ome · jburel · Jun 17, 2020 · Jun 3, 2020 · Jun 4, 2020 · Jun 4, 2020
diff --git a/docs/four-images.csv b/docs/four-images.csv
@@ -0,0 +1,6 @@
+# header s,s,d,l,s
+Image Name,Dataset Name,ROI_Area,Channel_Index,Channel_Name
+Centrin_PCNT_Cep215_20110506_Fri-1608_0_SIR_PRJ.dv,dataset01,0.0469,1,DAPI
+Cep215_PCNT_gtub_20110506_Fri-1721_0_SIR_PRJ.dv,dataset01,0.142,2,GFP
+Cep215_PCNT_NEDD1_20110505_Thu-1403_0_SIR_PRJ.dv,dataset01,0.093,3,TRITC
+siControl_N20_Cep215_I_20110411_Mon-1509_0_SIR_PRJ.dv,dataset01,0.429,4,Cy5
diff --git a/docs/images/metadata1.png b/docs/images/metadata1.png
diff --git a/docs/images/metadata2.png b/docs/images/metadata2.png
diff --git a/docs/images/metadata3.png b/docs/images/metadata3.png
diff --git a/docs/images/metadata3a.png b/docs/images/metadata3a.png
diff --git a/docs/images/metadata4.png b/docs/images/metadata4.png
diff --git a/docs/images/metadata5.png b/docs/images/metadata5.png
diff --git a/docs/images/metadata6.png b/docs/images/metadata6.png
diff --git a/docs/images/metadata7.png b/docs/images/metadata7.png
diff --git a/docs/images/metadata8.png b/docs/images/metadata8.png
diff --git a/docs/images/metadata9.png b/docs/images/metadata9.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -8,3 +8,4 @@ Contents:
 
    import
    render
+   metadata
diff --git a/docs/metadata.rst b/docs/metadata.rst
@@ -0,0 +1,165 @@
+Import metadata using the Command Line Interface (CLI)
+======================================================
+
+Description:
+------------
+
+This chapter will show how to import metadata starting from a local CSV file and ending with OMERO.tables on images or Key-Value pairs on images using the Command Line Interface (CLI) and the OMERO server-side scripts.
+
+This action is typically done after a successful import of images.
+
+We will show:
+
+- How to import metadata from local CSV file in a bulk manner and turn them into OMERO.tables on images using CLI
+
+- How to turn the OMERO.tables on images into Key-Value pairs on images in bulk manner using CLI
+
+- How to import metadata from local CSV file and use a server-side script in OMERO to turn these into OMERO.tables on images
+
+- How to construct a simple file to turn the metadata stored in OMERO.tables into Key-Value pairs on images using CLI
+
+**Resources:**
+--------------
+
+-  Documentation:
+
+   -  https://docs.openmicroscopy.org/omero/latest/users/cli/installation.html
+
+   -  `https://docs.openmicroscopy.org/omero/latest/users/cli/index.html <https://docs.openmicroscopy.org/omero/latest/users/cli/index.html>`__
+
+-  Data: example images from
+
+   -  IDR data https://idr.openmicroscopy.org/webclient/?show=project-51
+   -  siRNAi-HeLa dataset from https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/
+
+-  Metadata plugin for OMERO
+
+   - https://pypi.org/project/omero-metadata/
+
+-  Bulkmap config yml files defining the various Key-Value pairs parameters, such as the groups and other parameters.
+
+   - https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-bulkmap-config.yml
+   - :download:`simple-annotation-bulkmap-config.yml <simple-annotation-bulkmap-config.yml>`
+
+-  Annotation CSV files define the content of OMERO.tables for each image.
+
+   - https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-annotation.csv
+   - :download:`simple-annotation.csv <simple-annotation.csv>`
+   - :download:`four-images.csv <four-images.csv>`
+
+Setup:
+------
+
+**Metadata plugin installation**
+
+- Go to the environment where you installed your OMERO.cli as specified under -  https://docs.openmicroscopy.org/omero/latest/users/cli/installation.html.
+
+- Activate the virtual environment.
+
+- Run::
+
+    $ pip install omero-metadata
+
+Step-by-step:
+-------------
+
+#.  On your local machine, open a terminal
+
+#.  If you did not do so already, activate the virtual environment where ``omero-py`` is installed or add it to ``PATH`` e.g.::
+
+    $ export PATH=/opt/omero/server/venv3/bin:$PATH
+
+#.  Download the CSV from https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-annotation.csv if you have access to the idr0021 data https://idr.openmicroscopy.org/webclient/?show=project-51 in your OMERO.server. Alternatively, download :download:`simple-annotation.csv <simple-annotation.csv>`, which will allow you to work with the siRNAi-HeLa dataset, which you can download from https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/.
+
+#.  The variable ``$ID`` below is the ID of the Project, in this example case it is the Project containing the idr0021 study. If you are working with the siRNAi-HeLa data, replace in the following example the "Project" with a "Dataset" and the ``idr0021-experimentA-annotation.csv`` with ``simple-annotation.csv``. To add annotations from a local CSV file to the images in the said Project or Dataset in the form of OMERO.tables, run::
+
+    $ omero metadata populate --report --batch 1000 --file local/path/to/idr0021-experimentA-annotation.csv Project:$ID
+
+#.  Open your browser and login to the OMERO.web. Navigate to the Project or Dataset you just worked with, expand the "Attachments" harmonica in the right-hand pane and verify that a new attachment is on that Project named ``bulk_annotations``.
+
+    |image0|
+
+#.  You can inspect its content by clicking on the "eye" icon |image1| inside the annotation.
+
+#.  Select an image inside the Project/Dataset and expand the "Tables" harmonica in the right-hand pane. These tables contain the appropriate line from the ``bulk_annotations`` attachment you just created for that particular image.
+
+    |image2|
+
+#.  Go back to your terminal. Download the idr0021-experimentA-bulkmap-config.yml file https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-bulkmap-config.yml. Alternatively, in case you are working with the siRNAi-HeLa Dataset, download :download:`simple-annotation-bulkmap-config.yml <simple-annotation-bulkmap-config.yml>`.
+
+#.  If you are working with the IDR data, open the downloaded ``idr0021-experimentA-bulkmap-config.yml`` file in a text editor and delete the ``Advanced options...`` section. Save the file and run::
+
+    $ omero metadata populate --context bulkmap --cfg local/path/to/idr0021-experimentA-bulkmap-config.yml --batch 100 Project:$ID
+
+#.  If you work with the siRNAi-HeLa data, open the downloaded ``simple-annotation-bulkmap-config.yml`` and study the comments in the file itself, which will give you hints about how to manipulate the file to fit your particular needs with respect to the resulting Key-Value pairs layout. Make your changes (no need to change anything if you do not want), save the file locally and run::
+
+    $ omero metadata populate --context bulkmap --cfg local/path/to/simple-annotation-bulkmap-config.yml --batch 100 Dataset:$ID
+
+#.  Go to your browser and OMERO.web, select the images in the Project or Dataset you targeted and verify that they have now new Key-Value pairs displayed in the right-hand pane.
+
+    |image3a|
+
+#.  Still in OMERO.web, create a new Dataset and copy into it four images, preferably images which have neither OMERO.tables on them nor any Key-Value pairs attached. Note the names of the images you are copying in.
+
+    |image4|
+
+#.  Go to the https://pypi.org/project/omero-metadata/ and find the section named ``populate``. Study the ``project.csv``. You can either take the ``project.csv`` file from there, or more conveniently, you can download directly its copy :download:`four-images.csv <four-images.csv>`. Open the CSV in Excel and edit the names of the images in the first column to match the names of the images you copied into your Dataset in the previous step. Also, edit the name of the Dataset in the second column to match the name of your Dataset in OMERO.web. Save the file locally as CSV.
+
+#.  In your OMERO.web, upload the CSV you just saved and attach it onto the Dataset you created previously.
+
+    |image5|
+
+#.  Select the Dataset you created and attached to it the CSV. Find the script icon |image6| above the central pane, expand it and find the ``Import scripts`` section. In there, select the ``Populate metadata`` script.
+
+    |image7| 
+
+#.  Run the script.
+
+#.  Click again onto the Dataset in the left-hand pane to refresh and observe that there is a new Attachment in the right hand pane under "Attachments" harmonica. 
+
+    |image8|
+
+#.  Click on single images inside the Dataset and observe that in the "Tables" harmonica in the right-hand pane there are new values coming originally from your edited CSV.
+
+    |image9|
+
+
+.. |image0| image:: images/metadata1.png
+   :width: 4in
+   :height: 1in
+
+.. |image1| image:: images/metadata2.png
+   :width: 0.35in
+   :height: 0.3in
+
+.. |image2| image:: images/metadata3.png
+   :width: 4in
+   :height: 3.5in
+
+.. |image3a| image:: images/metadata3a.png
+   :width: 4in
+   :height: 3.3in
+
+.. |image4| image:: images/metadata4.png
+   :width: 5in
+   :height: 1.5in
+
+.. |image5| image:: images/metadata5.png
+   :width: 4in
+   :height: 1in
+
+.. |image6| image:: images/metadata6.png
+   :width: 0.35in
+   :height: 0.3in
+
+.. |image7| image:: images/metadata7.png
+   :width: 2in
+   :height: 0.7in
+
+.. |image8| image:: images/metadata8.png
+   :width: 4in
+   :height: 1.3in
+
+.. |image9| image:: images/metadata9.png
+   :width: 4in
+   :height: 2in
diff --git a/docs/simple-annotation-bulkmap-config.yml b/docs/simple-annotation-bulkmap-config.yml
@@ -0,0 +1,135 @@
+---
+name: simple-annotation
+version: 1
+
+defaults:
+    # Should the column be processed when creating bulk-annotations (yes/no)
+    include: no
+    # Columns type of the bulk-annotations column
+    type: string
+
+    # If non-empty a string used to separate multiple fields in a column
+    # White space will be stripped
+    split:
+    # Should this column be included in the clients (yes/no)
+    includeclient: yes
+    # Should this column be visible in the clients, if no the column should be
+    # hidden in the client but will still be indexed by the searcher (yes/no)
+    visible: yes
+    # Should empty values be omitted from the client display
+    omitempty: yes
+
+# This is the list of column names taken from simple-annotation.csv:
+#
+#   Dataset Name
+#   Image Name
+#   Characteristics [Organism]
+#   Characteristics [Cell Line]
+#   Characteristics [Cell Cycle Phase]
+#   Experimental Condition [Antibody Target]
+#   Comment [Targeted Protein]
+#   Comment [Gene Identifier]
+#   Comment [Gene Symbol]
+#   Comment [Gene Symbol Synonyms]
+#   Has Phenotype
+#   Phenotype Annotation Level
+#   Phenotype 1
+#   Phenotype 1 Term Name
+#   Phenotype 1 Term Accession
+#
+# You can choose which of these appear in the default map annotations.
+# In the defaults section of this configuration "include" is set to
+# "no" which means if you do not add a column it won't be displayed in
+# the map annotations.
+
+columns:
+
+  ######################################################################
+  # These columns will appear in the default map annotation namespace
+  # openmicroscopy.org/omero/bulk_annotations
+  ######################################################################
+  - name: Dataset Name
+    include: yes
+  - name: Image Name
+    include: yes
+  - name: Characteristics [Cell Cycle Phase]
+    # "clientname" can be used to override the column name in the
+    # key of the map-annotation key-value. The default is to use
+    # the column name
+    clientname: Cell Cycle Phase
+    include: yes
+  - name: Experimental Condition [Antibody Target]
+    clientname: Antibody Target
+    include: yes
+  - name: Comment [Targeted Protein]
+    clientname: Targeted Protein
+    include: yes
+  - name: Has Phenotype
+    include: yes
+  - name: Phenotype Annotation Level
+    include: yes
+
+  ######################################################################
+  # The columns in these groups will appear as separate namespaced map-
+  # annotations. Mapr can be configured to restrict a query to one of
+  # these namespaces.
+  ######################################################################
+
+  - group:
+      namespace: openmicroscopy.org/mapr/organism
+      columns:
+      - name: Characteristics [Organism]
+        clientname: Organism
+        include: yes
+
+  - group:
+      namespace: openmicroscopy.org/mapr/cell_line
+      columns:
+      - name: Characteristics [Cell Line]
+        clientname: Cell Line
+        include: yes
+
+  - group:
+      namespace: openmicroscopy.org/mapr/gene
+      columns:
+      # If mapr finds two sets of key-value pairs with names
+      # "Column Name" and "Column Name URL" it will automatically
+      # combine them into one hyperlinked value
+      # This is why "Comment [Gene Identifier]" is listed twice, the
+      # first indicates the text, the second indicates the hyperlink
+      - name: Comment [Gene Identifier]
+        clientname: Gene Identifier
+        include: yes
+        omitempty: no
+      - name: Comment [Gene Identifier]
+        clientname: Gene Identifier URL
+        # "clientvalue" can be used to override the value of the map-
+        # annotation key-value. The "value" is substituted using
+        # Jinja2 templates.
+        clientvalue: http://www.ensembl.org/id/{{ value|urlencode }}
+        include: yes
+      - name: Comment [Gene Symbol]
+        clientname: Gene Symbol
+        include: yes
+        omitempty: no
+      - name: Comment [Gene Symbol Synonyms]
+        clientname: Gene Symbol Synonyms
+        include: yes
+        omitempty: no
+
+  - group:
+      namespace: openmicroscopy.org/mapr/phenotype
+      columns:
+      - name: Phenotype 1
+        clientname: Phenotype
+        include: yes
+      - name: Phenotype 1 Term Name
+        clientname: Phenotype Term Name
+        include: yes
+      - name: Phenotype 1 Term Accession
+        clientname: Phenotype Term Accession
+        include: yes
+      - name: Phenotype 1 Term Accession
+        clientname: Phenotype Term Accession URL
+        clientvalue: http://www.ebi.ac.uk/cmpo/{{ value|urlencode }}
+        include: yes