# HG changeset patch
# User lldelisle
# Date 1716299408 0
# Node ID d041125db5230bd1b567255e4ca4d42589c327d6

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images commit b97db80733147cc920de70c59e1d283ef11fa879

diff -r 000000000000 -r d041125db523 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue May 21 13:50:08 2024 +0000
@@ -0,0 +1,20 @@
+# OMERO get full images
+
+## Set up user credentials on Galaxy to connect to other omero instance
+
+To enable users to set their credentials for this tool,
+make sure the file `config/user_preferences_extra.yml` has the following section:
+
+```
+    omero_account:
+        description: Your OMERO instance connection credentials
+        inputs:
+            - name: username
+              label: Username
+              type: text
+              required: False
+            - name: password
+              label: Password
+              type:  password
+              required: False
+```
diff -r 000000000000 -r d041125db523 omero_get_full_images.groovy
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_get_full_images.groovy	Tue May 21 13:50:08 2024 +0000
@@ -0,0 +1,284 @@
+// This macro was written by
+// Lucille Delisle using templates available at
+// https://github.com/BIOP/OMERO-scripts/tree/025047955b5c1265e1a93b259c1de4600d00f107/Fiji
+
+// Last modification: 2024-05-21
+
+// The input image(s) may have multiple time stacks
+// and multiple channels
+
+// This macro works both in headless
+// or GUI
+
+// In both modes,
+// Images of all omero object are written to the output directory
+
+import fr.igred.omero.Client
+import fr.igred.omero.repository.DatasetWrapper
+import fr.igred.omero.repository.GenericRepositoryObjectWrapper
+import fr.igred.omero.repository.ImageWrapper
+import fr.igred.omero.repository.PlateWrapper
+import fr.igred.omero.repository.WellWrapper
+
+import ij.ImagePlus
+import ij.IJ
+import ij.io.FileSaver
+
+import java.awt.GraphicsEnvironment
+import java.io.File
+import java.util.concurrent.TimeUnit
+
+import org.apache.commons.io.FileUtils
+
+
+// Global variable with times in minutes to wait:
+waiting_times = [0, 10, 60, 360, 600]
+
+def robustlyGetAll(GenericRepositoryObjectWrapper obj_wrp, String object_type, Client user_client) {
+    for (waiting_time in waiting_times) {
+        try {
+            wrappers = null
+            switch (object_type) {
+                case "image":
+                    wrappers = obj_wrp.getImages(user_client)
+                    break
+                case "dataset":
+                    wrappers = obj_wrp.getDatasets(user_client)
+                    break
+                case "well":
+                    wrappers = obj_wrp.getWells(user_client)
+                    break
+                case "project":
+                    wrappers = obj_wrp.getProjects(user_client)
+                    break
+                case "plate":
+                    wrappers = obj_wrp.getPlates(user_client)
+                    break
+                case "screen":
+                    wrappers = obj_wrp.getScreens(user_client)
+                    break
+            }
+            return wrappers
+        } catch(Exception e) {
+            println("Could not get " + object_type + " for " + obj_wrp + " waiting " + waiting_time + " minutes and trying again.")
+            println e
+            TimeUnit.MINUTES.sleep(waiting_time)
+            last_exception = e
+            if (!user_client.isConnected()) {
+                println("Has been deconnected. Will reconnect.")
+                user_client.connect(host, port, USERNAME, PASSWORD.toCharArray())
+            }
+        }
+    }
+    throw last_exception
+}
+
+def robustlyGetOne(Long id, String object_type, Client user_client) {
+    for (waiting_time in waiting_times) {
+        try {
+
+            wrapper = null
+            switch (object_type) {
+                case "image":
+                    warpper = user_client.getImage(id)
+                    break
+                case "dataset":
+                    warpper = user_client.getDataset(id)
+                    break
+                case "well":
+                    warpper = user_client.getWell(id)
+                    break
+                case "project":
+                    warpper = user_client.getProject(id)
+                    break
+                case "plate":
+                    warpper = user_client.getPlate(id)
+                    break
+                case "screen":
+                    warpper = user_client.getScreen(id)
+                    break
+            }
+            return warpper
+        } catch(Exception e) {
+            println("Could not get " + object_type + " id " + id + " waiting " + waiting_time + " minutes and trying again.")
+            println e
+            TimeUnit.MINUTES.sleep(waiting_time)
+            last_exception = e
+            if (!user_client.isConnected()) {
+                println("Has been deconnected. Will reconnect.")
+                user_client.connect(host, port, USERNAME, PASSWORD.toCharArray())
+            }
+        }
+    }
+    throw last_exception
+}
+
+def robustlytoImagePlus(ImageWrapper image_wrp, Client user_client) {
+    for (waiting_time in waiting_times) {
+        try {
+            return image_wrp.toImagePlus(user_client)
+        } catch(Exception e) {
+            println("Could not convert to image plus " + image_wrp + " waiting " + waiting_time + " minutes and trying again.")
+            println e
+            TimeUnit.MINUTES.sleep(waiting_time)
+            last_exception = e
+            if (!user_client.isConnected()) {
+                println("Has been deconnected. Will reconnect.")
+                user_client.connect(host, port, USERNAME, PASSWORD.toCharArray())
+            }
+        }
+    }
+    throw last_exception
+}
+
+def processDataset(Client user_client, DatasetWrapper dataset_wrp,
+                   File output_directory,
+                   Boolean headless_mode) {
+    robustlyGetAll(dataset_wrp, "image", user_client).each{ ImageWrapper img_wrp ->
+        processImage(user_client, img_wrp,
+                     output_directory,
+                     headless_mode)
+    }
+}
+
+def processSinglePlate(Client user_client, PlateWrapper plate_wrp,
+                       File output_directory,
+                       Boolean headless_mode) {
+    robustlyGetAll(plate_wrp, "well", user_client).each{ well_wrp ->
+        processSingleWell(user_client, well_wrp,
+                     output_directory,
+                     headless_mode)
+    }
+}
+
+def processSingleWell(Client user_client, WellWrapper well_wrp,
+                      File output_directory,
+                      Boolean headless_mode) {
+    well_wrp.getWellSamples().each{
+        ImageWrapper img_wrp = it.getImage()
+        processImage(user_client, img_wrp,
+                     output_directory,
+                     headless_mode)
+    }
+}
+
+def processImage(Client user_client, ImageWrapper image_wrp,
+                 File output_directory,
+                 Boolean headless_mode) {
+    IJ.run("Close All", "")
+
+    // Print image information
+    println "\n Image infos"
+    String image_basename = image_wrp.getName()
+    println ("Image_name : " + image_basename + " / id : " + image_wrp.getId())
+
+    println "Getting image from OMERO"
+
+    ImagePlus imp = robustlytoImagePlus(image_wrp, user_client)
+	// ImagePlus imp = IJ.openImage("/home/ldelisle/Desktop/EXP095_LE_PEG_CTGF_PLATE_120h.companion.ome [C2_1_merge].tif")
+
+    if (!headless_mode) {
+        imp.show()
+    }
+
+    // Write to file
+    File output_path = new File (output_directory, image_basename + ".tiff" )
+                // save file
+    FileSaver fs = new FileSaver(imp)
+    fs.saveAsTiff(output_path.toString())
+    return
+}
+
+// User set variables
+
+#@ String(visibility=MESSAGE, value="Inputs", required=false) msg
+#@ String(label="User name") USERNAME
+#@ String(label="PASSWORD", style='PASSWORD', value="", persist=false) PASSWORD
+#@ String(label="File path with omero credentials") credentials
+#@ String(label="omero host server") host
+#@ Integer(label="omero host server port", value=4064) port
+#@ String(label="Object", choices={"image","dataset","well","plate"}) object_type
+#@ Long(label="ID", value=119273) id
+
+#@ String(visibility=MESSAGE, value="Parameters for output", required=false) msg5
+#@ File(style = "directory", label="Directory where measures are put") output_directory
+
+// Detect if is headless
+// java.awt.GraphicsEnvironment.checkheadless_mode(GraphicsEnvironment.java:204)
+Boolean headless_mode = GraphicsEnvironment.isHeadless()
+if (headless_mode) {
+    println "Running in headless mode"
+}
+
+if (PASSWORD == "") {
+    File cred_file = new File(credentials)
+    if (!cred_file.exists()) {
+        throw new Exception("Password or credential file need to be set.")
+    }
+    String creds = FileUtils.readFileToString(cred_file, "UTF-8")
+    if (creds.split("\n").size() < 2) {
+        throw new Exception("Credential file requires 2 lines")
+    }
+    USERNAME = creds.split("\n")[0]
+    PASSWORD = creds.split("\n")[1]
+}
+
+// Connection to server
+Client user_client = new Client()
+user_client.connect(host, port, USERNAME, PASSWORD.toCharArray())
+
+if (user_client.isConnected()) {
+    println "\nConnected to "+host
+    println "Images will be in " + output_directory.toString()
+
+    try {
+
+        switch (object_type) {
+            case "image":
+                ImageWrapper image_wrp = robustlyGetOne(id, "image", user_client)
+                processImage(user_client, image_wrp,
+                    output_directory,
+                    headless_mode)
+                break
+            case "dataset":
+                DatasetWrapper dataset_wrp = robustlyGetOne(id, "dataset", user_client)
+                processDataset(user_client, dataset_wrp,
+                     output_directory,
+                     headless_mode)
+                break
+            case "well":
+                WellWrapper well_wrp = robustlyGetOne(id, "well", user_client)
+                processSingleWell(user_client, well_wrp,
+                     output_directory,
+                     headless_mode)
+                break
+            case "plate":
+                PlateWrapper plate_wrp = robustlyGetOne(id, "plate", user_client)
+                processSinglePlate(user_client, plate_wrp,
+                     output_directory,
+                     headless_mode)
+                break
+        }
+
+    } catch(Exception e) {
+        println("Something went wrong: " + e)
+        e.printStackTrace()
+
+        if (headless_mode){
+            // This is due to Rank Filter + GaussianBlur
+            System.exit(1)
+        }
+    } finally {
+        user_client.disconnect()
+        println "Disonnected " + host
+    }
+    if (headless_mode) {
+        // This is due to Rank Filter + GaussianBlur
+        System.exit(0)
+    }
+
+} else {
+    throw new Exception("Not able to connect to " + host)
+}
+
+return
diff -r 000000000000 -r d041125db523 omero_get_full_images.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_get_full_images.xml	Tue May 21 13:50:08 2024 +0000
@@ -0,0 +1,115 @@
+<tool id="omero_get_full_images" name="Omero: get full images" profile="20.01" version="@TOOL_VERSION@+galaxy0">
+    <macros>
+        <token name="@TOOL_VERSION@">20240521</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="20231211">fiji</requirement>
+        <requirement type="package" version="5.8.3">fiji-omero_ij</requirement>
+        <requirement type="package" version="5.18.0">fiji-simple_omero_client</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $omero_instance_type.omero_instance == "priv":
+            ## the user wants to use a non-public OMERO instance
+            ## check if credentials are set in the user-preferences, if not warn the user and exit
+            #set $username = $__user__.extra_preferences.get('omero_account|username', "")
+            #set $password = $__user__.extra_preferences.get('omero_account|password', "")
+
+            #if $omero_instance_type.galaxy_test_param != 'true' and ($username == "" or $password ==""):
+                echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 &&
+                exit 1 &&
+            #end if
+        #end if
+        mkdir output &&
+        ImageJ --ij2 --headless --console --run '$__tool_directory__/'omero_get_full_images.groovy 
+            'USERNAME="",PASSWORD="",credentials="${credentials}",host="${omero_instance_type.omero_host}",port="${omero_instance_type.omero_port}",object_type="${omero_object.object_type}",id="${omero_object.omero_id}",output_directory="output"' > output.log
+        ]]>
+    </command>
+    <configfiles>
+        <configfile name="credentials"><![CDATA[#if $omero_instance_type.omero_instance == 'idr' or ($omero_instance_type.omero_instance =='priv' and $omero_instance_type.galaxy_test_param == 'true'):
+    ## as a test for a private instance we actually use a public instance, but with credentials
+    #set $username = 'public'
+    #set $password = 'public'
+#else:
+    #set $username = $__user__.extra_preferences.get('omero_account|username', "")
+    #set $password = $__user__.extra_preferences.get('omero_account|password', "")
+#end if
+$username
+$password
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <conditional name="omero_instance_type">
+            <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
+                   help="By default, the tool will request children ID from IDR. If you 
+                   need to connect to your own instance, set your connection username and password from User->Preference->Manage Information" >
+                <option value="idr">IDR</option>
+                <option value="priv">other OMERO instance</option>
+            </param>
+            <when value="priv">
+                <param name="omero_host" type="text" label="OMERO host URL">
+                    <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
+                    <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
+                </param>
+                <param name="omero_port" type="integer" value="4064" label="Omero port" />
+                <param name="galaxy_test_param" type="hidden" value="false" />
+            </when>
+            <when value="idr">
+                <param name="omero_host" type="hidden" value="idr.openmicroscopy.org"/>
+                <param name="omero_port" type="hidden" value="4064" />
+            </when>
+        </conditional>
+        <conditional name="omero_object">
+            <param name="object_type" type="select" label="Type of object to analyze">
+                <option value="image">Single Omero Image</option>
+                <option value="well">All images of a Well</option>
+                <option value="plate">All images of a Plate</option>
+                <option value="dataset">All images of a Dataset</option>
+            </param>
+            <when value="image">
+                <param name="omero_id" type="integer" value="" label="Image ID on omero" />
+            </when>
+            <when value="well">
+                <param name="omero_id" type="integer" value="" label="Well ID on omero" />
+            </when>
+            <when value="plate">
+                <param name="omero_id" type="integer" value="" label="Plate ID on omero" />
+            </when>
+            <when value="dataset">
+                <param name="omero_id" type="integer" value="" label="Dataset ID on omero" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" from_work_dir="output.log" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id}: logfile">
+        </data>
+        <collection name="images" type="list" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id}: Images">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tiff" directory="output" format="tiff"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <conditional name="omero_instance_type">
+                <param name="omero_instance" value="idr"/>
+            </conditional>
+            <conditional name="omero_object">
+                <param name="object_type" value="image"/>
+                <param name="omero_id" value="14788706"/>
+            </conditional>
+            <output_collection name="images" type="list" count="1">
+                <element name="15303_CS20_PAS">
+                    <assert_contents>
+                        <has_size value="48063821" delta="1000000"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+**Overview**
+
+This tool will get images from omero and write them to disk. It uses ImageJ.
+
+]]>
+    </help>
+</tool>