Annotation scripts

Convert KeyVal namespace

Convert_KeyVal_namespace.py

Convert the namespace of objects key-value pairs.

it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 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 General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Convert_KeyVal_namespace.annotate_object(conn, obj, kv_list, namespace)

Create a new MapAnnotation with specified Key-Value pairs on an OMERO object.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection object for annotation.
obj (omero.model.<ObjectType>) – OMERO object to annotate.
kv_list (list of tuples) – Key-Value pairs to include in the annotation.
namespace (str) – Namespace for the new annotation.

Returns

The annotation is linked to the object within the OMERO database.

Return type

None

Convert_KeyVal_namespace.get_children_recursive(source_object, target_type)

Recursively retrieve child objects of a specified type from a source OMERO object.

Parameters

source_object (omero.model.<ObjectType>) – The OMERO source object from which child objects are retrieved.
target_type (str) – The OMERO object type to be retrieved as children.

Returns

A list of child objects of the specified target type.

Return type

list

Convert_KeyVal_namespace.get_existing_map_annotations(obj, namespace_l)

Retrieve existing map annotations with specified Namespaces from an OMERO object.

Parameters

obj (omero.model.<ObjectType>) – OMERO object from which annotations are retrieved.
namespace_l (list of str) – List of namespaces used to filter annotations.

Returns

A tuple containing a list of Key-Value pairs and a list of MapAnnotation objects.

Return type

tuple

Convert_KeyVal_namespace.main_loop(conn, script_params)

Process OMERO objects, updating or merging Namespaces of Key-Value annotations.

This function iterates over objects, identifies annotations with specified Namespaces, and either updates or merges them according to provided parameters.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection object for database operations.
script_params (dict) – Dictionary of parameters required by the script.

Returns

Summary message indicating update counts, and the result object.

Return type

tuple

Convert_KeyVal_namespace.parameters_parsing(client)

Parse input parameters from the OMERO client, establishing defaults and validating specific combinations for data types and Namespaces.

Parameters: client – The OMERO client object from which input parameters are

retrieved. :type client: omero.gateway.BlitzGateway :return: A dictionary of parsed parameters, including validated and default

values for processing the script logic.

Return type: dict

Convert_KeyVal_namespace.remove_map_annotations(conn, ann_l)

Delete specified MapAnnotations from OMERO.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
ann_l (list of omero.model.MapAnnotationWrapper) – List of map annotation objects to delete.

Returns

Returns 1 if deletion succeeds, otherwise 0.

Return type

int

Convert_KeyVal_namespace.run_script()

Execute the OMERO script to convert Namespaces for key-value pair annotations.

This function initializes the script parameters, processes input from the OMERO client, and orchestrates the execution of the main script logic, including handling target data types and merging annotations.

Parameters: None – This function does not take any parameters.
Returns: This function does not return a value; it sets outputs directly to the client.
Return type: None

Convert_KeyVal_namespace.target_iterator(conn, source_object, target_type, is_tag)

Iterate over and yield target objects of a specified type from a source OMERO object.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
source_object (omero.model.<ObjectType>) – Source OMERO object to iterate over.
target_type (str) – Target object type to retrieve.
is_tag (bool) – Flag indicating if the source object is a tag.

Yield

Target objects of the specified type.

Return type

omero.model.<ObjectType>

Export to CSV

Export_to_csv.py

Reads the metadata associated with the images in a dataset and creates a csv file attached to dataset

it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 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 General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Export_to_csv.attach_csv(conn, obj_, rows, separator, csv_name)

Attaches a generated CSV file to an OMERO object.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
obj (omero.model.<ObjectType>) – OMERO object to which the CSV file will be attached.
rows (list) – Data rows to write into the CSV.
separator (str) – Separator character for CSV file.
csv_name (str) – Name for the generated CSV file.

Returns

File annotation object if the file is attached, None otherwise.

Return type

omero.model.FileAnnotation

Export_to_csv.build_rows(annotation_dict_l, tagannotation_l, include_namespace)

Constructs rows for CSV export by organizing annotations and Tags.

Parameters

annotation_dict_l (defaultdict(list)) – Dictionary of annotations organized by Namespace.
tagannotation_l (list) – List of Tag annotations.
include_namespace (bool) – Flag indicating if Namespace should be included in the CSV.

Returns

Tuple containing Namespace row, header row, and data rows for the CSV.

Return type

tuple

Export_to_csv.get_all_tags(conn)

Retrieves all Tag annotations and Tagsets from OMERO.

Parameters: conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
Returns: Dictionary mapping tag IDs to Tag names or Tagset names.
Return type: dict

Export_to_csv.get_children_recursive(source_object, target_type)

Recursively retrieve child objects of a specified type from a source OMERO object.

Parameters: source_object – The OMERO source object from which child objects

are retrieved. :type source_object: omero.model.<ObjectType> :param target_type: The OMERO object type to be retrieved as children. :type target_type: str :return: A list of child objects of the specified target type. :rtype: list

Export_to_csv.get_existing_map_annotations(obj, namespace)

Retrieves existing Key-Value pair annotations from an OMERO object.

Parameters

obj (omero.model.<ObjectType>) – OMERO object to retrieve annotations from.
namespace (str) – Specific Namespace of annotations to retrieve; ‘*’ retrieves all.

Returns

List of MapAnnotationWrapper objects for the specified Namespace.

Return type

list

Export_to_csv.get_existing_tag_annotations(obj, all_tag_d)

Retrieves existing Tag annotations from an OMERO object.

Parameters

obj (omero.model.<ObjectType>) – OMERO object to retrieve Tags from.
all_tag_d (dict) – Dictionary of all Tags with Tagset names, if applicable.

Returns

List of Tag names associated with the specified OMERO object.

Return type

list

Export_to_csv.get_obj_name(omero_obj): Helper function

Export_to_csv.group_keyvalues(objannotation_l)

Groups Key-Value pairs of each object into a unified structure for CSV export.

Parameters: objannotation_l (list) – List of object annotations to be grouped.
Returns: Tuple containing the header row and data rows for each object’s annotations.
Return type: tuple

Export_to_csv.main_loop(conn, script_params)

Main loop to process each object, gathering annotations, ancestry, and writing to a single CSV file.

Final steps: - Combine all annotations into a single structure. - Sort rows for better organization. - Write the collected data to a single CSV file.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
script_params (dict) – Dictionary of script parameters including data types, IDs, namespaces, and flags for options like including ancestry and tags.

Returns

Message regarding CSV attachment status, file annotation, and result object.

Return type

tuple

Export_to_csv.parameters_parsing(client)

Parses and validates input parameters from the client.

Parameters: client (omero.scripts.ScriptClient) – Script client used to obtain input parameters.
Returns: Parsed parameters dictionary with defaults for unspecified options.
Return type: dict

Export_to_csv.run_script()

Entry point for the script, called by the client.

Sets up and executes the main loop based on user-defined parameters, and generates output message or URL for the CSV file download.

Returns: Sets output messages and result objects for OMERO client session.
Return type: None

Export_to_csv.sort_concat_rows(ns_row, header_row, rows, obj_id_l, obj_name_l, obj_ancestry_l)

Sorts and concatenates rows, including object IDs, names, and ancestry if applicable.

Parameters

ns_row (list) – Namespace row for CSV.
header_row (list) – Column headers for CSV.
rows (list) – Data rows for CSV.
obj_id_l (list) – List of object IDs.
obj_name_l (list) – List of object names.
obj_ancestry_l (list) – List of ancestry details for each object.

Returns

Tuple containing updated Namespace row, header row, and sorted data rows.

Return type

tuple

Export_to_csv.target_iterator(conn, source_object, target_type, is_tag)

Iterate over and yield target objects of a specified type from a source OMERO object.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
source_object (omero.model.<ObjectType>) – Source OMERO object to iterate over.
target_type (str) – Target object type to retrieve.
is_tag (bool) – Flag indicating if the source object is a tag.

Yield

Target objects of the specified type.

Return type

omero.model.<ObjectType>

Import from CSV

Import_from_csv.py

Adds key-value pairs to a target object on OMERO from a CSV file.

it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 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 General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Import_from_csv.annotate_object(conn, obj, row, header, namespaces, exclude_empty_value, tagid_d, split_on)

Annotate a target object with Key-Value pairs and tags based on a row of CSV data.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
obj (omero.model.<ObjectType>) – OMERO object to be annotated.
row (list of str) – Data row containing Values for annotations.
header (list of str) – Column headers corresponding to the row Values.
namespaces (list of str) – Namespace for each header, specifying context of annotation.
exclude_empty_value (bool) – If True, excludes empty Values in annotations.
tagid_d (dict) – Dictionary of Tag IDs to their Tag objects.
split_on (str) – Character to split multi-value fields.

Returns

True if the object was updated with new annotations; False otherwise.

Return type

bool

Import_from_csv.get_children_recursive(source_object, target_type)

Recursively retrieve child objects of a specified type from a source OMERO object.

Parameters: source_object – The OMERO source object from which child objects

are retrieved. :type source_object: omero.model.<ObjectType> :param target_type: The OMERO object type to be retrieved as children. :type target_type: str :return: A list of child objects of the specified target type. :rtype: list

Import_from_csv.get_obj_name(omero_obj): Helper function

Import_from_csv.get_original_file(omero_obj)

Retrieve the latest CSV or TSV file annotation linked to an OMERO object.

Parameters: omero_obj (omero.model.<ObjectType>) – OMERO object to retrieve file annotation from.
Returns: The most recent CSV or TSV file annotation.
Return type: omero.model.FileAnnotation

Import_from_csv.get_tag_dict(conn, use_personal_tags)

Create dictionaries of Tags, Tagsets, and Tags in Tagsets for annotation.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
use_personal_tags (bool) – If True, only Tags owned by the user are used.

Returns

Four dictionaries: tag_d, tagset_d, tagtree_d, and tagid_d for Tags and Tag relationships.

Return type

tuple

Returns

tag_d: dictionary of tag_ids {“tagA”: [12], “tagB”:[34,56]}

Returns

tagset_d: dictionary of tagset_ids {“tagsetX”:[78]}

Returns

tagtree_d: dictionary of tags in tagsets {“tagsetX”:{“tagA”:[12]}}

Returns

tagid_d: dictionary of tag objects {12:tagA_obj, 34:tagB_obj}

Import_from_csv.link_file_ann(conn, obj_to_link, file_ann)

Link a File Annotation to a specified OMERO object if not already linked.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
obj_to_link (omero.model.<ObjectType>) – OMERO object to which the file annotation will be linked.
file_ann (omero.model.FileAnnotation) – File Annotation object to link to the OMERO object.

Returns

The file annotation is linked directly within the OMERO database.

Return type

None

Import_from_csv.main_loop(conn, script_params)

Main function to annotate objects in OMERO based on CSV input.

This function reads a CSV file, identifies objects in OMERO based on specified criteria, and annotates them with metadata from the CSV.

Startup:

Find CSV and reads it

For every object:

Gather name and ID

Finalize:

Find a match between CSV rows and objects
Annotate the objects
(opt) attach the CSV to the source object

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for interacting with the OMERO server.
script_params (dict) – Dictionary of parameters passed to the script, specifying the source and target data types, IDs, annotations, CSV separator, namespaces, and other options.

Returns

Message with annotation summary and the first annotated target object.

Return type

tuple

Import_from_csv.parameters_parsing(client)

Parse and validate input parameters for the OMERO CSV import script.

This function collects and prepares the input parameters provided by the client. It sets defaults for optional parameters, verifies the consistency of input values, and transforms certain parameters into appropriate formats for use in annotation.

Parameters: client (omero.scripts.client) – OMERO client providing the interface for parameter input.
Returns: Dictionary of parsed and validated input parameters, with defaults applied and necessary transformations made.
Return type: dict

Import_from_csv.preprocess_tag_rows(conn, header, rows, tag_d, tagset_d, tagtree_d, tagid_d, create_new_tags, split_on)

Convert Tag names in CSV rows to Tag IDs for efficient processing. In case of an error, the script fails here before the annotation process starts.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
header (list of str) – Headers from the CSV file.
rows (list of list of str) – Rows of CSV data with Tag information.
tag_d (dict) – Dictionary mapping Tag names to their IDs.
tagset_d (dict) – Dictionary mapping Tagset names to their IDs.
tagtree_d (dict) – Dictionary of Tags grouped by Tagset names.
tagid_d (dict) – Dictionary mapping Tag IDs to their tag objects.
create_new_tags (bool) – If True, new Tags are created if not found.
split_on (str) – Character to split multi-value Tag cells.

Returns

Processed rows with Tag IDs, updated dictionaries for tags and tagsets.

Return type

tuple

Import_from_csv.read_csv(conn, original_file, delimiter, import_tags)

Read a CSV file linked to an OMERO FileAnnotation and process its contents.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for accessing the server.
original_file (omero.model.OriginalFileI) – File object containing the CSV data.
delimiter (str) – Delimiter for the CSV file; detected if None.
import_tags (bool) – If True, columns named “Tag” are included for annotation.

Returns

Parsed rows, header, and namespaces from the CSV file.

Return type

tuple

Import_from_csv.run_script()

Execute the main OMERO import script for annotating OMERO objects from CSV.

This function establishes a client connection, gathers user input parameters, and initializes a connection to the OMERO server to parse a CSV file for Key-Value pairs, tags, and other metadata to annotate objects in the OMERO database.

Returns: Sets output messages and result objects for OMERO client session.
Return type: None

Import_from_csv.target_iterator(conn, source_object, target_type, is_tag)

Iterate over and yield target objects of a specified type from a source OMERO object.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
source_object (omero.model.<ObjectType>) – Source OMERO object to iterate over.
target_type (str) – Target object type to retrieve.
is_tag (bool) – Flag indicating if the source object is a tag.

Yield

Target objects of the specified type.

Return type

omero.model.<ObjectType>

Remove KeyVal

Remove_KeyVal.py”

Remove all key-value pairs associated with a namespace from objects on OMERO.

it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 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 General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Remove_KeyVal.get_children_recursive(source_object, target_type)

Recursively retrieve child objects of a specified type from a source OMERO object.

Parameters: source_object – The OMERO source object from which child objects

are retrieved. :type source_object: omero.model.<ObjectType> :param target_type: The OMERO object type to be retrieved as children. :type target_type: str :return: A list of child objects of the specified target type. :rtype: list

Remove_KeyVal.main_loop(conn, script_params)

Iterates through specified OMERO objects and removes Key-Value pair annotations within given Namespaces.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
script_params (dict) – Dictionary of script parameters including source data type, target data type, object IDs, and Namespace list.

Returns

Message indicating the success of the deletions, and the result object if any annotation was removed.

Return type

tuple

Remove_KeyVal.parameters_parsing(client)

Parses and validates input parameters from the client, with defaults for optional inputs.

Parameters: client (omero.scripts.ScriptClient) – Script client used to obtain input parameters.
Returns: Dictionary of parsed parameters, ready for processing.
Return type: dict

Remove_KeyVal.remove_map_annotations(conn, obj, namespace_l)

Deletes map annotations within the specified Namespaces from an OMERO object.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
obj (omero.model.<ObjectType>) – OMERO object from which MapAnnotations will be removed.
namespace_l (list) – List of Namespaces to remove annotations from; ‘*’ denotes all namespaces.

Returns

1 if annotations were successfully deleted, 0 otherwise.

Return type

int

Remove_KeyVal.run_script()

Main entry point, called by the client to initiate the script, collect parameters, and execute annotation deletion based on user input.

Returns: Sets output messages and result objects for OMERO client session.
Return type: None

Remove_KeyVal.target_iterator(conn, source_object, target_type, is_tag)

Iterate over and yield target objects of a specified type from a source OMERO object.

Parameters

conn (omero.gateway.BlitzGateway) – OMERO connection for server interaction.
source_object (omero.model.<ObjectType>) – Source OMERO object to iterate over.
target_type (str) – Target object type to retrieve.
is_tag (bool) – Flag indicating if the source object is a Tag.

Yield

Target objects of the specified type.

Return type

omero.model.<ObjectType>

Annotation scripts

Convert KeyVal namespace

Export to CSV

Import from CSV

Remove KeyVal

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