Merge pull request #46 from GReD-Clermont/5_9_4

5.9.4

.editorconfig

@@ -0,0 +1,303 @@
+# Topmost editor config file
+root = true
+
+[*]
+charset = utf-8
+indent_size = 4
+indent_style = space
+insert_final_newline = false
+max_line_length = 120
+tab_width = 4
+ij_continuation_indent_size = 8
+ij_formatter_off_tag = @formatter:off
+ij_formatter_on_tag = @formatter:on
+ij_formatter_tags_enabled = false
+ij_smart_tabs = false
+ij_visual_guides = none
+ij_wrap_on_typing = false
+
+[*.java]
+ij_visual_guides = 80
+ij_java_align_consecutive_assignments = false
+ij_java_align_consecutive_variable_declarations = true
+ij_java_align_group_field_declarations = true
+ij_java_align_multiline_annotation_parameters = false
+ij_java_align_multiline_array_initializer_expression = true
+ij_java_align_multiline_assignment = true
+ij_java_align_multiline_binary_operation = true
+ij_java_align_multiline_chained_methods = true
+ij_java_align_multiline_extends_list = true
+ij_java_align_multiline_for = true
+ij_java_align_multiline_method_parentheses = false
+ij_java_align_multiline_parameters = true
+ij_java_align_multiline_parameters_in_calls = true
+ij_java_align_multiline_parenthesized_expression = true
+ij_java_align_multiline_records = true
+ij_java_align_multiline_resources = true
+ij_java_align_multiline_ternary_operation = true
+ij_java_align_multiline_text_blocks = true
+ij_java_align_multiline_throws_list = true
+ij_java_align_subsequent_simple_methods = false
+ij_java_align_throws_keyword = true
+ij_java_annotation_parameter_wrap = off
+ij_java_array_initializer_new_line_after_left_brace = false
+ij_java_array_initializer_right_brace_on_new_line = false
+ij_java_array_initializer_wrap = on_every_item
+ij_java_assert_statement_colon_on_next_line = false
+ij_java_assert_statement_wrap = normal
+ij_java_assignment_wrap = normal
+ij_java_binary_operation_sign_on_next_line = false
+ij_java_binary_operation_wrap = normal
+ij_java_blank_lines_after_anonymous_class_header = 0
+ij_java_blank_lines_after_class_header = 1
+ij_java_blank_lines_after_imports = 2
+ij_java_blank_lines_after_package = 2
+ij_java_blank_lines_around_class = 2
+ij_java_blank_lines_around_field = 0
+ij_java_blank_lines_around_field_in_interface = 0
+ij_java_blank_lines_around_initializer = 1
+ij_java_blank_lines_around_method = 2
+ij_java_blank_lines_around_method_in_interface = 2
+ij_java_blank_lines_before_class_end = 1
+ij_java_blank_lines_before_imports = 1
+ij_java_blank_lines_before_method_body = 0
+ij_java_blank_lines_before_package = 0
+ij_java_block_brace_style = end_of_line
+ij_java_block_comment_at_first_column = true
+ij_java_call_parameters_new_line_after_left_paren = false
+ij_java_call_parameters_right_paren_on_new_line = false
+ij_java_call_parameters_wrap = normal
+ij_java_case_statement_on_separate_line = true
+ij_java_catch_on_new_line = false
+ij_java_class_annotation_wrap = split_into_lines
+ij_java_class_brace_style = end_of_line
+ij_java_class_count_to_use_import_on_demand = 10
+ij_java_class_names_in_javadoc = 1
+ij_java_do_not_indent_top_level_class_members = false
+ij_java_do_not_wrap_after_single_annotation = false
+ij_java_do_while_brace_force = never
+ij_java_doc_add_blank_line_after_description = true
+ij_java_doc_add_blank_line_after_param_comments = true
+ij_java_doc_add_blank_line_after_return = true
+ij_java_doc_add_p_tag_on_empty_lines = true
+ij_java_doc_align_exception_comments = true
+ij_java_doc_align_param_comments = true
+ij_java_doc_do_not_wrap_if_one_line = true
+ij_java_doc_enable_formatting = true
+ij_java_doc_enable_leading_asterisks = true
+ij_java_doc_indent_on_continuation = false
+ij_java_doc_keep_empty_lines = true
+ij_java_doc_keep_empty_parameter_tag = true
+ij_java_doc_keep_empty_return_tag = true
+ij_java_doc_keep_empty_throws_tag = true
+ij_java_doc_keep_invalid_tags = true
+ij_java_doc_param_description_on_new_line = false
+ij_java_doc_preserve_line_breaks = false
+ij_java_doc_use_throws_not_exception_tag = true
+ij_java_else_on_new_line = false
+ij_java_enum_constants_wrap = on_every_item
+ij_java_extends_keyword_wrap = off
+ij_java_extends_list_wrap = on_every_item
+ij_java_field_annotation_wrap = split_into_lines
+ij_java_finally_on_new_line = false
+ij_java_for_brace_force = never
+ij_java_for_statement_new_line_after_left_paren = false
+ij_java_for_statement_right_paren_on_new_line = false
+ij_java_for_statement_wrap = on_every_item
+ij_java_generate_final_locals = false
+ij_java_generate_final_parameters = false
+ij_java_if_brace_force = never
+ij_java_imports_layout = *, |, javax.**, java.**, |, $*
+ij_java_indent_case_from_switch = true
+ij_java_insert_inner_class_imports = false
+ij_java_insert_override_annotation = true
+ij_java_keep_blank_lines_before_right_brace = 2
+ij_java_keep_blank_lines_between_package_declaration_and_header = 2
+ij_java_keep_blank_lines_in_code = 2
+ij_java_keep_blank_lines_in_declarations = 2
+ij_java_keep_control_statement_in_one_line = true
+ij_java_keep_first_column_comment = true
+ij_java_keep_indents_on_empty_lines = false
+ij_java_keep_line_breaks = true
+ij_java_keep_multiple_expressions_in_one_line = false
+ij_java_keep_simple_blocks_in_one_line = false
+ij_java_keep_simple_classes_in_one_line = false
+ij_java_keep_simple_lambdas_in_one_line = false
+ij_java_keep_simple_methods_in_one_line = false
+ij_java_label_indent_absolute = false
+ij_java_label_indent_size = 0
+ij_java_lambda_brace_style = end_of_line
+ij_java_layout_static_imports_separately = true
+ij_java_line_comment_add_space = false
+ij_java_line_comment_at_first_column = true
+ij_java_method_annotation_wrap = split_into_lines
+ij_java_method_brace_style = end_of_line
+ij_java_method_call_chain_wrap = normal
+ij_java_method_parameters_new_line_after_left_paren = false
+ij_java_method_parameters_right_paren_on_new_line = false
+ij_java_method_parameters_wrap = normal
+ij_java_modifier_list_wrap = false
+ij_java_names_count_to_use_import_on_demand = 10
+ij_java_new_line_after_lparen_in_record_header = false
+ij_java_packages_to_use_import_on_demand = javax.swing.*
+ij_java_parameter_annotation_wrap = off
+ij_java_parentheses_expression_new_line_after_left_paren = false
+ij_java_parentheses_expression_right_paren_on_new_line = false
+ij_java_place_assignment_sign_on_next_line = false
+ij_java_prefer_longer_names = true
+ij_java_prefer_parameters_wrap = false
+ij_java_record_components_wrap = normal
+ij_java_repeat_synchronized = true
+ij_java_replace_instanceof_and_cast = false
+ij_java_replace_null_check = true
+ij_java_replace_sum_lambda_with_method_ref = true
+ij_java_resource_list_new_line_after_left_paren = false
+ij_java_resource_list_right_paren_on_new_line = false
+ij_java_resource_list_wrap = on_every_item
+ij_java_rparen_on_new_line_in_record_header = false
+ij_java_space_after_closing_angle_bracket_in_type_argument = false
+ij_java_space_after_colon = true
+ij_java_space_after_comma = true
+ij_java_space_after_comma_in_type_arguments = true
+ij_java_space_after_for_semicolon = true
+ij_java_space_after_quest = true
+ij_java_space_after_type_cast = true
+ij_java_space_before_annotation_array_initializer_left_brace = false
+ij_java_space_before_annotation_parameter_list = false
+ij_java_space_before_array_initializer_left_brace = false
+ij_java_space_before_catch_keyword = true
+ij_java_space_before_catch_left_brace = true
+ij_java_space_before_catch_parentheses = true
+ij_java_space_before_class_left_brace = true
+ij_java_space_before_colon = true
+ij_java_space_before_colon_in_foreach = true
+ij_java_space_before_comma = false
+ij_java_space_before_do_left_brace = true
+ij_java_space_before_else_keyword = true
+ij_java_space_before_else_left_brace = true
+ij_java_space_before_finally_keyword = true
+ij_java_space_before_finally_left_brace = true
+ij_java_space_before_for_left_brace = true
+ij_java_space_before_for_parentheses = true
+ij_java_space_before_for_semicolon = false
+ij_java_space_before_if_left_brace = true
+ij_java_space_before_if_parentheses = true
+ij_java_space_before_method_call_parentheses = false
+ij_java_space_before_method_left_brace = true
+ij_java_space_before_method_parentheses = false
+ij_java_space_before_opening_angle_bracket_in_type_parameter = false
+ij_java_space_before_quest = true
+ij_java_space_before_switch_left_brace = true
+ij_java_space_before_switch_parentheses = true
+ij_java_space_before_synchronized_left_brace = true
+ij_java_space_before_synchronized_parentheses = true
+ij_java_space_before_try_left_brace = true
+ij_java_space_before_try_parentheses = true
+ij_java_space_before_type_parameter_list = false
+ij_java_space_before_while_keyword = true
+ij_java_space_before_while_left_brace = true
+ij_java_space_before_while_parentheses = true
+ij_java_space_inside_one_line_enum_braces = false
+ij_java_space_within_empty_array_initializer_braces = false
+ij_java_space_within_empty_method_call_parentheses = false
+ij_java_space_within_empty_method_parentheses = false
+ij_java_spaces_around_additive_operators = true
+ij_java_spaces_around_assignment_operators = true
+ij_java_spaces_around_bitwise_operators = true
+ij_java_spaces_around_equality_operators = true
+ij_java_spaces_around_lambda_arrow = true
+ij_java_spaces_around_logical_operators = true
+ij_java_spaces_around_method_ref_dbl_colon = false
+ij_java_spaces_around_multiplicative_operators = true
+ij_java_spaces_around_relational_operators = true
+ij_java_spaces_around_shift_operators = true
+ij_java_spaces_around_type_bounds_in_type_parameters = true
+ij_java_spaces_around_unary_operator = false
+ij_java_spaces_within_angle_brackets = false
+ij_java_spaces_within_annotation_parentheses = false
+ij_java_spaces_within_array_initializer_braces = false
+ij_java_spaces_within_braces = false
+ij_java_spaces_within_brackets = false
+ij_java_spaces_within_cast_parentheses = false
+ij_java_spaces_within_catch_parentheses = false
+ij_java_spaces_within_for_parentheses = false
+ij_java_spaces_within_if_parentheses = false
+ij_java_spaces_within_method_call_parentheses = false
+ij_java_spaces_within_method_parentheses = false
+ij_java_spaces_within_parentheses = false
+ij_java_spaces_within_record_header = false
+ij_java_spaces_within_switch_parentheses = false
+ij_java_spaces_within_synchronized_parentheses = false
+ij_java_spaces_within_try_parentheses = false
+ij_java_spaces_within_while_parentheses = false
+ij_java_special_else_if_treatment = true
+ij_java_subclass_name_suffix = Impl
+ij_java_ternary_operation_signs_on_next_line = false
+ij_java_ternary_operation_wrap = normal
+ij_java_test_name_suffix = Test
+ij_java_throws_keyword_wrap = normal
+ij_java_throws_list_wrap = on_every_item
+ij_java_use_external_annotations = false
+ij_java_use_fq_class_names = false
+ij_java_use_relative_indents = false
+ij_java_use_single_class_imports = true
+ij_java_variable_annotation_wrap = off
+ij_java_visibility = public
+ij_java_while_brace_force = never
+ij_java_while_on_new_line = false
+ij_java_wrap_comments = true
+ij_java_wrap_first_method_in_call_chain = false
+ij_java_wrap_long_lines = false
+
+[.editorconfig]
+ij_editorconfig_align_group_field_declarations = false
+ij_editorconfig_space_after_colon = false
+ij_editorconfig_space_after_comma = true
+ij_editorconfig_space_before_colon = false
+ij_editorconfig_space_before_comma = false
+ij_editorconfig_spaces_around_assignment_operators = true
+
+[{*.ant, *.fxml, *.jhm, *.jnlp, *.jrxml, *.jspx, *.pom, *.rng, *.tagx, *.tld, *.wsdl, *.xml, *.xsd, *.xsl, *.xslt, *.xul}]
+ij_xml_align_attributes = true
+ij_xml_align_text = false
+ij_xml_attribute_wrap = normal
+ij_xml_block_comment_at_first_column = true
+ij_xml_keep_blank_lines = 2
+ij_xml_keep_indents_on_empty_lines = false
+ij_xml_keep_line_breaks = true
+ij_xml_keep_line_breaks_in_text = true
+ij_xml_keep_whitespaces = false
+ij_xml_keep_whitespaces_around_cdata = preserve
+ij_xml_keep_whitespaces_inside_cdata = false
+ij_xml_line_comment_at_first_column = true
+ij_xml_space_after_tag_name = false
+ij_xml_space_around_equals_in_attribute = false
+ij_xml_space_inside_empty_tag = false
+ij_xml_text_wrap = normal
+ij_xml_use_custom_settings = false
+
+[{*.markdown, *.md}]
+ij_markdown_force_one_space_after_blockquote_symbol = true
+ij_markdown_force_one_space_after_header_symbol = true
+ij_markdown_force_one_space_after_list_bullet = true
+ij_markdown_force_one_space_between_words = true
+ij_markdown_keep_indents_on_empty_lines = false
+ij_markdown_max_lines_around_block_elements = 1
+ij_markdown_max_lines_around_header = 1
+ij_markdown_max_lines_between_paragraphs = 1
+ij_markdown_min_lines_around_block_elements = 1
+ij_markdown_min_lines_around_header = 1
+ij_markdown_min_lines_between_paragraphs = 1
+
+[{*.yaml, *.yml}]
+indent_size = 2
+ij_yaml_align_values_properties = do_not_align
+ij_yaml_autoinsert_sequence_marker = true
+ij_yaml_block_mapping_on_new_line = false
+ij_yaml_indent_sequence_value = true
+ij_yaml_keep_indents_on_empty_lines = false
+ij_yaml_keep_line_breaks = true
+ij_yaml_sequence_on_new_line = false
+ij_yaml_space_before_colon = false
+ij_yaml_spaces_within_braces = true
+ij_yaml_spaces_within_brackets = true

README.md

@@ -1,6 +1,6 @@
 [![Java CI with Maven](https://github.com/GReD-Clermont/simple-omero-client/actions/workflows/maven.yml/badge.svg)](https://github.com/GReD-Clermont/simple-omero-client/actions/workflows/maven.yml)
 [![codecov](https://codecov.io/gh/GReD-Clermont/simple-omero-client/branch/main/graph/badge.svg)](https://codecov.io/gh/GReD-Clermont/simple-omero-client)
-[![DOI](https://img.shields.io/badge/DOI-10.12688%2Ff1000research.110385.1-GREEN)](https://doi.org/10.12688/f1000research.110385.1)
+[![DOI](https://img.shields.io/badge/DOI-10.12688%2Ff1000research.110385.2-GREEN)](https://doi.org/10.12688/f1000research.110385.2)
 
 # simple-omero-client
 
@@ -107,7 +107,7 @@ List<ROIWrapper> rois = image.getROIs(client);
 They can also be converted from or to ImageJ Rois:
 
 ```java
-// The property is a string used to create 3D/4D ROIs in OMERO, by grouping shapes sharing the same value
+// The property is a string used to create 3D/4D ROIs in OMERO, by grouping shapes sharing the same value (used to name the ROI)
 List<ROIWrapper> omeroRois = ROIWrapper.fromImageJ(ijRois, property);
 
 ROIWrapper roi = new ROIWrapper();

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>fr.igred</groupId>
     <artifactId>simple-omero-client</artifactId>
-    <version>5.9.3</version>
+    <version>5.9.4</version>
     <packaging>jar</packaging>
 
     <name>Simple OMERO Client</name>
@@ -19,7 +19,7 @@
 
     <organization>
         <name>GReD</name>
-        <url>https://www.gred-clermont.fr</url>
+        <url>https://www.igred.fr</url>
     </organization>
 
     <licenses>
@@ -35,9 +35,9 @@
             <id>ppouchin</id>
             <name>Pierre Pouchin</name>
             <email>[email protected]</email>
-            <url>https://www.gred-clermont.fr/directory/member/pierre-pouchin/</url>
+            <url>https://www.igred.fr/directory/member/pierre-pouchin/</url>
             <organization>GReD (INSERM U1103 / CNRS UMR 6293 / UCA)</organization>
-            <organizationUrl>https://www.gred-clermont.fr</organizationUrl>
+            <organizationUrl>https://www.igred.fr</organizationUrl>
             <roles>
                 <role>lead</role>
                 <role>developer</role>
@@ -54,6 +54,9 @@
         <contributor>
             <name>Rémi Valarcher</name>
         </contributor>
+        <contributor>
+            <name>Rémy Dornier</name>
+        </contributor>
     </contributors>
 
     <mailingLists>

src/main/java/fr/igred/omero/Client.java

@@ -1,5 +1,5 @@
 /*
- *  Copyright (C) 2020-2022 GReD
+ *  Copyright (C) 2020-2023 GReD
  *
  * This program is free software; you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software

src/main/java/fr/igred/omero/GatewayWrapper.java

@@ -1,5 +1,5 @@
 /*
- *  Copyright (C) 2020-2022 GReD
+ *  Copyright (C) 2020-2023 GReD
  *
  * This program is free software; you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software

src/main/java/fr/igred/omero/GenericObjectWrapper.java

@@ -1,5 +1,5 @@
 /*
- *  Copyright (C) 2020-2022 GReD
+ *  Copyright (C) 2020-2023 GReD
  *
  * This program is free software; you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software
@@ -167,6 +167,7 @@ public Timestamp getCreated() {
      *
      * @return owner id.
      */
+    @SuppressWarnings("ClassReferencesSubclass")
     public ExperimenterWrapper getOwner() {
         return new ExperimenterWrapper(data.getOwner());
     }

src/main/java/fr/igred/omero/annotations/FileAnnotationWrapper.java

@@ -1,5 +1,5 @@
 /*
- *  Copyright (C) 2020-2022 GReD
+ *  Copyright (C) 2020-2023 GReD
  *
  * This program is free software; you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software