**
+ * Transform the HTML table with the version history to tsv.
+ *
+ * @param {HTMLElement} history_table - the HTML representation of the
+ * version history.
+ * @return {string} the version history as downloadable tsv string,
+ * suitable for the href attribute of a link or window.location.
+ */
+ this.get_history_tsv = function (history_table) {
+ const rows = [];
+ for (let row of $(history_table).find("tr")) {
+ const cells = $(row).find(".export-data").toArray().map(x => x.textContent);
+ rows.push(cells);
+ }
+ return caosdb_utils.create_tsv_table(rows);
+ }
+
+ /**
+ * Initialize the export buttons of `entity`.
+ *
+ * The buttons are only visible when the version history is visible and
+ * trigger a download of a tsv file which contains the version history.
+ *
+ * The buttons trigger the download of a tsv file with the version history.
+ *
+ * @param {HTMLElement} [entity] - if undefined, the export buttons of all
+ * page entities are initialized.
+ */
+ this.init_export_history_buttons = function (entity) {
+ entity = entity || $(".caosdb-entity-panel");
+ for (let version_info of $(entity)
+ .find(".caosdb-f-entity-version-info")) {
+ $(version_info).find(".caosdb-f-entity-version-export-history-btn")
+ .click(async () => {
+ const html_table = $(version_info).find("table")[0];
+ const history_tsv = this.get_history_tsv(html_table);
+ version_history._download_tsv(history_tsv);
+ });
+ }
+ }
+
+ this._download_tsv = function(tsv_link) {
+ window.location.href = tsv_link;
+ }
+
+
+ this.init = function () {
+ this.init_load_history_buttons();
+ this.init_export_history_buttons();
+ }
+}
var paging = new function () {
@@ -979,6 +1173,9 @@ var paging = new function () {
return null;
}
+ // remove fragment
+ uri_old = uri_old.split("#")[0];
+
var pattern = /(\?(.*&)?)P=([^&]*)/;
if (pattern.test(uri_old)) {
// replace existing P=...
@@ -1003,7 +1200,7 @@ var paging = new function () {
if (uri == null) {
throw new Error("uri was null.");
}
- var pattern = /\?(.*&)?P=([^&]*)/;
+ var pattern = /\?(.*&)?P=([^&#]*)/;
var ret = pattern.exec(uri);
return (ret != null ? ret[2] : null);
}
@@ -1121,7 +1318,6 @@ var queryForm = new function () {
See https://developer.mozilla.org/en-US/docs/Web/Events/submit why this is necessary.
*/
var submithandler = function () {
-
// store current query
var queryField = form.query;
var value = queryField.value.toUpperCase();
@@ -1141,6 +1337,13 @@ var queryForm = new function () {
queryForm.redirect(queryField.value, paging);
};
+ $("#caosdb-query-textarea").on("keydown", (e) => {
+ // prevent submit on enter
+ if(e.originalEvent.which == 13) {
+ e.originalEvent.preventDefault();
+ }
+ })
+
// handler for the form
form.onsubmit = function (e) {
@@ -1503,13 +1706,13 @@ function insertParam(xsl, name, value = null) {
/**
* When the page is scrolled down 100 pixels, the scroll-back button appears.
*
- * @return
+ * @return FIXME
*/
/**
* Every initial function calling is done here.
*
- * @return
+ * @return TODO
*/
function initOnDocumentReady() {
hintMessages.init();
@@ -1534,6 +1737,7 @@ function initOnDocumentReady() {
}
caosdb_modules.init();
navbar.init();
+ version_history.init();
}
diff --git a/src/core/xsl/entity.xsl b/src/core/xsl/entity.xsl
index 299b1dac37a1029e5bc7c48008efa3735d61037b..cac9e87ea40bf6a687a19a1942b5534276c8faf7 100644
--- a/src/core/xsl/entity.xsl
+++ b/src/core/xsl/entity.xsl
@@ -103,6 +103,7 @@
<xsl:attribute name="data-entity-id">
<xsl:value-of select="@id"/>
</xsl:attribute>
+ <xsl:apply-templates mode="entity-permissions" select="Permissions"/>
<!-- A page-unique ID for this entity -->
<xsl:variable name="entityid" select="concat('entity_',generate-id())"/>
<div class="panel-heading caosdb-entity-panel-heading">
@@ -156,6 +157,16 @@
<span class="label caosdb-id caosdb-id-button hidden">
<xsl:value-of select="@id"/>
</span>
+ <button class="btn btn-link caosdb-v-bookmark-button">
+ <xsl:attribute name="data-bmval">
+ <xsl:value-of select="@id"/>
+ <xsl:if test="Version/Successor">
+ <!-- this is not the head -->
+ <xsl:value-of select="concat('@', Version/@id)"/>
+ </xsl:if>
+ </xsl:attribute>
+ <span class="glyphicon glyphicon-bookmark"/>
+ </button>
<xsl:apply-templates mode="entity-heading-attributes-version" select="Version">
<xsl:with-param name="entityId" select="@id"/>
</xsl:apply-templates>
@@ -392,8 +403,8 @@
<xsl:otherwise>
<xsl:choose>
<!-- the referenced entities have been returned. -->
- <xsl:when test="*[@id]">
- <xsl:for-each select="*[@id]">
+ <xsl:when test="Record|RecordType|Property|File">
+ <xsl:for-each select="Record|RecordType|Property|File">
<xsl:call-template name="single-value">
<xsl:with-param name="reference">
<xsl:value-of select="'true'"/>
@@ -518,78 +529,197 @@
</xsl:attribute>
<span class="glyphicon glyphicon-time"/>
</button>
+
<!-- the following div.modal is the window that pops up when the user clicks on the clock button -->
<div class="caosdb-f-entity-version-info modal fade" tabindex="-1" role="dialog">
<xsl:attribute name="id"><xsl:value-of select="$versionModalId"/></xsl:attribute>
+ <xsl:attribute name="data-entity-versioned-id"><xsl:value-of select="concat($entityId, '@', @id)"/></xsl:attribute>
<div class="modal-dialog modal-lg" role="document">
<div class="modal-content text-left">
+ <!-- modal-header start -->
<div>
<xsl:attribute name="class">
modal-header
- <xsl:if test="Successor">
+ <xsl:if test="not(@head='true')">
<!-- indicate old version by color -->
<xsl:value-of select="' bg-danger'"/>
</xsl:if>
</xsl:attribute>
<button type="button" class="close" data-dismiss="modal" aria-label="Close" title="Close"><span aria-hidden="true">×</span></button>
<h4 class="modal-title">Version Info</h4>
- <p class="caosdb-entity-heading-attr">
+ <p class="caosdb-entity-heading-attr">
<em class="caosdb-entity-heading-attr-name">
This is
- <xsl:if test="Successor"><b>not</b></xsl:if>
+ <xsl:if test="not(@head='true')"><b>not</b></xsl:if>
the latest version of this entity.
+ <xsl:apply-templates mode="entity-version-modal-head" select="Successor">
+ <xsl:with-param name="entityId" select="$entityId"/>
+ </xsl:apply-templates>
</em>
</p>
</div>
- <div class="modal-body">
- <xsl:apply-templates mode="entity-version-modal-head" select="Successor">
+ <!-- modal-header end -->
+ <div class="caosdb-f-entity-version-history">
+ <!-- modal-body and modal-footer are added by this template -->
+ <xsl:apply-templates select="." mode="entity-version-history-table">
<xsl:with-param name="entityId" select="$entityId"/>
</xsl:apply-templates>
- <xsl:apply-templates mode="entity-version-modal-successor" select="Successor">
+ </div>
+ </div>
+ </div>
+ </div>
+ </xsl:template>
+
+ <xsl:template match="Version[@completeHistory='true']" mode="entity-version-history-table">
+ <!-- contains the table of the full version history -->
+ <xsl:param name="entityId"/>
+ <div class="modal-body">
+ <table class="table table-hover">
+ <thead>
+ <tr><div class="export-data">Entity ID</div><th/>
+ <th class="export-data">Version ID</th>
+ <th class="export-data">Date</th>
+ <th class="export-data">User</th>
+ <div class="export-data">URI</div>
+ </tr></thead>
+ <tbody>
+ <xsl:apply-templates mode="entity-version-modal-successor" select="Successor">
+ <xsl:with-param name="entityId" select="$entityId"/>
+ </xsl:apply-templates>
+ <tr>
+ <div class="export-data"><xsl:value-of select="$entityId"/></div>
+ <td class="caosdb-v-entity-version-hint caosdb-v-entity-version-hint-cur">This Version</td>
+ <td><xsl:apply-templates select="@id" mode="entity-version-id"/>
+ </td><td>
+ <xsl:apply-templates select="@date" mode="entity-version-date"/>
+ </td><td class="export-data">
+ <xsl:value-of select="@username"/>@<xsl:value-of select="@realm"/>
+ </td>
+ <div class="export-data"><xsl:value-of select="concat($entitypath, $entityId, '@', @id)"/></div>
+ </tr>
+ <xsl:apply-templates mode="entity-version-modal-predecessor" select="Predecessor">
+ <xsl:with-param name="entityId" select="$entityId"/>
+ </xsl:apply-templates>
+ </tbody>
+ </table>
+ </div>
+ <div class="modal-footer">
+ <button type="button" class="caosdb-f-entity-version-export-history-btn btn btn-default">Export history</button>
+ </div>
+ </xsl:template>
+
+ <xsl:template match="Version[not(@completeHistory='true')]" mode="entity-version-history-table">
+ <!-- contains the table of the simple version info (not the full history)-->
+ <xsl:param name="entityId"/>
+ <div class="modal-body">
+ <table class="table">
+ <thead><tr><th>Previous Version</th><th>This Version</th><th>Next Version</th></tr></thead>
+ <tbody>
+ <tr>
+ <td>
+ <xsl:if test="not(Predecessor)">
+ <div class="caosdb-v-entity-version-no-related">No predecessor</div>
+ </xsl:if>
+ <xsl:apply-templates select="Predecessor/@id" mode="entity-version-link-to-other-version">
<xsl:with-param name="entityId" select="$entityId"/>
</xsl:apply-templates>
- <p class="caosdb-entity-heading-attr">
- <em class="caosdb-entity-heading-attr-name">This version:</em>
- <xsl:value-of select="@id"/> (<xsl:value-of select="@date"/>)
- </p>
- <xsl:apply-templates mode="entity-version-modal-predecessor" select="Predecessor">
+ </td>
+ <td>
+ <xsl:apply-templates select="@id" mode="entity-version-id"/>
+ </td>
+ <td>
+ <xsl:if test="not(Successor)">
+ <div class="caosdb-v-entity-version-no-related">No successor</div>
+ </xsl:if>
+ <xsl:apply-templates select="Successor/@id" mode="entity-version-link-to-other-version">
<xsl:with-param name="entityId" select="$entityId"/>
</xsl:apply-templates>
- </div>
- </div>
- </div>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div class="modal-footer">
+ <button type="button" style="display: none" class="caosdb-f-entity-version-load-history-btn btn btn-default">Load full history</button>
</div>
</xsl:template>
+
+ <xsl:template match="@id" mode="entity-version-id">
+ <!-- a versions'id (abbreviated) -->
+ <xsl:attribute name="title">Full Version ID: <xsl:value-of select="."/></xsl:attribute>
+ <xsl:value-of select="substring(.,1,8)"/>
+ <div class="export-data"><xsl:value-of select="."/></div>
+ </xsl:template>
+
+ <xsl:template match="@date" mode="entity-version-date">
+ <!-- a version's date (abbreviated)-->
+ <xsl:attribute name="title"><xsl:value-of select="."/></xsl:attribute>
+ <xsl:value-of select="substring(.,0,11)"/>
+ <xsl:value-of select="' '"/>
+ <xsl:value-of select="substring(.,12,8)"/>
+ <div class="export-data"><xsl:value-of select="."/></div>
+ </xsl:template>
+
+ <xsl:template match="Predecessor|Successor" mode="entity-version-modal-single-history-item">
+ <!-- a single row of the version history table -->
+ <xsl:param name="entityId"/>
+ <xsl:param name="hint"/>
+ <tr>
+ <div class="export-data"><xsl:value-of select="$entityId"/></div>
+ <td class="caosdb-v-entity-version-hint"><xsl:value-of select="$hint"/></td>
+ <td>
+ <xsl:apply-templates select="@id" mode="entity-version-link-to-other-version">
+ <xsl:with-param name="entityId" select="$entityId"/>
+ </xsl:apply-templates>
+ </td><td>
+ <xsl:apply-templates select="@date" mode="entity-version-date"/>
+ </td><td class="export-data">
+ <xsl:value-of select="@username"/>@<xsl:value-of select="@realm"/>
+ </td>
+ <div class="export-data"><xsl:value-of select="concat($entitypath, $entityId, '@', @id)"/></div>
+ </tr>
+ </xsl:template>
+
+ <xsl:template match="@id" mode="entity-version-link-to-other-version">
+ <!-- link to other version (used by both version tables)-->
+ <xsl:param name="entityId"/>
+ <a><xsl:attribute name="href"><xsl:value-of select="$entityId"/>@<xsl:value-of select="."/></xsl:attribute>
+ <xsl:apply-templates select="." mode="entity-version-id"/></a>
+ </xsl:template>
+
<xsl:template match="Predecessor" mode="entity-version-modal-predecessor">
- <!-- content of the versioning window -->
+ <!-- content of the versioning info (not the full history) -->
<xsl:param name="entityId"/>
- <p class="caosdb-entity-heading-attr">
- <em class="caosdb-entity-heading-attr-name">Previous version:</em>
- <a><xsl:attribute name="href"><xsl:value-of select="$entityId"/>@<xsl:value-of select="@id"/></xsl:attribute>
- <xsl:value-of select="@id"/> (<xsl:value-of select="@date"/>)
- </a>
- </p>
+ <xsl:apply-templates mode="entity-version-modal-single-history-item" select=".">
+ <xsl:with-param name="entityId" select="$entityId"/>
+ <xsl:with-param name="hint" select="'Older Version'"/>
+ </xsl:apply-templates>
+ <xsl:apply-templates mode="entity-version-modal-predecessor" select="Predecessor">
+ <xsl:with-param name="entityId" select="$entityId"/>
+ </xsl:apply-templates>
</xsl:template>
+
<xsl:template match="Successor" mode="entity-version-modal-head">
- <!-- content of the versioning window -->
+ <!-- content of the versioning modal's header (if a newer version exists) -->
<xsl:param name="entityId"/>
- <p class="caosdb-entity-heading-attr">
- <em class="caosdb-entity-heading-attr-name">Newest version:</em>
- <a><xsl:attribute name="href"><xsl:value-of select="$entityId"/>@HEAD</xsl:attribute>
- <xsl:value-of select="$entityId"/>@HEAD
- </a>
- </p>
+ View the newest version here:
+ <a><xsl:attribute name="href"><xsl:value-of select="$entityId"/>@HEAD</xsl:attribute>
+ <xsl:value-of select="$entityId"/>@HEAD
+ </a>
</xsl:template>
+
<xsl:template match="Successor" mode="entity-version-modal-successor">
- <!-- content of the versioning window -->
+ <!-- content of the versioning info (not the full history) -->
<xsl:param name="entityId"/>
- <p class="caosdb-entity-heading-attr">
- <em class="caosdb-entity-heading-attr-name">Next version:</em>
- <a><xsl:attribute name="href"><xsl:value-of select="$entityId"/>@<xsl:value-of select="@id"/></xsl:attribute>
- <xsl:value-of select="@id"/> (<xsl:value-of select="@date"/>)
- </a>
- </p>
+ <xsl:apply-templates mode="entity-version-modal-successor" select="Successor">
+ <xsl:with-param name="entityId" select="$entityId"/>
+ </xsl:apply-templates>
+ <xsl:apply-templates mode="entity-version-modal-single-history-item" select=".">
+ <xsl:with-param name="entityId" select="$entityId"/>
+ <xsl:with-param name="hint" select="'Newer Version'"/>
+ </xsl:apply-templates>
</xsl:template>
+
<xsl:template match="Version/Successor" mode="entity-action-panel-version">
<!-- clickable warning message in the entity actions panel when there exists a newer version -->
<xsl:param name="entityId"/>
@@ -598,13 +728,15 @@
<strong>Warning</strong> A newer version exists!
</a>
</xsl:template>
+
<xsl:template match="Version" mode="entity-version-marker">
<!-- content of the data-version-id attribute -->
<xsl:attribute name="data-version-id">
- <xsl:value-of select="@id"/>
+ <xsl:value-of select="@id"/>
</xsl:attribute>
<xsl:apply-templates select="Successor" mode="entity-version-marker"/>
</xsl:template>
+
<xsl:template match="Successor" mode="entity-version-marker">
<!-- content of the data-version-successor attribute
This data-attribute marks entities which have a newer version.
@@ -613,4 +745,17 @@
<xsl:value-of select="@id"/>
</xsl:attribute>
</xsl:template>
+
+ <!-- PERMISSIONS -->
+ <xsl:template match="Permissions" mode="entity-permissions">
+ <div style="display: none">
+ <xsl:apply-templates select="Permission" mode="entity-permissions"/>
+ </div>
+ </xsl:template>
+
+ <xsl:template match="Permission" mode="entity-permissions">
+ <div>
+ <xsl:attribute name="data-permission"><xsl:value-of select="@name"/></xsl:attribute>
+ </div>
+ </xsl:template>
</xsl:stylesheet>
diff --git a/src/core/xsl/main.xsl b/src/core/xsl/main.xsl
index efbf2e6b6e4db0ad7b14cb1c2483157bc79001f1..e414f9af4147714c5f6ff8a03b70309a02ec1446 100644
--- a/src/core/xsl/main.xsl
+++ b/src/core/xsl/main.xsl
@@ -142,6 +142,16 @@
<xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/webcaosdb.js')"/>
</xsl:attribute>
</xsl:element>
+ <xsl:element name="script">
+ <xsl:attribute name="src">
+ <xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/pako.js')"/>
+ </xsl:attribute>
+ </xsl:element>
+ <xsl:element name="script">
+ <xsl:attribute name="src">
+ <xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/utif.js')"/>
+ </xsl:attribute>
+ </xsl:element>
<script>
$(document).ready(() => paging.initPaging(window.location.href, <xsl:value-of select="/Response/@count"/> ));
</script>
@@ -157,7 +167,7 @@
</xsl:element>
<xsl:element name="script">
<xsl:attribute name="src">
- <xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/autocomplete.js')"/>
+ <xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/ext_autocomplete.js')"/>
</xsl:attribute>
</xsl:element>
<xsl:element name="script">
@@ -170,6 +180,11 @@
<xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/ext_references.js')"/>
</xsl:attribute>
</xsl:element>
+ <xsl:element name="script">
+ <xsl:attribute name="src">
+ <xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/ext_table_preview.js')"/>
+ </xsl:attribute>
+ </xsl:element>
<xsl:element name="script">
<xsl:attribute name="src">
<xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/ext_xls_download.js')"/>
@@ -195,6 +210,11 @@
<xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/edit_mode.js')"/>
</xsl:attribute>
</xsl:element>
+ <xsl:element name="script">
+ <xsl:attribute name="src">
+ <xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/ext_file_download.js')"/>
+ </xsl:attribute>
+ </xsl:element>
<xsl:element name="script">
<xsl:attribute name="src">
<xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/leaflet.js')"/>
@@ -255,6 +275,11 @@
<xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/ext_trigger_crawler_form.js')"/>
</xsl:attribute>
</xsl:element>
+ <xsl:element name="script">
+ <xsl:attribute name="src">
+ <xsl:value-of select="concat($basepath,'webinterface/${BUILD_NUMBER}/js/ext_bookmarks.js')"/>
+ </xsl:attribute>
+ </xsl:element>
<!--JS_EXTENSIONS-->
</xsl:template>
<xsl:template name="caosdb-data-container">
diff --git a/src/core/xsl/navbar.xsl b/src/core/xsl/navbar.xsl
index 907f27e512250cf5fde0ff2fe93fe85f800428a6..6ce69e638efda10dbb95a066e8b59508854a4435 100644
--- a/src/core/xsl/navbar.xsl
+++ b/src/core/xsl/navbar.xsl
@@ -132,6 +132,23 @@
</ul>
</xsl:if>
<ul class="nav navbar-nav navbar-right">
+ <li class="dropdown">
+ <a class="dropdown-toggle" data-toggle="dropdown" href="#">
+ <span id="caosdb-f-bookmarks-collection-counter" class="badge">0</span>
+ Bookmarks
+ <span class="caret"></span></a>
+ <ul class="dropdown-menu">
+ <li class="disabled" id="caosdb-f-bookmarks-collection-link"
+ title="Show all bookmarked entities.">
+ <a>Show all</a></li>
+ <li class="disabled" id="caosdb-f-bookmarks-export-link"
+ title="Export all bookmarks to a file. The exported file is a spread sheet with columns for the id, the version, the complete URI of the bookmarked entities and the path, if the entity is a file.">
+ <a>Export to file</a></li>
+ <li class="disabled" id="caosdb-f-bookmarks-clear"
+ title="Empty the list of bookmarks.">
+ <a>Clear</a></li>
+ </ul>
+ </li>
<xsl:call-template name="caosdb-user-menu"/>
</ul>
</div>
@@ -191,17 +208,15 @@
</xsl:when>
<xsl:otherwise>
<li id="user-menu">
- <form class="navbar-form" method="POST">
+ <form id="caosdb-f-login-form" class="navbar-form visible-xs-inline-block" method="POST">
<xsl:attribute name="action">
<xsl:value-of select="concat($basepath, 'login')"/>
</xsl:attribute>
<input class="form-control" id="username" name="username" placeholder="username" type="text"/>
<input class="form-control" id="password" name="password" placeholder="password" type="password"/>
- <button class="btn btn-default" type="submit">
- <span class="glyphicon glyphicon-log-in"></span>
- Login
- </button>
+ <button class="btn btn-primary" type="submit">Login</button>
</form>
+ <button style="margin-right: 15px" class="btn btn-default navbar-btn hidden-xs" id="caosdb-f-login-show-button" type="button">Login</button>
</li>
</xsl:otherwise>
</xsl:choose>
diff --git a/src/core/xsl/query.xsl b/src/core/xsl/query.xsl
index be49ed7d889e920cfee87e723c4c5c3b8efb27b2..ca1884aea16d59c7df92de304d3154698dc471bf 100644
--- a/src/core/xsl/query.xsl
+++ b/src/core/xsl/query.xsl
@@ -89,7 +89,7 @@
</div>
<div class="col-xs-6 text-right">
<!-- Trigger the modal with a button -->
- <button class="btn btn-info btn-sm" data-target="#downloadModal" data-toggle="modal" type="button">Download this table</button>
+ <button class="btn btn-info btn-sm caosdb-v-btn-select" data-target="#downloadModal" data-toggle="modal" type="button">Export</button>
<!-- Modal -->
<div class="modal fade text-left" id="downloadModal" role="dialog">
<div class="modal-dialog">
@@ -102,16 +102,21 @@
<div class="modal-body">
<p>
<a id="caosdb-f-query-select-data-tsv" onclick="downloadTSV(this)" href="#selected_data.tsv" download="selected_data.tsv">
- Download TSV File
+ Download table as TSV File
</a>
<span class="checkbox" style="margin-top: 0; display: inline; position: absolute; right: 10px"><label><input type="checkbox" name="raw" id="caosdb-table-export-raw-flag-tsv" title="Export raw entity ids instead of the visible page content."/>raw</label></span>
</p>
<p>
<a class="caosdb-v-query-select-data-xsl" onclick="downloadXLS(this)" href="#selected_data.xsl" download="">
- Download XLS File
+ Download table as XLS File
</a>
<span class="checkbox" style="margin-top: 0; display: inline; position: absolute; right: 10px"><label><input type="checkbox" name="raw" id="caosdb-table-export-raw-flag-xls" title="Export raw entity ids instead of the visible page content."/>raw</label></span>
</p>
+ <p>
+ <a id="caosdb-f-query-select-files" onclick="ext_file_download.download_files(this)" href="#selected_data.tsv" download="files.zip" title="Collects file entities listed in the table in a zip file. If the entity belonging to a row is a file entity, it will be included.">
+ Download files referenced in the table
+ </a>
+ </p>
<hr/>
<p>
<small>Download this dataset in Python with:</small>
@@ -123,7 +128,13 @@
</p>
</div>
<div class="modal-footer">
- <button class="btn btn-default" data-dismiss="modal" type="button">Close</button>
+ <div class="row" style="margin:0px">
+ <div class="col-xs-6 caosdb-f-modal-footer-left">
+ </div>
+ <div class="col-xs-6">
+ <button class="btn btn-default" data-dismiss="modal" type="button">Close</button>
+ </div>
+ </div>
</div>
</div>
</div>
diff --git a/src/doc/Makefile b/src/doc/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..b3c35b4ddbc2849eb6b3bdc223095e275669ad39
--- /dev/null
+++ b/src/doc/Makefile
@@ -0,0 +1,51 @@
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+#
+# 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
+
+# This Makefile is a wrapper for sphinx scripts.
+#
+# It is based upon the autocreated makefile for Sphinx documentation.
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?= -a
+SPHINXBUILD ?= sphinx-build
+# SPHINXAPIDOC ?= javasphinx-apidoc
+SOURCEDIR = .
+BUILDDIR = ../../build/doc
+
+# npm is not always in the global PATH
+NPM_PATH = $(shell npm bin)
+
+.PHONY: doc-help Makefile apidoc
+
+# Put it first so that "make" without argument is like "make help".
+doc-help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ PATH=$(NPM_PATH):$$PATH $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+# sphinx-build -M html . ../../build/doc
+
+# Not necessary in this repository, apidoc is doone with the sphinx-autoapi extension
+# apidoc:
+# @$(SPHINXAPIDOC) -o _apidoc --update --title="CaosDB Server" ../main/
diff --git a/src/doc/concepts.rst b/src/doc/concepts.rst
new file mode 100644
index 0000000000000000000000000000000000000000..23e5fc4f6ddb666757fb9c79e192e07ffed8fb44
--- /dev/null
+++ b/src/doc/concepts.rst
@@ -0,0 +1,6 @@
+========================
+The concepts of pycaosdb
+========================
+
+Some text...
+
diff --git a/src/doc/conf.py b/src/doc/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..988df3c3a2340c6b6b6b7e34f808e0e0496f680e
--- /dev/null
+++ b/src/doc/conf.py
@@ -0,0 +1,209 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('../caosdb'))
+
+
+# -- Project information -----------------------------------------------------
+
+import sphinx_rtd_theme
+
+project = 'caosdb-webui'
+copyright = '2020, IndiScale GmbH'
+author = 'Daniel Hornung'
+
+# The short X.Y version
+version = '0.X.Y'
+# The full version, including alpha/beta/rc tags
+release = '0.x.y-beta-rc2'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+ 'sphinx_js',
+ 'sphinx.ext.todo',
+ "sphinx.ext.autodoc",
+ 'autoapi.extension',
+ "recommonmark", # For markdown files.
+ "sphinx_rtd_theme",
+ # 'sphinx.ext.intersphinx',
+ # 'sphinx.ext.napoleon', # For Google style docstrings
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself. Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'caosdb-webuidoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+ # The paper size ('letterpaper' or 'a4paper').
+ #
+ # 'papersize': 'letterpaper',
+
+ # The font size ('10pt', '11pt' or '12pt').
+ #
+ # 'pointsize': '10pt',
+
+ # Additional stuff for the LaTeX preamble.
+ #
+ # 'preamble': '',
+
+ # Latex figure (float) alignment
+ #
+ # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+# author, documentclass [howto, manual, or own class]).
+latex_documents = [
+ (master_doc, 'caosdb-webui.tex', 'caosdb-webui Documentation',
+ 'IndiScale GmbH', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ (master_doc, 'caosdb-webui', 'caosdb-webui Documentation',
+ [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ (master_doc, 'caosdb-webui', 'caosdb-webui Documentation',
+ author, 'caosdb-webui', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for sphinx-js ---------------------------------------------------
+# See also https://pypi.org/project/sphinx-js/
+
+js_source_path = '../core/js/'
+primary_domain = 'js' # Not strictly necessary?
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}
+
+# TODO Which options do we want?
+autodoc_default_options = {
+ 'members': None,
+ 'undoc-members': None,
+}
+
+# -- Options for sphinx-autoapi ----------------------------------------------
+# See also https://pypi.org/project/sphinx-js/
+
+autoapi_type = 'javascript'
+autoapi_dirs = ['../core/js/']
diff --git a/src/doc/genindex.rst b/src/doc/genindex.rst
new file mode 100644
index 0000000000000000000000000000000000000000..48ab71fd283bb48564ac30e4c69e62bbd463cd77
--- /dev/null
+++ b/src/doc/genindex.rst
@@ -0,0 +1,4 @@
+.. This file is a placeholder and will be replaced.
+
+Index
+=====
diff --git a/src/doc/getting_started.md b/src/doc/getting_started.md
new file mode 120000
index 0000000000000000000000000000000000000000..88332e357f5e06f3de522768ccdcd9e513c15f62
--- /dev/null
+++ b/src/doc/getting_started.md
@@ -0,0 +1 @@
+../../README_SETUP.md
\ No newline at end of file
diff --git a/src/doc/index.rst b/src/doc/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..b3a26c96df4f13e22f4b01a6cb0a9f00a1d33981
--- /dev/null
+++ b/src/doc/index.rst
@@ -0,0 +1,34 @@
+
+Welcome to the documentation of CaosDB's web UI!
+================================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+ :hidden:
+
+ Getting started <getting_started>
+ Concepts <concepts>
+ tutorials
+ API Index<genindex>
+
+
+This documentation helps you to :doc:`get started<getting_started>`, explains the most important
+:doc:`concepts<concepts>` and offers a range of :doc:`tutorials<tutorials>`.
+
+.. note::
+
+ TODO: Build the index (manually?) like here: https://github.com/mozilla/fathom/edit/master/docs/.
+ Note that :doc:`autoapi/index` still does not have any content.
+
+ .. js:autofunction:: input2caosdbDate
+
+ .. js:autofunction:: getEntityVersion
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`
diff --git a/src/ext/js/fileupload.js b/src/ext/js/fileupload.js
index fac11efadc3d1b6d364333d68b27904c37c3aa42..e21ccf7f6035a8170bd1a0f4c7f5868d56c83b37 100644
--- a/src/ext/js/fileupload.js
+++ b/src/ext/js/fileupload.js
@@ -93,7 +93,7 @@ var fileupload = new function() {
formData.append("FileRepresentation", request);
- // add the success and error handlers which put the
+ // add the success and error handlers
xhr.addEventListener("load", success_handler);
xhr.addEventListener("error", error_handler);
});
diff --git a/src/server_side_scripting/ext_file_download/zip_files.py b/src/server_side_scripting/ext_file_download/zip_files.py
new file mode 100755
index 0000000000000000000000000000000000000000..65f27c9d901a6790456b8addb636bd55b7fe0c7e
--- /dev/null
+++ b/src/server_side_scripting/ext_file_download/zip_files.py
@@ -0,0 +1,112 @@
+#!/usr/bin/env python3
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2019 IndiScale GmbH
+#
+# 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
+
+"""Creates a zip file from multiple file entities. """
+
+import argparse
+import datetime
+import io
+import logging
+import os
+import sys
+from tempfile import NamedTemporaryFile
+from zipfile import ZipFile
+
+import caosdb as db
+import pandas as pd
+from caosadvancedtools.serverside import helper
+from caosdb import CaosDBException, ConsistencyError, EntityDoesNotExistError
+
+
+def _parse_arguments():
+ """Parses the command line arguments.
+
+ Takes into account defaults from the environment (where known).
+ """
+ parser = argparse.ArgumentParser(description='__doc__')
+ parser.add_argument('-a', '--auth-token', required=False,
+ help=("An authentication token. If not provided caosdb"
+ " pylib will search for other methods of "
+ "authentication if necessary."))
+ parser.add_argument('ids', help="list of entity ids.")
+ parser.add_argument('table', help="tsv table to be saved (as string).")
+
+ return parser.parse_args()
+
+
+def collect_files_in_zip(ids, table):
+ # File output
+ now = datetime.datetime.now()
+ zip_name = "files.{time}.zip".format(
+ time=now.strftime("%Y-%m-%dT%H_%M_%S"))
+ zip_display_path, zip_internal_path = helper.get_shared_filename(zip_name)
+ with ZipFile(zip_internal_path, 'w') as zf:
+ nc = helper.NameCollector()
+
+ # add the table which has been genereated by the webui table exporter
+ with NamedTemporaryFile(delete=False) as table_file:
+ # the file has been transmitted as string and has to be written to
+ # a file first.
+ table_file.write(table.encode())
+ zf.write(table_file.name, "selected_table.tsv")
+
+ # download and add all files
+ for file_id in ids:
+ try:
+ tmp = db.execute_query("FIND {a:} WITH ID={a:}".format(
+ a=file_id),
+ unique=True)
+ except EntityDoesNotExistError as e:
+ # TODO
+ # Current behavior: script terminates with error if just one
+ # file cannot be retrieved.
+ # Desired behavior: The script should go on with the other
+ # ids, but the user should be informed about the missing files.
+ # How should we do this?
+ logger = logging.getLogger("caosadvancedtools")
+ logger.error("Did not find Entity with ID={}.".format(
+ file_id))
+
+ raise e
+ savename = nc.get_unique_savename(os.path.basename(tmp.path))
+ val_file = helper.get_file_via_download(
+ tmp, logger=logging.getLogger("caosadvancedtools"))
+
+ zf.write(val_file, savename)
+
+ return zip_display_path
+
+
+def main():
+ args = _parse_arguments()
+
+ if hasattr(args, "auth_token") and args.auth_token:
+ db.configure_connection(auth_token=args.auth_token)
+
+ id_list = [int(el) for el in args.ids.split(",")]
+
+ zip_file = collect_files_in_zip(id_list, args.table)
+
+ print(zip_file)
+
+
+if __name__ == "__main__":
+ main()
diff --git a/src/server_side_scripting/ext_table_preview/pandas_table_preview.py b/src/server_side_scripting/ext_table_preview/pandas_table_preview.py
new file mode 100755
index 0000000000000000000000000000000000000000..c0659d9b1839c43e0629a878d792c414577ea344
--- /dev/null
+++ b/src/server_side_scripting/ext_table_preview/pandas_table_preview.py
@@ -0,0 +1,145 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+#
+# 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
+#
+
+"""
+This script tries to read typical table data files (.csv etc.) with pandas and
+creates a html (partial) representation of the table.
+"""
+
+import logging
+import os
+import sys
+from datetime import datetime
+
+import caosdb as db
+import pandas as pd
+from caosadvancedtools.serverside.helper import get_argument_parser
+from caosadvancedtools.serverside.logging import configure_server_side_logging
+
+MAXIMUMFILESIZE = 1e8
+VALID_ENDINGS = [".csv", ".tsv", ".xls", ".xlsx"]
+
+
+def get_file(eid):
+ """ retrieves the file entity from caosdb """
+ try:
+ fi = db.File(id=eid)
+ fi.retrieve()
+ except db.exceptions.EntityDoesNotExistError:
+ print("Cannot create preview for Entity with ID={}, because it seems"
+ "not to exist.".format(eid), file=sys.stderr)
+ sys.exit(1)
+
+ return fi
+
+
+def size_is_ok(fi):
+ """ show previews only for files that are not too large """
+
+ return fi.size <= MAXIMUMFILESIZE
+
+
+def get_ending(fipath):
+ """ return which of the valid endings (tsv etc.) is the one present"""
+
+ for end in VALID_ENDINGS:
+ if fipath.lower().endswith(end):
+ return end
+
+ return None
+
+
+def ending_is_valid(fipath):
+ """ return whether the ending indicates a file type that can be treated"""
+
+ return get_ending(fipath) is not None
+
+
+def read_file(fipath, ftype):
+ """ tries to read the provided file """
+
+ try:
+ if ftype in [".xls", ".xlsx"]:
+ df = pd.read_excel(fipath)
+ elif ftype == ".tsv":
+ df = pd.read_csv(fipath, sep="\t", comment="#")
+ elif ftype == ".csv":
+ df = pd.read_csv(fipath, comment="#")
+ else:
+ print("File type unknown: {}".format(ftype))
+ raise RuntimeError("")
+ except Exception:
+ raise ValueError()
+
+ return df
+
+
+def create_table_preview(fi):
+ if not ending_is_valid(fi.path):
+ print("Cannot create preview for Entity with ID={}, because download"
+ "failed.".format(entity_id), file=sys.stderr)
+ sys.exit(5)
+
+ ending = get_ending(fi.path)
+
+ if not size_is_ok(fi):
+ print("Skipped creating a preview for Entity with ID={}, because the"
+ "file is large!".format(entity_id), file=sys.stderr)
+ sys.exit(2)
+
+ try:
+ tmpfile = fi.download()
+ except Exception:
+ print("Cannot create preview for Entity with ID={}, because download"
+ "failed.".format(entity_id), file=sys.stderr)
+
+ sys.exit(3)
+
+ try:
+ df = read_file(tmpfile, ending)
+ except ValueError:
+ print("Cannot read File Entity with ID={}.".format(entity_id),
+ file=sys.stderr)
+ sys.exit(4)
+
+ print(df.to_html(max_cols=10, max_rows=10))
+
+
+if __name__ == "__main__":
+ conlogger = logging.getLogger("connection")
+ conlogger.setLevel(level=logging.ERROR)
+
+ parser = get_argument_parser()
+ args = parser.parse_args()
+
+ debug_file = configure_server_side_logging()
+ logger = logging.getLogger("caosadvancedtools")
+
+ db.configure_connection(auth_token=args.auth_token)
+ entity_id = args.filename
+
+ fi = get_file(entity_id)
+
+ create_table_preview(fi)
diff --git a/test/core/index.html b/test/core/index.html
index 50d8cbef8003d6fb9ab383f94405bcfa07270774..ea7b63b9e37943f0bdd4e32499c6c1ea9310a618 100644
--- a/test/core/index.html
+++ b/test/core/index.html
@@ -37,6 +37,8 @@
<script src="js/bootstrap.js"></script>
<script src="js/bootstrap-select.js"></script>
<script src="js/bootstrap-autocomplete.min.js"></script>
+ <script src="js/utif.js"></script>
+ <script src="js/pako.js"></script>
<script src="js/webcaosdb.js"></script>
<script src="js/plotly.js"></script>
<script>
@@ -54,6 +56,7 @@
<script src="js/edit_mode.js"></script>
<script src="js/query_shortcuts.js"></script>
<script src="js/ext_references.js"></script>
+ <script src="js/ext_file_download.js"></script>
<script src="js/ext_xls_download.js"></script>
<script src="js/form_elements.js"></script>
<script src="js/tour.js"></script>
@@ -64,11 +67,13 @@
<script src="js/proj4.js"></script>
<script src="js/proj4leaflet.js"></script>
<script src="js/ext_map.js"></script>
+ <script src="js/ext_table_preview.js"></script>
<script src="js/ext_bottom_line.js"></script>
<script src="js/ext_revisions.js"></script>
- <script src="js/autocomplete.js"></script>
+ <script src="js/ext_autocomplete.js"></script>
<script src="js/ext_sss_markdown.js"></script>
<script src="js/ext_trigger_crawler_form.js"></script>
+ <script src="js/ext_bookmarks.js"></script>
<!--EXTENSIONS-->
<script src="js/modules/webcaosdb.js.js"></script>
<script src="js/modules/caosdb.js.js"></script>
@@ -80,14 +85,16 @@
<script src="js/modules/navbar.xsl.js"></script>
<script src="js/modules/edit_mode.js.js"></script>
<script src="js/modules/ext_xls_download.js.js"></script>
+ <script src="js/modules/ext_file_download.js.js"></script>
<script src="js/modules/query_shortcuts.js.js"></script>
<script src="js/modules/form_elements.js.js"></script>
<script src="js/modules/ext_references.js.js"></script>
<script src="js/modules/ext_map.js.js"></script>
<script src="js/modules/ext_bottom_line.js.js"></script>
<script src="js/modules/ext_revisions.js.js"></script>
- <script src="js/modules/autocomplete.js.js"></script>
+ <script src="js/modules/ext_autocomplete.js.js"></script>
<script src="js/modules/ext_sss_markdown.js.js"></script>
<script src="js/modules/ext_trigger_crawler_form.js.js"></script>
+ <script src="js/modules/ext_bookmarks.js.js"></script>
</body>
</html>
diff --git a/test/core/js/modules/autocomplete.js.js b/test/core/js/modules/autocomplete.js.js
deleted file mode 100644
index b75acdcad8b08e548423513ccdf78d7ca0ea7359..0000000000000000000000000000000000000000
--- a/test/core/js/modules/autocomplete.js.js
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2019 IndiScale GmbH
- *
- * 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
- */
-
-'use strict';
-
-QUnit.module("autocomplete.js", {
- before: function (assert){
- autocomplete.retrieve_names = async function () {
- return ['IceCore', 'Bag', 'IceSample', 'IceCream', 'Palette'];
- }
- }
-});
-
-QUnit.test("availability", function(assert) {
- //assert.ok(bootstrap..init, "init available");
- assert.equal(autocomplete.version, "0.1", "test version");
- assert.ok(autocomplete.init, "init available");
-});
-
-
-
-QUnit.test("filter", function(assert) {
- assert.equal(autocomplete.filter('IceCore','Ice'), true, 'test filter')
- assert.equal(autocomplete.filter('IceCore','iCe'), true, 'test filter')
- assert.equal(autocomplete.filter('IceCore','Core'), false, 'test filter')
- assert.equal(autocomplete.filter('Bag','Ice'), false, 'test filter')
-});
-
-QUnit.test("search", async function(assert) {
-
- var done = assert.async(2);
- var gcallback = function(expresults){
- return function (results) {
- assert.propEqual(
- results,
- expresults,
- "test list filter");
- done();
- };
- };
-
- await autocomplete.search("Ice", gcallback(
- ['IceCore', 'IceSample', 'IceCream']
- ));
-
- await autocomplete.search("Core", gcallback([]));
-});
-
-QUnit.test("class", function(assert) {
- assert.ok(autocomplete.toggle_completion , "toggle available");
- assert.ok(autocomplete.toggle_completion() , "toggle runs");
-});
diff --git a/test/core/js/modules/entity.xsl.js b/test/core/js/modules/entity.xsl.js
index c607ee28bf7888f94e3086abf8e033e1532d0d09..59a2f8a6f9a03cf4990fe11bfd751d437a3ffc3e 100644
--- a/test/core/js/modules/entity.xsl.js
+++ b/test/core/js/modules/entity.xsl.js
@@ -264,6 +264,67 @@ QUnit.test("data-version-successor attribute", function(assert) {
assert.equal($(html).find("div.caosdb-entity-panel[data-version-successor]").length, 0, "data-version-successor attribute not present");
});
+QUnit.test("version full history", function (assert) {
+ var xmlstr = `
+ <Response username="user1" realm="Realm1" srid="31ce8ea1-6c9b-4a82-82ec-9f6f3edd2622" timestamp="1606225647516" baseuri="https://localhost:10443" count="1">
+ <Record id="3373" name="TestRecord1-10thVersion" description="This is the 10th version.">
+ <Permissions>
+ <Permission name="RETRIEVE:HISTORY" />
+ </Permissions>
+ <Version id="vid6" username="user1" realm="Realm1" date="date6" completeHistory="true">
+ <Predecessor id="vid5" username="user1" realm="Realm1" date="date5">
+ <Predecessor id="vid4" username="user1" realm="Realm1" date="date4">
+ <Predecessor id="vid3" username="user1" realm="Realm1" date="date3">
+ <Predecessor id="vid2" username="user1" realm="Realm1" date="date2">
+ <Predecessor id="vid1" username="user1" realm="Realm1" date="date1" />
+ </Predecessor>
+ </Predecessor>
+ </Predecessor>
+ </Predecessor>
+ <Successor id="vid7" username="user1" realm="Realm1" date="date7">
+ <Successor id="vid8" username="user1" realm="Realm1" date="date8">
+ <Successor id="vid9" username="user1" realm="Realm1" date="date9">
+ <Successor id="vid10" username="user1" realm="Realm1" date="date10" />
+ </Successor>
+ </Successor>
+ </Successor>
+ </Version>
+ <Parent id="3372" name="TestRT" />
+ </Record>
+</Response>
+`;
+ var xml = str2xml(xmlstr);
+ var html = applyTemplates(xml, this.entityXSL, "entities", "*");
+ var version_info = $(html).find(".caosdb-f-entity-version-info");
+ var table_elem = $(version_info).find("table");
+
+ var TAB = "%09", NEWL = "%0A", usr = "user1@Realm1",
+ path = "/entitypath/3373";
+ var export_table = `data:text/csv;charset=utf-8,Entity ID${TAB}Version ID${TAB}Date${TAB}User${TAB}URI${NEWL}3373${TAB}vid10${TAB}date10${TAB}${usr}${TAB}${path}@vid10${NEWL}3373${TAB}vid9${TAB}date9${TAB}${usr}${TAB}${path}@vid9${NEWL}3373${TAB}vid8${TAB}date8${TAB}${usr}${TAB}${path}@vid8${NEWL}3373${TAB}vid7${TAB}date7${TAB}${usr}${TAB}${path}@vid7${NEWL}3373${TAB}vid6${TAB}date6${TAB}${usr}${TAB}${path}@vid6${NEWL}3373${TAB}vid5${TAB}date5${TAB}${usr}${TAB}${path}@vid5${NEWL}3373${TAB}vid4${TAB}date4${TAB}${usr}${TAB}${path}@vid4${NEWL}3373${TAB}vid3${TAB}date3${TAB}${usr}${TAB}${path}@vid3${NEWL}3373${TAB}vid2${TAB}date2${TAB}${usr}${TAB}${path}@vid2${NEWL}3373${TAB}vid1${TAB}date1${TAB}${usr}${TAB}${path}@vid1`
+ assert.equal(version_info.length, 1);
+ assert.equal(table_elem.length, 1);
+ assert.equal(version_history.get_history_tsv(table_elem[0]), export_table);
+});
+
+QUnit.test("Transforming abstract properties", function (assert) {
+ var xmlstr = `<Property id="3842" name="reftotestrt" datatype="TestRT">
+ <Version id="04ad505da057603a9177a1fcf6c9efd5f3690fe4" date="2020-11-23T10:38:02.936+0100" />
+ </Property>`;
+ var xml = str2xml(xmlstr);
+ var html = applyTemplates(xml, this.entityXSL, "entity-body", "Property");
+ var prop = getPropertyFromElement(html.firstElementChild);
+ assert.propEqual(prop, {
+ "datatype": "TestRT",
+ "html": {},
+ "id": "3842",
+ "list": false,
+ "name": "reftotestrt",
+ "reference": true,
+ "unit": undefined,
+ "value": ""}
+ );
+});
+
/* MISC FUNCTIONS */
function applyTemplates(xml, xsl, mode, select = "*") {
let entryRule = '<xsl:template priority="9" match="/"><xsl:apply-templates select="' + select + '" mode="' + mode + '"/></xsl:template>';
diff --git a/test/core/js/modules/ext_autocomplete.js.js b/test/core/js/modules/ext_autocomplete.js.js
new file mode 100644
index 0000000000000000000000000000000000000000..e8776f945b7bb46a0d431eb2d0ac0f7fe21419fc
--- /dev/null
+++ b/test/core/js/modules/ext_autocomplete.js.js
@@ -0,0 +1,72 @@
+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2019 IndiScale GmbH
+ *
+ * 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
+ */
+
+'use strict';
+
+QUnit.module("ext_autocomplete.js", {
+ before: function (assert){
+ ext_autocomplete.retrieve_names = async function () {
+ return ['IceCore', 'Bag', 'IceSample', 'IceCream', 'Palette'];
+ }
+ ext_autocomplete.init();
+
+ }
+});
+
+QUnit.test("availability", function(assert) {
+ //assert.ok(bootstrap..init, "init available");
+ assert.equal(ext_autocomplete.version, "0.1", "test version");
+ assert.ok(ext_autocomplete.init, "init available");
+});
+
+
+
+QUnit.test("starts_with_filter", function(assert) {
+ assert.equal(ext_autocomplete.starts_with_filter('IceCore','Ice'), true, 'test filter')
+ assert.equal(ext_autocomplete.starts_with_filter('IceCore','iCe'), true, 'test filter')
+ assert.equal(ext_autocomplete.starts_with_filter('IceCore','Core'), false, 'test filter')
+ assert.equal(ext_autocomplete.starts_with_filter('Bag','Ice'), false, 'test filter')
+});
+
+QUnit.test("search", async function(assert) {
+
+ var done = assert.async(2);
+ var gcallback = function(expresults){
+ return function (results) {
+ assert.propEqual(
+ results,
+ expresults,
+ "test list filter");
+ done();
+ };
+ };
+ await ext_autocomplete.search("Ice",
+ gcallback( ['IceCore', 'IceSample', 'IceCream'])
+ );
+
+ await ext_autocomplete.search("Core", gcallback([]));
+});
+
+QUnit.test("class", function(assert) {
+ assert.ok(ext_autocomplete.switch_on_completion , "toggle available");
+ assert.ok(ext_autocomplete.switch_on_completion() , "toggle runs");
+});
diff --git a/test/core/js/modules/ext_bookmarks.js.js b/test/core/js/modules/ext_bookmarks.js.js
new file mode 100644
index 0000000000000000000000000000000000000000..831df74231e479d5b4550524f6bc0da617c98fb3
--- /dev/null
+++ b/test/core/js/modules/ext_bookmarks.js.js
@@ -0,0 +1,181 @@
+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ *
+ * 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
+ */
+
+'use strict';
+
+QUnit.module("ext_bookmarks.js", {
+ before: function (assert) {
+ // setup before module
+ ext_bookmarks.set_collection_id("test");
+ // otherwise tests would collide with actual bookmarks
+ },
+ beforeEach: function (assert) {
+ // setup before each test
+ },
+ afterEach: function (assert) {
+ // teardown after each test
+ ext_bookmarks.clear_bookmark_storage();
+ connection._init();
+ },
+ after: function (assert) {
+ // teardown after module
+ }
+});
+
+QUnit.test("parse_uri", function(assert) {
+ assert.equal(typeof ext_bookmarks.parse_uri(""), "undefined");
+ assert.equal(typeof ext_bookmarks.parse_uri("asdf"), "undefined");
+ assert.equal(typeof ext_bookmarks.parse_uri("https://localhost:1234/Entity/sada?sadfasd#sdfgdsf"), "undefined");
+
+ assert.propEqual(ext_bookmarks.parse_uri("safgsa/123&456&789?sadfasdf#_bm_1"),
+ {bookmarks: ["123", "456", "789"], collection_id: "1"});
+});
+
+QUnit.test("get_bookmarks, clear_bookmark_storage", function(assert) {
+ assert.propEqual(ext_bookmarks.get_bookmarks(), []);
+
+ ext_bookmarks.bookmark_storage[ext_bookmarks.get_key("sdfg")] = "3456"
+ assert.propEqual(ext_bookmarks.get_bookmarks(), ["3456"]);
+
+ ext_bookmarks.clear_bookmark_storage();
+ assert.propEqual(ext_bookmarks.get_bookmarks(), []);
+});
+
+QUnit.test("get_export_table", async function (assert) {
+ connection.get = (id) => `<root><Response><File id="${id}" path="testpath_${id.split("/")[1]}"><Version id="abcHead"/></File></Response></root>`;
+ const TAB = "%09";
+ const NEWL = "%0A";
+ const context_root = connection.getBasePath() + "Entity/";
+ var table = await ext_bookmarks.get_export_table(
+ ["123@ver1", "456@ver2", "789@ver3", "101112", "@131415"]);
+ assert.equal(table,
+ `data:text/csv;charset=utf-8,ID${TAB}Version${TAB}URI${TAB}Path${TAB}Name${TAB}RecordType${NEWL}123${TAB}ver1${TAB}${context_root}123@ver1${TAB}testpath_123@ver1${TAB}${TAB}${NEWL}456${TAB}ver2${TAB}${context_root}456@ver2${TAB}testpath_456@ver2${TAB}${TAB}${NEWL}789${TAB}ver3${TAB}${context_root}789@ver3${TAB}testpath_789@ver3${TAB}${TAB}${NEWL}101112${TAB}abcHead${TAB}${context_root}101112@abcHead${TAB}testpath_101112${TAB}${TAB}${NEWL}${TAB}131415${TAB}${context_root}@131415${TAB}testpath_@131415${TAB}${TAB}`);
+
+});
+
+QUnit.test("update_clear_button", function (assert) {
+ const clear_button = $(`<div id="caosdb-f-bookmarks-clear"/>`);
+ $("body").append(clear_button);
+
+ assert.notOk(clear_button.is(".disabled"));
+ ext_bookmarks.update_clear_button([]);
+ assert.ok(clear_button.is(".disabled"));
+
+ ext_bookmarks.update_clear_button(["asdf"]);
+ assert.notOk(clear_button.is(".disabled"));
+
+ ext_bookmarks.update_clear_button(["asdf"]);
+ assert.notOk(clear_button.is(".disabled"));
+
+ ext_bookmarks.update_clear_button([]);
+ assert.ok(clear_button.is(".disabled"));
+
+ clear_button.remove();
+});
+
+QUnit.test("update_export_link", function (assert) {
+ const export_link = $(`<div id="caosdb-f-bookmarks-export-link"/>`);
+ $("body").append(export_link);
+
+ assert.notOk(export_link.is(".disabled"));
+ ext_bookmarks.update_export_link([]);
+ assert.ok(export_link.is(".disabled"));
+
+ ext_bookmarks.update_export_link(["asdf"]);
+ assert.notOk(export_link.is(".disabled"));
+
+ ext_bookmarks.update_export_link(["asdf"]);
+ assert.notOk(export_link.is(".disabled"));
+
+ ext_bookmarks.update_export_link([]);
+ assert.ok(export_link.is(".disabled"));
+
+ export_link.remove();
+});
+
+QUnit.test("update_collection_link", function (assert) {
+ const collection_link = $(
+ `<div id="caosdb-f-bookmarks-collection-link"><a/></div>`);
+ const a = collection_link.find("a")[0];
+ $("body").append(collection_link);
+
+ assert.notOk(collection_link.is(".disabled"));
+ assert.notOk(a.href);
+
+ ext_bookmarks.update_collection_link([]);
+ assert.ok(collection_link.is(".disabled"));
+ assert.notOk(a.href);
+
+ ext_bookmarks.update_collection_link(["asdf"]);
+ assert.notOk(collection_link.is(".disabled"));
+ assert.equal(a.href, ext_bookmarks.get_collection_link(["asdf"]));
+
+ ext_bookmarks.update_collection_link(["asdf", "sdfg"]);
+ assert.notOk(collection_link.is(".disabled"));
+ assert.equal(a.href, ext_bookmarks.get_collection_link(["asdf", "sdfg"]));
+
+ ext_bookmarks.update_collection_link([]);
+ assert.ok(collection_link.is(".disabled"));
+ assert.notOk(a.href);
+
+ collection_link.remove();
+});
+
+QUnit.test("bookmark buttons", function (assert) {
+ const inactive_button = $(`<div data-bmval="id1"/>`);
+ const active_button = $(`<div class="active" data-bmval="id2"/>`);
+ const broken_button = $(`<div data-bmval=""/>`);
+ const non_button = $(`<div data-bla="sadf"/>)`);
+ const outside_button = $(`<div data-bmval="id3"/>`);
+ const inside_buttons = $("<div/>").append([inactive_button, active_button,
+ broken_button, non_button]);
+
+ // get_bookmark_buttons
+ assert.equal(ext_bookmarks.get_bookmark_buttons("body").length, 0);
+
+ $("body").append([outside_button, inside_buttons]);
+
+ assert.equal(ext_bookmarks.get_bookmark_buttons("body").length, 4, "all but no_button");
+ assert.equal(ext_bookmarks.get_bookmark_buttons(inside_buttons).length, 3, "all but non_button and outside_button");
+
+ // get_value
+ assert.equal(ext_bookmarks.get_value(inactive_button), "id1");
+ assert.notOk(ext_bookmarks.get_value(non_button));
+ assert.notOk(ext_bookmarks.get_value(broken_button));
+
+ // init_button
+ assert.ok(active_button.is(".active"));
+ ext_bookmarks.init_button(active_button);
+ assert.notOk(active_button.is(".active"));
+
+ ext_bookmarks.bookmark_storage[ext_bookmarks.get_key("id1")] = "id1"
+ assert.notOk(inactive_button.is(".active"));
+ ext_bookmarks.init_button(inactive_button);
+ assert.ok(inactive_button.is(".active"));
+
+ ext_bookmarks.clear_bookmark_storage();
+ assert.notOk(inactive_button.is(".active"), "clear_bookmark_storage removes active class");
+
+ inside_buttons.remove();
+ outside_button.remove();
+});
diff --git a/test/core/js/modules/ext_bottom_line.js b/test/core/js/modules/ext_bottom_line.js.js
similarity index 88%
rename from test/core/js/modules/ext_bottom_line.js
rename to test/core/js/modules/ext_bottom_line.js.js
index 21c92167271f87554a9af881554d33db686d9194..610d95d1b00b3a8bf220a6d39e12ed71ecaa9090 100644
--- a/test/core/js/modules/ext_bottom_line.js
+++ b/test/core/js/modules/ext_bottom_line.js.js
@@ -45,7 +45,7 @@ var ext_bottom_line_test_suite = function ($, ext_bottom_line, QUnit) {
},
{ "id": "test.success-2",
"is_applicable": "(entity) => getParents(entity).map(par => par.name).includes('TestPreviewRecordType') && getEntityName(entity) !== 'TestPreviewRecord-fall-back'",
- "create": "(entity) => { return plotly_preview.create_plot([{x: [1,2,3,4,5], y: [1,2,4,8,16]}], { 'xaxis': {'title': 'time [samples]'}}); }"
+ "create": "(entity) => { return plotly_preview.create_plot([{x: [1,2,3,4,5], y: [1,2,4,8,16]}], { 'xaxis': {'title': 'time [samples]'}}, {displaylogo: false}); }"
}
]
};
@@ -67,7 +67,7 @@ var ext_bottom_line_test_suite = function ($, ext_bottom_line, QUnit) {
});
QUnit.test("_creators", function (assert) {
- assert.equal(ext_bottom_line._creators.length, 7, "seven creators");
+ assert.equal(ext_bottom_line._creators.length, 9, "nine creators, 5 default ones, 4 from these tests.");
});
QUnit.test("add_preview_container", function(assert) {
@@ -105,7 +105,7 @@ var ext_bottom_line_test_suite = function ($, ext_bottom_line, QUnit) {
assert.equal(container.text(), "blablabla");
break;
case "error":
- assert.equal(container.text(), "An error occured while loading this preview");
+ assert.equal(container.text(), "An error occured while loading this preview.Test Error");
break;
case "load-forever":
assert.equal(container.text(), "Please wait...");
@@ -121,4 +121,12 @@ var ext_bottom_line_test_suite = function ($, ext_bottom_line, QUnit) {
});
+ QUnit.test("tiff converter", async function(assert) {
+ let entity_xml = `<Response><File path="../pics/saturn.tif"/></Response>`;
+ const entity = (await transformation.transformEntities(str2xml(entity_xml)))[0];
+ const tiff_preview = await ext_bottom_line._creators.filter((c) => c.id == "_default_creators.tiff_images")[0].create(entity);
+
+ assert.equal($(tiff_preview).find("img").attr("src").slice(0,21), "data:image/png;base64", "decoded tiff to png");
+ });
+
}($, ext_bottom_line, QUnit);
diff --git a/test/core/js/modules/ext_file_download.js.js b/test/core/js/modules/ext_file_download.js.js
new file mode 100644
index 0000000000000000000000000000000000000000..1103f61304c56259cc1a54a94c0c6b6b201d2aa5
--- /dev/null
+++ b/test/core/js/modules/ext_file_download.js.js
@@ -0,0 +1,65 @@
+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+ *
+ * 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
+ */
+
+'use strict';
+
+QUnit.module("ext_file_download.js", {
+ before: function (assert) {
+ // setup before module
+ },
+ beforeEach: function (assert) {
+ // setup before each test
+ },
+ afterEach: function (assert) {
+ // teardown after each test
+ },
+ after: function (assert) {
+ // teardown after module
+ }
+});
+
+QUnit.test("chunk_list ", function(assert) {
+ const li = [1,2,3,4,5,6,7];
+ const res = ext_file_download.chunk_list(li, 3);
+ assert.equal(res.length, 3, "number of parts");
+ assert.propEqual(res[2], [7], "number of parts");
+});
+
+QUnit.test("collect_ids ", function (assert) {
+ const line = id => $(`<tr data-entity-id="${id}"/>`);
+ const prop_val = x => $(`<div class="caosdb-f-property-value"/>`);
+ const single_val =x => $(`<div class="caosdb-f-property-single-raw-value caosdb-id">${x}</div>`);
+
+
+ const line1 = line("34");
+ line1.append([prop_val().append(single_val("5")),prop_val().append(single_val("6"))])
+ $("body").append([line1]);
+
+ const res = ext_file_download.collect_ids()
+ assert.ok(res.indexOf("5") > -1, "missing id");
+ assert.ok(res.indexOf("6") > -1, "missing id");
+ assert.ok(res.indexOf("34") > -1, "missing id");
+
+ line1.remove();
+
+});
diff --git a/test/core/js/modules/ext_xls_download.js.js b/test/core/js/modules/ext_xls_download.js.js
index 4f9dc6c59b156f1f2265acb4b315887536667194..997a89ec21d4a22f49746cbda1c46bb56268f80d 100644
--- a/test/core/js/modules/ext_xls_download.js.js
+++ b/test/core/js/modules/ext_xls_download.js.js
@@ -79,16 +79,14 @@ QUnit.module("ext_xls_download", {
return str2xml('<response><script code="0" /><stdout>bla</stdout></response>');
}
- caosdb_table_export._go_to_script_results = function(xls_link, filename) {
- xls_link.setAttribute(
- "href",
- location.protocol + "//" +location.host + "/Shared/" + filename);
+ caosdb_table_export.go_to_script_results = function(filename) {
assert.equal(filename, "bla", "filename correct");
done();
}
var tsv_data = $('<a id="caosdb-f-query-select-data-tsv" />');
- $(document.body).append(tsv_data);
+ var modal = $('<div id="downloadModal"><div>');
+ $(document.body).append([tsv_data, modal]);
var xsl_link = $("<a/>");
@@ -96,12 +94,15 @@ QUnit.module("ext_xls_download", {
await sleep(500);
- assert.ok(xsl_link.attr("href").endsWith("Shared/bla"), xsl_link.attr("href") + " ends with Shared/bla");
-
tsv_data.remove();
+ modal.remove();
});
}
+QUnit.test("_clean_cell", function(assert) {
+ assert.equal(caosdb_table_export._clean_cell("\n\t\n\t"), " ", "No valid content");
+});
+
QUnit.test("_get_property_value", function(assert) {
var f = caosdb_table_export._get_property_value;
@@ -116,9 +117,15 @@ QUnit.test("_get_tsv_string", function(assert) {
const entities = $(table).find("tbody tr").toArray();
assert.equal(entities.length, 2, "two example entities");
- var f = caosdb_table_export._get_tsv_string
+ var f = caosdb_table_export._create_tsv_string
var tsv_string = f(entities, ["Bag", "Number"], true);
- assert.equal(tsv_string, "data:text/csv;charset=utf-8,ID%09Bag%09Number%0A242%096366, 6406, 6407, 6408, 6409, 6410, 6411, 6412, 6413%090284%0A2112%09%091101", "tsv generated");
+ var prefix = "data:text/csv;charset=utf-8,"
+ assert.equal(tsv_string,
+ "ID\tBag\tNumber\n242\t6366, 6406, 6407, 6408, 6409, 6410, 6411, 6412, 6413\t02 8 4aaa a\n2112\t\t1101", "tsv generated");
+ tsv_string = caosdb_table_export._encode_tsv_string(tsv_string);
+ assert.equal(tsv_string.slice(0,prefix.length), prefix);
+ assert.equal(decodeURIComponent(tsv_string.slice(prefix.length, tsv_string.length)),
+ "ID\tBag\tNumber\n242\t6366, 6406, 6407, 6408, 6409, 6410, 6411, 6412, 6413\t02 8 4aaa a\n2112\t\t1101", "tsv generated");
});
QUnit.test("_get_property_value", function (assert) {
diff --git a/test/core/js/modules/form_elements.js.js b/test/core/js/modules/form_elements.js.js
index 7f5930cd4253f408edf785045db10290697cd6c3..f8bf1ed1ac1495a8a3688aeb7b0cce387c8b69fb 100644
--- a/test/core/js/modules/form_elements.js.js
+++ b/test/core/js/modules/form_elements.js.js
@@ -541,3 +541,91 @@ QUnit.test("field_ready", function(assert) {
});
});
+{
+const sleep = (ms) => {
+ return new Promise(res => setTimeout(res, ms))
+}
+
+QUnit.test("make_alert - cancel", async function(assert) {
+ var cancel_callback = assert.async()
+ var _alert = form_elements.make_alert({
+ message: "message",
+ proceed_callback: () => {assert.ok(false, "this should not be called");},
+ cancel_callback: cancel_callback,
+ });
+ $("body").append(_alert);
+
+ assert.equal($("body").find(".caosdb-f-form-elements-alert").length, 1, "alert is there");
+ $(_alert).find("button.caosdb-f-btn-alert-cancel")[0].click();
+ await sleep(500);
+
+ assert.equal($("body").find(".caosdb-f-form-elements-alert").length, 0, "has been removed");
+
+
+});
+
+QUnit.test("make_alert - proceed", async function(assert) {
+ var proceed_callback = assert.async();
+ var _alert = form_elements.make_alert({
+ message: "message",
+ proceed_callback: proceed_callback,
+ });
+ assert.equal($(_alert).find("[type='checkbox']").length, 0, "no remember checkbox");
+
+ $("body").append(_alert);
+ assert.equal($("body").find(".caosdb-f-form-elements-alert").length, 1, "alert is there");
+ $(_alert).find("button.caosdb-f-btn-alert-proceed")[0].click();
+ await sleep(500);
+
+ assert.equal($("body").find(".caosdb-f-form-elements-alert").length, 0, "has been removed");
+
+});
+
+QUnit.test("make_alert - remember", async function(assert) {
+ form_elements._set_alert_decision("unittests", "");
+
+ var proceed_callback = assert.async(3);
+ var _alert = form_elements.make_alert({
+ message: "message",
+ proceed_callback: proceed_callback,
+ remember_my_decision_id: "unittests",
+ });
+ assert.equal($(_alert).find("[type='checkbox']").length, 1, "has remember checkbox");
+
+ // append for the first time
+ $("body").append(_alert);
+ assert.equal($("body").find(".caosdb-f-form-elements-alert").length, 1, "alert is there");
+
+ // click proceed without "don't ask me again".
+ $(_alert).find("button.caosdb-f-btn-alert-proceed")[0].click();
+ await sleep(500);
+
+ form_elements._set_alert_decision("unittests", "");
+
+ assert.equal($("body").find(".caosdb-f-form-elements-alert").length, 0, "has been removed");
+
+ // append 2nd time
+ _alert = form_elements.make_alert({
+ message: "message",
+ proceed_callback: proceed_callback,
+ remember_my_decision_id: "unittests",
+ });
+ assert.equal($(_alert).find("[type='checkbox']").length, 1, "has remember checkbox");
+ $("body").append(_alert);
+ assert.equal($("body").find(".caosdb-f-form-elements-alert").length, 1, "alert is there");
+ $(_alert).find("[type='checkbox']").prop("checked", true);
+
+ $(_alert).find("button.caosdb-f-btn-alert-proceed")[0].click();
+ await sleep(500);
+ form_elements._set_alert_decision("unittests", "proceed");
+
+ // try 3rd time
+ _alert = form_elements.make_alert({
+ message: "message",
+ proceed_callback: proceed_callback,
+ remember_my_decision_id: "unittests",
+ });
+ assert.equal(typeof _alert, "undefined", "alert was not created, proceed callback was called third time");
+});
+
+}
diff --git a/test/core/js/modules/webcaosdb.js.js b/test/core/js/modules/webcaosdb.js.js
index 239758161b8419a8a5e15799c67c909977f1fbf0..7b3f7abf404f261668c18690df337b73794dd8bd 100644
--- a/test/core/js/modules/webcaosdb.js.js
+++ b/test/core/js/modules/webcaosdb.js.js
@@ -324,7 +324,7 @@ QUnit.test("createUpdateForm", function(assert) {
QUnit.test("createUpdateEntityHeading", function(assert) {
let cueh = transaction.update.createUpdateEntityHeading;
assert.ok(cueh, "function available");
- let eh = $('<div class="panel-heading"><div class="1strow"/><div class="2ndrow"/></div>')[0];
+ let eh = $('<div class="panel-heading"><div class="1strow"></div><div class="2ndrow"></div></div>')[0];
assert.equal($(eh).children('.1strow').length, 1, "eh has 1st row");
assert.equal($(eh).children('.2ndrow').length, 1, "eh has 2nd row");
let uh = cueh(eh);
@@ -957,10 +957,6 @@ QUnit.test("createCarouselNav", function(assert) {
let original_get = connection.get;
ref_property_elem.find('div').append(refLinks);
- const sleep = function sleep(ms) {
- return new Promise(resolve => setTimeout(resolve, ms));
- }
-
QUnit.test("initProperty", async function(assert) {
var done = assert.async(2);
assert.ok(preview.initProperty, "function available");
@@ -1939,3 +1935,80 @@ QUnit.test("toolbox example", function(assert) {
assert.equal($('.caosdb-f-navbar-toolbox[data-toolbox-name="Tools"]').length, 1, "one 'Tools' toolbox");
assert.equal($('.caosdb-f-navbar-toolbox[data-toolbox-name="Tools"] button').length, 3, "three 'Tools' buttons");
});
+
+QUnit.module("webcaosdb.js - version_history", {
+ before: function(assert) {
+ connection._init();
+ },
+ after: function(assert) {
+ connection._init();
+ },
+});
+
+QUnit.test("available", function (assert) {
+ assert.equal(typeof version_history.init, "function");
+ assert.equal(typeof version_history.get_history_tsv, "function");
+ assert.equal(typeof version_history.init_export_history_buttons, "function");
+ assert.equal(typeof version_history.init_load_history_buttons, "function");
+ assert.equal(typeof version_history.retrieve_history, "function");
+})
+
+QUnit.test("init_load_history_buttons and init_load_history_buttons", async function (assert) {
+ var xml_str = `<Response username="user1" realm="Realm1" srid="bc2f8f6b-71d6-49ca-890c-eebea3e38e18" timestamp="1606253365632" baseuri="https://localhost:10443" count="1">
+ <UserInfo username="user1" realm="Realm1">
+ <Roles>
+ <Role>role1</Role>
+ </Roles>
+ </UserInfo>
+ <Record id="8610" name="TestRecord1-6thVersion" description="This is the 6th version.">
+ <Permissions>
+ <Permission name="RETRIEVE:HISTORY" />
+ </Permissions>
+ <Version id="efa5ac7126c722b3f43284e150d070d6deac0ba6">
+ <Predecessor id="f09114b227d88f23d4e23645ae471d688b1e82f7" />
+ <Successor id="5759d2bccec3662424db5bb005acea4456a299ef" />
+ </Version>
+ <Parent id="8609" name="TestRT" />
+ </Record>
+</Response>
+`;
+ var done = assert.async(2);
+ var xml = str2xml(xml_str);
+ version_history._get = async function (entity) {
+ assert.equal(entity, "Entity/8610@efa5ac7126c722b3f43284e150d070d6deac0ba6?H");
+ done();
+ $(xml).find("Version").attr("completeHistory", "true");
+ return xml;
+ }
+ var html = await transformation.transformEntities(xml);
+ var load_button = $(html).find(".caosdb-f-entity-version-load-history-btn");
+ $("body").append(html);
+
+ assert.notOk(load_button.is(":visible"), "load_button hidden");
+ load_button.click(); // nothing happens
+
+ version_history.init_load_history_buttons();
+ assert.ok(load_button.is(":visible"), "load_button is not hidden anymore");
+
+ // load_button triggers retrieval of history
+ load_button.click();
+ await sleep(200);
+
+ var gone_button = $(html).find(".caosdb-f-entity-version-load-history-btn");
+ assert.equal(gone_button.length, 0, "button is gone");
+
+ export_button = $(html).find(".caosdb-f-entity-version-export-history-btn");
+ assert.ok(export_button.is(":visible"), "export_button is visible");
+
+ version_history._download_tsv = function (tsv) {
+ assert.equal(tsv.indexOf("data:text/csv;charset=utf-8,Entity ID%09"), 0);
+ done();
+ }
+ export_button.click();
+
+ $(html).remove();
+});
+
+const sleep = function sleep(ms) {
+ return new Promise(resolve => setTimeout(resolve, ms));
+}
diff --git a/test/core/pics/saturn.tif b/test/core/pics/saturn.tif
new file mode 100644
index 0000000000000000000000000000000000000000..f226ebab7fca3c9caa306f78d80eaa7b4068f994
Binary files /dev/null and b/test/core/pics/saturn.tif differ
diff --git a/test/core/xml/table_export/test_case_select_table_1.xml b/test/core/xml/table_export/test_case_select_table_1.xml
index 12f26180b89bdf3f2ba3280d4546783f54bfa8ea..ae0a856f106557be3712f303b06a99f6220ef827 100644
--- a/test/core/xml/table_export/test_case_select_table_1.xml
+++ b/test/core/xml/table_export/test_case_select_table_1.xml
@@ -10,7 +10,7 @@
</Query>
<Record id="242">
<Property id="117" name="Number" datatype="TEXT" importance="FIX">
- 0284
+ 02	8


4aaa	a
</Property>
<Property id="104" name="Bag" datatype="Bag" importance="FIX">
6366
diff --git a/test/docker/Dockerfile b/test/docker/Dockerfile
index a19843fb3de11bbedf1c01f71619470bcc99f75c..7340ee5a7bb94aacc13ff582f1d05221419a312b 100644
--- a/test/docker/Dockerfile
+++ b/test/docker/Dockerfile
@@ -1,7 +1,15 @@
-FROM debian:latest
-RUN apt-get update && \
- apt-get install firefox-esr gettext-base pylint3 python3-pip \
- python3-httpbin git curl x11-apps xvfb unzip -y
-RUN git clone -b dev https://gitlab.com/caosdb/caosdb-pylib.git && \
- cd caosdb-pylib && pip3 install .
+FROM debian:10
+RUN echo "deb http://deb.debian.org/debian buster-backports main" >> /etc/apt/sources.list \
+ && apt-get update \
+ && apt-get install -y \
+ firefox-esr gettext-base pylint3 python3-pip \
+ python3-httpbin git curl x11-apps xvfb unzip python3-pytest \
+ && apt-get install -y -t buster-backports \
+ npm
+RUN pip3 install caosdb
+RUN pip3 install pandas xlrd
+RUN pip3 install git+https://gitlab.com/caosdb/caosdb-advanced-user-tools.git@dev
+# For automatic documentation
+RUN npm install -g jsdoc
+RUN pip3 install sphinx-js sphinx-autoapi recommonmark sphinx-rtd-theme
diff --git a/test/server_side_scripting/ext_table_preview/__pycache__/pandas_table_preview.cpython-37.pyc b/test/server_side_scripting/ext_table_preview/__pycache__/pandas_table_preview.cpython-37.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..613d9dce64b94c3b4c66891f22cd02a6c337dff6
Binary files /dev/null and b/test/server_side_scripting/ext_table_preview/__pycache__/pandas_table_preview.cpython-37.pyc differ
diff --git a/test/server_side_scripting/ext_table_preview/__pycache__/test_pandas_table_preview.cpython-37-pytest-6.0.2.pyc b/test/server_side_scripting/ext_table_preview/__pycache__/test_pandas_table_preview.cpython-37-pytest-6.0.2.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..c3563a411e0c836d2613ab7189dc6833be735e00
Binary files /dev/null and b/test/server_side_scripting/ext_table_preview/__pycache__/test_pandas_table_preview.cpython-37-pytest-6.0.2.pyc differ
diff --git a/test/server_side_scripting/ext_table_preview/data/bad.csv b/test/server_side_scripting/ext_table_preview/data/bad.csv
new file mode 100644
index 0000000000000000000000000000000000000000..d29a9312a387186beb8bf4f77a8ec0e4b0ab80fa
Binary files /dev/null and b/test/server_side_scripting/ext_table_preview/data/bad.csv differ
diff --git a/test/server_side_scripting/ext_table_preview/data/bad.tsv b/test/server_side_scripting/ext_table_preview/data/bad.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..d29a9312a387186beb8bf4f77a8ec0e4b0ab80fa
Binary files /dev/null and b/test/server_side_scripting/ext_table_preview/data/bad.tsv differ
diff --git a/test/server_side_scripting/ext_table_preview/data/bad.xls b/test/server_side_scripting/ext_table_preview/data/bad.xls
new file mode 100644
index 0000000000000000000000000000000000000000..1f31bf2754258e3d07f88fd1e6bdee4d7b11bee1
Binary files /dev/null and b/test/server_side_scripting/ext_table_preview/data/bad.xls differ
diff --git a/test/server_side_scripting/ext_table_preview/data/bad.xlsx b/test/server_side_scripting/ext_table_preview/data/bad.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..1f31bf2754258e3d07f88fd1e6bdee4d7b11bee1
Binary files /dev/null and b/test/server_side_scripting/ext_table_preview/data/bad.xlsx differ
diff --git a/test/server_side_scripting/ext_table_preview/data/server_error.csv b/test/server_side_scripting/ext_table_preview/data/server_error.csv
new file mode 100644
index 0000000000000000000000000000000000000000..3e770df012f65d73ce4721a5f65d7e3f39959519
--- /dev/null
+++ b/test/server_side_scripting/ext_table_preview/data/server_error.csv
@@ -0,0 +1 @@
+Hi, this line contains a unicode backspace. This causes a server error, when pandas_table_preview.py's output is serialized into XML.
\ No newline at end of file
diff --git a/test/server_side_scripting/ext_table_preview/data/test.csv b/test/server_side_scripting/ext_table_preview/data/test.csv
new file mode 100644
index 0000000000000000000000000000000000000000..7c9bfd1354393439f551021cfe340577433ce2aa
--- /dev/null
+++ b/test/server_side_scripting/ext_table_preview/data/test.csv
@@ -0,0 +1,12 @@
+# test header
+# two lines
+A1,B1,C1,D1,E1,F1,G1,H1,I1,J1,K1,L1,M1,N1,O1,P1,Q1,R1,S1,T1
+A2,B2,C2,D2,E2,F2,G2,H2,I2,J2,K2,L2,M2,N2,O2,P2,Q2,R2,S2,T2
+A3,B3,csvfile,D3,E3,F3,G3,H3,I3,J3,K3,L3,M3,N3,O3,P3,Q3,R3,S3,T3
+A5,B5,C5,D5,E5,F5,G5,H5,I5,J5,K5,L5,M5,N5,O5,P5,Q5,R5,S5,T5
+A6,B6,C6,D6,E6,F6,G6,H6,I6,J6,K6,L6,M6,N6,O6,P6,Q6,R6,S6,T6
+A7,B7,csvfile,D7,E7,F7,G7,H7,I7,J7,K7,L7,M7,N7,O7,P7,Q7,R7,S7,T7
+A8,B8,C8,D8,E8,F8,G8,H8,I8,J8,K8,L8,M8,N8,O8,P8,Q8,R8,S8,T8
+A9,B9,C9,D9,E9,F9,G9,H9,I9,J9,K9,L9,M9,N9,O9,P9,Q9,R9,S9,T9
+A10,B10,C10,D10,E10,F10,G10,H10,I10,J10,K10,L10,M10,N10,O10,P10,Q10,R10,S10,T10
+A11,B11,C11,D11,E11,F11,G11,H11,I11,J11,K11,L11,M11,N11,O11,P11,Q11,R11,S11,T11
diff --git a/test/server_side_scripting/ext_table_preview/data/test.tsv b/test/server_side_scripting/ext_table_preview/data/test.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..863f692bf64e7dcabf74703587a93e37adf27e67
--- /dev/null
+++ b/test/server_side_scripting/ext_table_preview/data/test.tsv
@@ -0,0 +1,12 @@
+# test header
+# two lines
+A1 B1 C1 D1 E1 F1 G1 H1 I1 J1 K1 L1 M1 N1 O1 P1 Q1 R1 S1 T1
+A2 B2 C2 D2 E2 F2 G2 H2 I2 J2 K2 L2 M2 N2 O2 P2 Q2 R2 S2 T2
+A3 B3 csvfile D3 E3 F3 G3 H3 I3 J3 K3 L3 M3 N3 O3 P3 Q3 R3 S3 T3
+A5 B5 C5 D5 E5 F5 G5 H5 I5 J5 K5 L5 M5 N5 O5 P5 Q5 R5 S5 T5
+A6 B6 C6 D6 E6 F6 G6 H6 I6 J6 K6 L6 M6 N6 O6 P6 Q6 R6 S6 T6
+A7 B7 tsvfile D7 E7 F7 G7 H7 I7 J7 K7 L7 M7 N7 O7 P7 Q7 R7 S7 T7
+A8 B8 C8 D8 E8 F8 G8 H8 I8 J8 K8 L8 M8 N8 O8 P8 Q8 R8 S8 T8
+A9 B9 C9 D9 E9 F9 G9 H9 I9 J9 K9 L9 M9 N9 O9 P9 Q9 R9 S9 T9
+A10 B10 C10 D10 E10 F10 G10 H10 I10 J10 K10 L10 M10 N10 O10 P10 Q10 R10 S10 T10
+A11 B11 C11 D11 E11 F11 G11 H11 I11 J11 K11 L11 M11 N11 O11 P11 Q11 R11 S11 T11
diff --git a/test/server_side_scripting/ext_table_preview/data/test.xls b/test/server_side_scripting/ext_table_preview/data/test.xls
new file mode 100644
index 0000000000000000000000000000000000000000..a355756b9ab72f9035246c5303800a2076d9bfc0
Binary files /dev/null and b/test/server_side_scripting/ext_table_preview/data/test.xls differ
diff --git a/test/server_side_scripting/ext_table_preview/data/test.xlsx b/test/server_side_scripting/ext_table_preview/data/test.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..bc291f1aa86cd6d550320f07a7ce69cf813b8116
Binary files /dev/null and b/test/server_side_scripting/ext_table_preview/data/test.xlsx differ
diff --git a/test/server_side_scripting/ext_table_preview/data/xss_attack.csv b/test/server_side_scripting/ext_table_preview/data/xss_attack.csv
new file mode 100644
index 0000000000000000000000000000000000000000..e7d43505aef42c397f1859805bc87aab8b6da1a2
--- /dev/null
+++ b/test/server_side_scripting/ext_table_preview/data/xss_attack.csv
@@ -0,0 +1,8 @@
+# as it seems all these characters are escaped correctly.
+"","%3C","<","<","<","<","<","<","<","<"
+"<","<","<","<","<","<","<","<","<","<"
+"<","<","<","<","<","<","<","<","<","<"
+"<","<","<","<","<","<","<","<","<","<"
+"<","<","<","<","<","<","<","<","<","<"
+"<","<","<","<","<","<","<","<","<","<"
+"<","<","<","<","<","<","\x3c","\x3C","\u003c","\u003C"
diff --git a/test/server_side_scripting/ext_table_preview/pandas_table_preview.py b/test/server_side_scripting/ext_table_preview/pandas_table_preview.py
new file mode 120000
index 0000000000000000000000000000000000000000..f24b3901ce8610fd02fc28468b747b7171834307
--- /dev/null
+++ b/test/server_side_scripting/ext_table_preview/pandas_table_preview.py
@@ -0,0 +1 @@
+../../../src/server_side_scripting/ext_table_preview/pandas_table_preview.py
\ No newline at end of file
diff --git a/test/server_side_scripting/ext_table_preview/requirements.txt b/test/server_side_scripting/ext_table_preview/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4628529ba9dce50a08d574e21d3b4a71b50af2b1
--- /dev/null
+++ b/test/server_side_scripting/ext_table_preview/requirements.txt
@@ -0,0 +1,3 @@
+caosdb
+caosadvancedtools
+pandas
diff --git a/test/server_side_scripting/ext_table_preview/test_pandas_table_preview.py b/test/server_side_scripting/ext_table_preview/test_pandas_table_preview.py
new file mode 100644
index 0000000000000000000000000000000000000000..00d1c7f38746abe437abc76cd51b29600adcd049
--- /dev/null
+++ b/test/server_side_scripting/ext_table_preview/test_pandas_table_preview.py
@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+#
+# 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
+#
+
+import os
+import unittest
+
+import caosdb as db
+from caosdb.common.models import _parse_single_xml_element
+from lxml import etree
+from pandas_table_preview import (MAXIMUMFILESIZE, create_table_preview,
+ ending_is_valid, read_file, size_is_ok)
+
+
+class PreviewTest(unittest.TestCase):
+ def test_file_ending(self):
+ self.assertFalse(ending_is_valid("/this/is/no/xls.lol"))
+ self.assertFalse(ending_is_valid("xls.lol"))
+ self.assertFalse(ending_is_valid("ag.xls.lol"))
+ assert ending_is_valid("/this/is/a/lol.xls")
+ assert ending_is_valid("/this/is/a/lol.csv")
+ assert ending_is_valid("/this/is/a/lol.cSv")
+ assert ending_is_valid("/this/is/a/lol.CSV")
+ assert ending_is_valid("lol.CSV")
+
+ def test_file_size(self):
+ entity_xml = ('<File id="1234" name="SomeFile" '
+ 'path="/this/path.tsv" size="{size}"></File>')
+ small = _parse_single_xml_element(
+ etree.fromstring(entity_xml.format(size="20000")))
+
+ assert size_is_ok(small)
+ large = _parse_single_xml_element(
+ etree.fromstring(entity_xml.format(
+ size=str(int(MAXIMUMFILESIZE+1)))))
+ assert not size_is_ok(large)
+
+ def test_output(self):
+ files = [os.path.join(os.path.dirname(__file__), "data", f)
+ for f in ["test.csv", "test.tsv", "test.xls", "test.xlsx"]]
+
+ for fi in files:
+ table = read_file(fi, ftype="."+fi.split(".")[-1])
+ searchkey = fi.split(".")[-1]+"file"
+ print(table)
+ assert (table == searchkey).any(axis=None)
+
+ badfiles = [os.path.join(os.path.dirname(__file__), "data", f)
+ for f in ["bad.csv", "bad.tsv", "bad.xls", "bad.xlsx"]]
+
+ for bfi in badfiles:
+ self.assertRaises(ValueError, read_file,
+ bfi, "."+bfi.split(".")[-1])