OMERO Docker compose example
License: BSD 2-Clause "Simplified" License
This is an example of running OMERO.server and OMERO.web in Docker.
OMERO.server is listening on the standard OMERO ports 4063 and 4064.
OMERO.web is listening on port 4080 (http://localhost:4080/).
Log in as user root password omero.
The initial password can be changed in docker-compose.yml.
First pull the latest major versions of the containers:
docker compose pull
Then start the containers:
docker compose up -d
docker compose logs -f
For more configuration options see:
Hi,
A user pointed out that the export options are disabled. I then stumbled upon #6 but following the instructions there isn't working for me:
Dockerfile:
FROM openmicroscopy/omero-server:5
USER root
RUN wget https://raw.githubusercontent.com/ome/omero-figure/master/omero_figure/scripts/omero/figure_scripts/F
igure_To_Pdf.py -O /opt/omero/server/OMERO.server/lib/scripts/omero/figure_scripts/Figure_To_Pdf.py
RUN /opt/omero/server/venv3/bin/pip install reportlab markdown
USER omero-server
Then building via: docker build -t local/omero-server:5 .
Sending build context to Docker daemon 6.144kB
Step 1/5 : FROM openmicroscopy/omero-server:5
---> e4c5633c6b61
Step 2/5 : USER root
---> Using cache
---> 5b7b9b9f76b2
Step 3/5 : RUN wget https://raw.githubusercontent.com/ome/omero-figure/master/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py -O /opt/omero/server/OMERO.server/lib/scripts/omero/figure_scripts/Figure_To_Pdf.py
---> Using cache
---> 93b1d44b4fff
Step 4/5 : RUN /opt/omero/server/venv3/bin/pip install reportlab markdown
---> Running in ab68b49f8f84
Collecting reportlab
Downloading reportlab-3.6.8.tar.gz (4.5 MB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting markdown
Downloading Markdown-3.3.7-py3-none-any.whl (97 kB)
Requirement already satisfied: pillow>=4.0.0 in /opt/omero/server/venv3/lib/python3.6/site-packages (from reportlab) (8.4.0)
Collecting importlib-metadata>=4.4
Downloading importlib_metadata-4.8.3-py3-none-any.whl (17 kB)
Collecting zipp>=0.5
Downloading zipp-3.6.0-py3-none-any.whl (5.3 kB)
Collecting typing-extensions>=3.6.4
Downloading typing_extensions-4.1.1-py3-none-any.whl (26 kB)
Using legacy 'setup.py install' for reportlab, since package 'wheel' is not installed.
Installing collected packages: zipp, typing-extensions, importlib-metadata, reportlab, markdown
Running setup.py install for reportlab: started
Running setup.py install for reportlab: finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /opt/omero/server/venv3/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2dvy4iwb/reportlab_64c92fbac7eb4e69b7d4527d09fbfedd/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2dvy4iwb/reportlab_64c92fbac7eb4e69b7d4527d09fbfedd/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-vzvu9yws/install-record.txt --single-version-externally-managed --compile --install-headers /opt/omero/server/venv3/include/site/python3.6/reportlab
cwd: /tmp/pip-install-2dvy4iwb/reportlab_64c92fbac7eb4e69b7d4527d09fbfedd/
Complete output (232 lines):
##### setup-python-3.6.8-linux-x86_64: ================================================
##### setup-python-3.6.8-linux-x86_64: Attempting build of _rl_accel
##### setup-python-3.6.8-linux-x86_64: extensions from 'src/rl_addons/rl_accel'
##### setup-python-3.6.8-linux-x86_64: ================================================
##### setup-python-3.6.8-linux-x86_64: ===================================================
##### setup-python-3.6.8-linux-x86_64: Attempting build of _renderPM
##### setup-python-3.6.8-linux-x86_64: extensions from 'src/rl_addons/renderPM'
##### setup-python-3.6.8-linux-x86_64: ===================================================
##### setup-python-3.6.8-linux-x86_64: will use package libart 2.3.21
##### setup-python-3.6.8-linux-x86_64: # installing without freetype no ttf, sorry!
##### setup-python-3.6.8-linux-x86_64: # You need to install a static library version of the freetype2 software
##### setup-python-3.6.8-linux-x86_64: # If you need truetype support in renderPM
##### setup-python-3.6.8-linux-x86_64: # You may need to edit setup.cfg (win32)
##### setup-python-3.6.8-linux-x86_64: # or edit this file to access the library if it is installed
##### setup-python-3.6.8-linux-x86_64: ################################################
##### setup-python-3.6.8-linux-x86_64: Downloading standard T1 font curves
##### setup-python-3.6.8-linux-x86_64: Finished download of standard T1 font curves
##### setup-python-3.6.8-linux-x86_64: The _glyphlist module already exists
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/reportlab
copying src/reportlab/__init__.py -> build/lib.linux-x86_64-3.6/reportlab
copying src/reportlab/rl_config.py -> build/lib.linux-x86_64-3.6/reportlab
copying src/reportlab/rl_settings.py -> build/lib.linux-x86_64-3.6/reportlab
creating build/lib.linux-x86_64-3.6/reportlab/graphics
creating build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/__init__.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/areas.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/axes.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/barcharts.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/dotbox.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/doughnut.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/legends.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/linecharts.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/lineplots.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/markers.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/piecharts.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/slidebox.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/spider.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/textlabels.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/utils.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
copying src/reportlab/graphics/charts/utils3d.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/charts
creating build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/__init__.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/bubble.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/clustered_bar.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/clustered_column.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/excelcolors.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/exploded_pie.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/filled_radar.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/line_chart.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/linechart_with_markers.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/radar.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/runall.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/scatter.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/scatter_lines.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/scatter_lines_markers.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/simple_pie.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/stacked_bar.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
copying src/reportlab/graphics/samples/stacked_column.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/samples
creating build/lib.linux-x86_64-3.6/reportlab/graphics/widgets
copying src/reportlab/graphics/widgets/__init__.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/widgets
copying src/reportlab/graphics/widgets/adjustableArrow.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/widgets
copying src/reportlab/graphics/widgets/eventcal.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/widgets
copying src/reportlab/graphics/widgets/flags.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/widgets
copying src/reportlab/graphics/widgets/grids.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/widgets
copying src/reportlab/graphics/widgets/markers.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/widgets
copying src/reportlab/graphics/widgets/signsandsymbols.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/widgets
copying src/reportlab/graphics/widgets/table.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/widgets
creating build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/__init__.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/code128.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/code39.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/code93.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/common.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/dmtx.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/eanbc.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/ecc200datamatrix.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/fourstate.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/lto.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/qr.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/qrencoder.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/test.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/usps.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/usps4s.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/barcode/widgets.py -> build/lib.linux-x86_64-3.6/reportlab/graphics/barcode
copying src/reportlab/graphics/__init__.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/renderPDF.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/renderPM.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/renderPS.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/renderSVG.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/renderbase.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/shapes.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/testdrawings.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/testshapes.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/transform.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/utils.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
copying src/reportlab/graphics/widgetbase.py -> build/lib.linux-x86_64-3.6/reportlab/graphics
creating build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/PyFontify.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/__init__.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/abag.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/arciv.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/attrmap.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/boxstuff.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/codecharts.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/colors.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/corp.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/enums.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/extformat.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/fontfinder.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/fonts.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/formatters.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/geomutils.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/logger.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/normalDate.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/pagesizes.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/pdfencrypt.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/pygments2xpre.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/randomtext.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/rl_accel.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/rl_safe_eval.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/rltempfile.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/rparsexml.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/sequencer.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/styles.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/testutils.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/textsplit.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/units.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/utils.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/validators.py -> build/lib.linux-x86_64-3.6/reportlab/lib
copying src/reportlab/lib/yaml.py -> build/lib.linux-x86_64-3.6/reportlab/lib
creating build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/__init__.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_can_cmap_data.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_cidfontdata.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_enc_macexpert.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_enc_macroman.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_enc_pdfdoc.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_enc_standard.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_enc_symbol.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_enc_winansi.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_enc_zapfdingbats.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_courier.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_courierbold.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_courierboldoblique.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_courieroblique.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_helvetica.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_helveticabold.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_helveticaboldoblique.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_helveticaoblique.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_symbol.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_timesbold.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_timesbolditalic.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_timesitalic.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_timesroman.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_fontdata_widths_zapfdingbats.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/_glyphlist.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/acroform.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/cidfonts.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/pdfdoc.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/pdfform.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/pdfmetrics.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/pdfpattern.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/pdfutils.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/rl_codecs.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
copying src/reportlab/pdfbase/ttfonts.py -> build/lib.linux-x86_64-3.6/reportlab/pdfbase
creating build/lib.linux-x86_64-3.6/reportlab/pdfgen
copying src/reportlab/pdfgen/__init__.py -> build/lib.linux-x86_64-3.6/reportlab/pdfgen
copying src/reportlab/pdfgen/canvas.py -> build/lib.linux-x86_64-3.6/reportlab/pdfgen
copying src/reportlab/pdfgen/pathobject.py -> build/lib.linux-x86_64-3.6/reportlab/pdfgen
copying src/reportlab/pdfgen/pdfgeom.py -> build/lib.linux-x86_64-3.6/reportlab/pdfgen
copying src/reportlab/pdfgen/pdfimages.py -> build/lib.linux-x86_64-3.6/reportlab/pdfgen
copying src/reportlab/pdfgen/textobject.py -> build/lib.linux-x86_64-3.6/reportlab/pdfgen
creating build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/__init__.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/doctemplate.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/figures.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/flowables.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/frames.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/multicol.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/para.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/paragraph.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/paraparser.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/tableofcontents.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/tables.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
copying src/reportlab/platypus/xpreformatted.py -> build/lib.linux-x86_64-3.6/reportlab/platypus
creating build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/00readme.txt -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/bitstream-vera-license.txt -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/DarkGarden-changelog.txt -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/DarkGarden-copying-gpl.txt -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/DarkGarden-copying.txt -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/DarkGarden-readme.txt -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/DarkGarden.sfd -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/DarkGardenMK.afm -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/DarkGardenMK.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/Vera.ttf -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/VeraBd.ttf -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/VeraBI.ttf -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/VeraIt.ttf -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/_abi____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/_ab_____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/_ai_____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/_a______.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/cobo____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/cob_____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/com_____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/coo_____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/_ebi____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/_eb_____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/_ei_____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/_er_____.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/sy______.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/zd______.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/zx______.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/zy______.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/callig15.pfb -> build/lib.linux-x86_64-3.6/reportlab/fonts
copying src/reportlab/fonts/callig15.afm -> build/lib.linux-x86_64-3.6/reportlab/fonts
running build_ext
building 'reportlab.lib._rl_accel' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/src
creating build/temp.linux-x86_64-3.6/src/rl_addons
creating build/temp.linux-x86_64-3.6/src/rl_addons/rl_accel
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/opt/omero/server/venv3/include -I/usr/include/python3.6m -c src/rl_addons/rl_accel/_rl_accel.c -o build/temp.linux-x86_64-3.6/src/rl_addons/rl_accel/_rl_accel.o
unable to execute 'gcc': No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/omero/server/venv3/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2dvy4iwb/reportlab_64c92fbac7eb4e69b7d4527d09fbfedd/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2dvy4iwb/reportlab_64c92fbac7eb4e69b7d4527d09fbfedd/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-vzvu9yws/install-record.txt --single-version-externally-managed --compile --install-headers /opt/omero/server/venv3/include/site/python3.6/reportlab Check the logs for full command output.
The command '/bin/sh -c /opt/omero/server/venv3/bin/pip install reportlab markdown' returned a non-zero code: 1
I'm not a python dev so I can't suss out what it's not happy about?
Hi
Thanks for making it possible to use OMERO via docker. It has simplified the process a lot.
I can get the omero server running on a virtual machine using:
docker-compose up -d
docker-compose logs -f
I can also login to OMERO.web and access the webclient.
I was running out of storage as the server has limited space. I have attached an external volume and mounted it. I would like to change the OMERO data directory to this external volume. This is under the assumption that all the image data will be stored in OMERO data directory.
If I've used the above 2 commands to setup the server, how do I access the configuration options within docker to change the data directory? Also, do I have to stop it, set it up and restart it? I only have a basic understanding of docker.
Thanks a lot.
Pradeep
Hello,
I have uploaded the below given dataset into my container based omero server and could visualize and properly work with it via omero-web client
https://downloads.openmicroscopy.org/images/Leica-SCN/openslide/Leica-1/Leica-1.scn
The problem occurs when I try to download this data or render it using omero-py based BlitzGateway functions (gateway::renderImage), I get the following exception:
_WARNING:omero.gateway:InternalException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <f725d875-4ee1-49d3-8bff-9a50db95126aomero.api.RenderingEngine> renderCompressed((object #0 (::omero::romio::PlaneDef)
{
slice = 0
x = 0
y = 0
z = 0
t = 0
region = <nil>
stride = 0
}, <ServiceOptsDict: {'omero.client.uuid': 'f9272c8a-7a4a-40d1-bd88-0ec44be2643b', 'omero.event': 'Internal', 'omero.session.uuid': 'e38406ac-84c1-4fcb-9c4c-69b138cbc4fa'}>), {})
Traceback (most recent call last):
File "C:\Python38\lib\site-packages\omero\gateway\__init__.py", line 4793, in __call__
return self.f(*args, **kwargs)
File "C:\Python38\lib\site-packages\omero_api_RenderingEngine_ice.py", line 913, in renderCompressed
return _M_omero.api.RenderingEngine._op_renderCompressed.invoke(self, ((_def, ), _ctx))
omero.InternalException: exception ::omero::InternalException
{
serverStackTrace = ome.conditions.InternalException: Wrapped Exception: (java.lang.OutOfMemoryError):
Java heap space
at ome.io.bioformats.BfPixelBuffer.getPlane(BfPixelBuffer.java:208)
at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:208)
at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:100)
at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:231)
at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:328)
at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:292)
at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:558)
at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:512)
at ome.services.RenderingBean.renderCompressed(RenderingBean.java:542)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy106.renderCompressed(Unknown Source)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
serverExceptionClass = ome.conditions.InternalException
message = Wrapped Exception: (java.lang.OutOfMemoryError):
Java heap space
}_
I can see the same error been thrown inside the server side /opt/omero/server/OMERO.server/var/log/Blitz-0.log also
..................
_2021-03-29 13:22:03,952 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Meth: interface omeis.providers.re.RenderingEngine.renderCompressed
2021-03-29 13:22:03,952 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Args: [Type: XY, z=0, t=0, renderShapes=false, shapeIds=[]]
2021-03-29 13:22:03,953 INFO [ omeis.providers.re.Renderer] (l.Server-3) Using: 'omeis.providers.re.HSBStrategy' rendering strategy.
2021-03-29 13:24:00,001 INFO [ ome.services.blitz.fire.SessionManagerI] (1-thread-4) Performing requestHeartbeats
2021-03-29 13:26:34,770 INFO [ org.perf4j.TimingLogger] (l.Server-3) start[1617024123952] time[270818] tag[omero.call.exception]
2021-03-29 13:26:34,774 ERROR [ ome.services.util.ServiceHandler] (l.Server-3) java.lang.Error: Wrapped Exception: (java.lang.OutOfMemoryError):
Java heap space
java.lang.OutOfMemoryError: Java heap space
at ome.io.bioformats.BfPixelBuffer.getPlane(BfPixelBuffer.java:208) ~[omero-romio.jar:5.6.2]
at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:208) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:100) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:231) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:328) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:292) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:558) ~[omero-renderer.jar:5.5.7]
at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:512) ~[omero-server.jar:5.6.1]
at ome.services.RenderingBean.renderCompressed(RenderingBean.java:542) ~[omero-server.jar:5.6.1]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:na]
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
at java.base/java.lang.reflect.Method.invoke(Method.java:566) ~[na:na]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) ~[spring-aop.jar:4.3.14.RELEASE]
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) ~[omero-server.jar:5.6.1]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) ~[spring-aop.jar:4.3.14.RELEASE]
at com.sun.proxy.$Proxy106.renderCompressed(Unknown Source) ~[na:na]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:na]
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
at java.base/java.lang.reflect.Method.invoke(Method.java:566) ~[na:na]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) ~[spring-aop.jar:4.3.14.RELEASE]
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) ~[omero-server.jar:5.6.1]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop.jar:4.3.14.RELEASE]
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) ~[omero-blitz.jar:5.5.8]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) ~[spring-aop.jar:4.3.14.RELEASE]
2021-03-29 13:26:34,775 WARN [ ome.services.util.ServiceHandler] (l.Server-3) Unknown exception thrown.
java.lang.OutOfMemoryError: Java heap space
at ome.io.bioformats.BfPixelBuffer.getPlane(BfPixelBuffer.java:208) ~[omero-romio.jar:5.6.2]
at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:208) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:100) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:231) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:328) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:292) ~[omero-renderer.jar:5.5.7]
at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:558) ~[omero-renderer.jar:5.5.7]
at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:512) ~[omero-server.jar:5.6.1]
at ome.services.RenderingBean.renderCompressed(RenderingBean.java:542) ~[omero-server.jar:5.6.1]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:na]
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
at java.base/java.lang.reflect.Method.invoke(Method.java:566) ~[na:na]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) ~[spring-aop.jar:4.3.14.RELEASE]
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) ~[omero-server.jar:5.6.1]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) ~[spring-aop.jar:4.3.14.RELEASE]
at com.sun.proxy.$Proxy106.renderCompressed(Unknown Source) ~[na:na]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:na]
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
at java.base/java.lang.reflect.Method.invoke(Method.java:566) ~[na:na]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) ~[spring-aop.jar:4.3.14.RELEASE]
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) ~[omero-server.jar:5.6.1]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop.jar:4.3.14.RELEASE]
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) ~[omero-blitz.jar:5.5.8]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop.jar:4.3.14.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) ~[spring-aop.jar:4.3.14.RELEASE]
2021-03-29 13:26:34,776 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Excp: java.lang.OutOfMemoryError: Java heap space
2021-03-29 13:26:34,776 ERROR [ ome.services.util.ServiceHandler] (l.Server-3) Method interface omeis.providers.re.RenderingEngine.renderCompressed invocation took 270818
2021-03-29 13:27:00,001 INFO [ ome.services.blitz.fire.SessionManagerI] (1-thread-5) Performing requestHeartbeats_
I think, I have to adjust the heapsize of server side JVM, which all config has to be adapted? Would it be better to have enough size defined for the docker images already?
Also could you let me know which is the python gateway function to be used to download the 'Leica-1.scn' image locally to my directory from omero-server?
See feedback on https://forum.image.sc/t/enable-fpbioimage-in-omeroweb-docker/39361
Something like the equivalent of -v ./web/50-config-extra-apps.omero:/opt/omero/web/config/50-config-extra-apps.omero to provide an example of configuring the optional web apps.
Hello, could you please let me know where inside the omero-server container will be the log files be generated?
e.g. I attach to the server container using command: docker exec -it $(docker ps -aqf "name=dockerexampleomeromaster_omeroserver_1") /bin/bash
I see there are some files are written here: /OMERO/ManagedRepository/root_0/
Is this the right location or do you have a different location for the log files,
Specifically I am trying to use python omero-py (BlitzGateway) client in order to retrieve the image data from server.
................
from omero.gateway import BlitzGateway
................
For such data retrievals, where are the respective logs generated in omero-server container (name=dockerexampleomeromaster_omeroserver_1)?
After following the README, I have a working OMERO.web but cannot log in to OMERO.server as it reports server not responding.
My admin diagnostics say
omero admin diagnostics
================================================================================
OMERO Diagnostics (admin) 5.11.2
================================================================================
Commands: java -version 11.0.15 (/usr/bin/java)
Commands: python -V 3.6.8 (/opt/omero/server/venv3/bin/python -- 2 others)
Commands: icegridnode --version 3.6.5 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.5 (/usr/bin/icegridadmin)
Commands: psql --version 11.16 (/usr/bin/psql)
Commands: openssl version 1.0.2 (/usr/bin/openssl)
Server: icegridnode running
Server: Blitz-0 activation timed out (pid = 1144, enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 1027, enabled)
Server: Indexer-0 active (pid = 1039, enabled)
Server: MonitorServer active (pid = 1030, enabled)
Server: OMERO.Glacier2 active (pid = 1033, enabled)
Server: OMERO.IceStorm active (pid = 1135, enabled)
Server: PixelData-0 active (pid = 1051, enabled)
Server: Processor-0 activating (enabled)
Server: Tables-0 activating (enabled)
Server: TestDropBox inactive (enabled)
Log dir: /opt/omero/server/OMERO.server/var/log exists
Log files: Blitz-0.log 1.4 KB errors=0 warnings=2
Log files: DropBox.log 4.3 KB errors=4 warnings=6
Log files: FileServer.log 114 B
Log files: Indexer-0.log 2.9 KB errors=0 warnings=2
Log files: MonitorServer.log 117 B
Log files: PixelData-0.log 3.5 KB errors=0 warnings=2
Log files: Processor-0.log 28.1 KB errors=5 warnings=20
Log files: Tables-0.log 29.4 KB errors=5 warnings=20
Log files: TestDropBox.log n/a
Log files: master.err 2.7 KB errors=1 warnings=2
Log files: master.out empty
Log files: Total size 0.07 MB
Environment:OMERO_HOME=(unset)
Environment:OMERODIR=/opt/omero/server/OMERO.server
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/opt/omero/server/venv3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/OMERO' Exists? True Is writable? True
OMERO temp dir:'/opt/omero/server/omero/tmp' Exists? True Is writable? True (Size: 0)
JVM settings: Blitz-${index} -Xmx1234m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx823m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx1234m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx823m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
Jar: lib/server/formats-api.jar Bio-Formats API 6.10.0 31 May 2022 f8b46c2458c43cffdf5bc67cc4bf9dfc6e93167b
Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 6.10.0 31 May 2022 f8b46c2458c43cffdf5bc67cc4bf9dfc6e93167b
Jar: lib/server/formats-gpl.jar Bio-Formats library 6.10.0 31 May 2022 f8b46c2458c43cffdf5bc67cc4bf9dfc6e93167b
Jar: lib/server/ome-codecs.jar OME Codecs 0.3.2 19 May 2022 5aa67ccc5d04208d5ea78a1f58d49716130f89a6
Jar: lib/server/ome-common.jar OME Common Java 6.0.9 19 May 2022 1a61b42905228d596d80107e7a02853e77e0d7a7
Jar: lib/server/ome-jai.jar OME JAI 0.1.3 3 August 2018 489959cb7d24c279249bc08181aa9f734158ca4e
Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.2 7 August 2018 68ffca2a95750cbb96f0d11785851aa4a554c0a4
Jar: lib/server/ome-poi.jar OME POI 5.3.6 19 May 2022 bb8f9406af613d4d1b088149d979f994f7aa1650
Jar: lib/server/ome-xml.jar OME XML library 6.3.1 19 May 2022 f2abe457b296d37c8d6a5a6774ebcf0017dc51a8
Jar: lib/server/omero-blitz.jar jar 5.5.12
Jar: lib/server/omero-common.jar jar 5.5.10
Jar: lib/server/omero-gateway.jar jar 5.6.10
Jar: lib/server/omero-model.jar jar 5.6.7
Jar: lib/server/omero-renderer.jar jar 5.5.10
Jar: lib/server/omero-romio.jar jar 5.7.0
Jar: lib/server/omero-server.jar jar 5.6.4
My master.err
cat master.err
OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by javassist.util.proxy.SecurityActions (file:/opt/omero/server/OMERO.server-5.6.5-ice36-b233/lib/server/javassist.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of javassist.util.proxy.SecurityActions
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by javassist.util.proxy.SecurityActions (file:/opt/omero/server/OMERO.server-5.6.5-ice36-b233/lib/server/javassist.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of javassist.util.proxy.SecurityActions
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by javassist.util.proxy.SecurityActions (file:/opt/omero/server/OMERO.server-5.6.5-ice36-b233/lib/server/javassist.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of javassist.util.proxy.SecurityActions
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
-! 09/22/22 14:40:07.263 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1637: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters'
-! 09/22/22 14:40:07.273 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1637: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters'
!! 09/22/22 14:40:22.772 error: communicator not destroyed during global destruction.!! 09/22/22 14:40:46.682 error: communicator not destroyed during global destruction
My Blitz log is very short
2022-09-22 14:39:23,620 INFO [ ome.services.blitz.Entry] ( main) Creating OMERO.blitz. Please wait...
2022-09-22 14:39:34,078 INFO [ ome.services.util.ReadOnlyStatus] ( main) read-only status: db=false, repo=false
2022-09-22 14:39:34,549 WARN [ omero.security] ( main) trustStore property is empty, not setting
2022-09-22 14:39:34,556 WARN [ omero.security] ( main) trustStorePassword property is empty, not setting
2022-09-22 14:39:34,605 INFO [.s.ShutdownSafeEhcacheManagerFactoryBean] ( main) Initializing EhCache CacheManager
2022-09-22 14:39:35,829 INFO [ ome.services.util.DBPatchCheck] ( main) Verified database patch: OMERO5.4__0
2022-09-22 14:39:36,170 INFO [ ome.services.util.DBUserCheck] ( main) User root.id = 0
2022-09-22 14:39:36,171 INFO [ ome.services.util.DBUserCheck] ( main) User guest.id = 1
2022-09-22 14:39:36,171 INFO [ ome.services.util.DBUserCheck] ( main) Group system.id = 0
2022-09-22 14:39:36,171 INFO [ ome.services.util.DBUserCheck] ( main) Group user.id = 1
2022-09-22 14:39:36,172 INFO [ ome.services.util.DBUserCheck] ( main) Group guest.id = 2
2022-09-22 14:39:39,721 INFO [ ome.services.fulltext.FullTextAnalyzer] ( main) Initialized FullTextAnalyzer
This works perfectly fine on Mac Book Pro , but on M1 I have probs as above.
Any ideas please @joshmoore @sbesson ?
Hello,
When I try to log in after a fresh installation, I get the following error:
Thank you for you help,
Gabriel
Omero server is failing? I did a git clone and then from the docker-example-omero directory ran
docker-compose up -d
docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
5194f138bba9 openmicroscopy/omero-web-standalone:5.5 "/usr/local/bin/entr…" 20 seconds ago Up 18 seconds 0.0.0.0:4080->4080/tcp docker-example-omero_omeroweb_1
c67df2fb8c9b postgres:10 "docker-entrypoint.s…" 20 seconds ago Up 18 seconds 5432/tcp docker-example-omero_database_1
baeb73e1a25f openmicroscopy/omero-server:5.5 "/usr/local/bin/entr…" 20 seconds ago Exited (1) 12 seconds ago docker-example-omero_omeroserver_1
docker logs -t docker-example-omero_omeroserver_1
2019-06-25T23:58:27.882034265Z CREATE FUNCTION
2019-06-25T23:58:27.882036244Z CREATE TRIGGER
2019-06-25T23:58:27.882038199Z ALTER TABLE
2019-06-25T23:58:27.882040138Z ALTER TABLE
2019-06-25T23:58:27.882042092Z
2019-06-25T23:58:27.882044581Z stderr: psql:omero-20190625-235824-637626.sql:2842: NOTICE: identifier "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapco"
2019-06-25T23:58:27.882048220Z psql:omero-20190625-235824-637626.sql:4712: NOTICE: identifier "fklogicalchannel_photometricinterpretation_photometricinterpretation" will be truncated to "fklogicalchannel_photometricinterpretation_photometricinterpret"
2019-06-25T23:58:27.882050571Z psql:omero-20190625-235824-637626.sql:5697: NOTICE: identifier "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcont"
2019-06-25T23:58:27.882052861Z psql:omero-20190625-235824-637626.sql:9478: ERROR: relation "i_logicalchannel_emissionwave" already exists
2019-06-25T23:58:27.882054960Z
I am on macOS Mojave, Docker Desktop Community 2..0.0.3 (31259)
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