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app: generate cli automatically, #TASK-4248
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@pfurio
pfurio committed Sep 1, 2023
1 parent 48babe1 commit 48889d0
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Showing 80 changed files with 765 additions and 427 deletions.
2 changes: 1 addition & 1 deletion opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
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@@ -1,5 +1,5 @@
/*
* Copyright 2015-2023-08-30 OpenCB
* Copyright 2015-2023-09-01 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
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@@ -1,5 +1,5 @@
/*
* Copyright 2015-2023-08-30 OpenCB
* Copyright 2015-2023-09-01 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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16 changes: 8 additions & 8 deletions ...src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
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Expand Up @@ -275,7 +275,7 @@ public class DistinctCommandOptions {
@Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
public String study;

@Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String id;

@Parameter(names = {"--uuid"}, description = "Comma separated list of Clinical Analysis UUIDs up to a maximum of 100", required = false, arity = 1)
Expand All @@ -284,7 +284,7 @@ public class DistinctCommandOptions {
@Parameter(names = {"--type"}, description = "Clinical Analysis type", required = false, arity = 1)
public String type;

@Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder", required = false, arity = 1)
@Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String disorder;

@Parameter(names = {"--files"}, description = "Clinical Analysis files", required = false, arity = 1)
Expand Down Expand Up @@ -364,7 +364,7 @@ public class DistinctInterpretationCommandOptions {
@Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
public String study;

@Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String id;

@Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1)
Expand All @@ -376,7 +376,7 @@ public class DistinctInterpretationCommandOptions {
@Parameter(names = {"--analyst-id"}, description = "Analyst ID", required = false, arity = 1)
public String analystId;

@Parameter(names = {"--method-name"}, description = "Interpretation method name", required = false, arity = 1)
@Parameter(names = {"--method-name"}, description = "Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String methodName;

@Parameter(names = {"--panels"}, description = "Interpretation panels", required = false, arity = 1)
Expand Down Expand Up @@ -432,7 +432,7 @@ public class SearchInterpretationCommandOptions {
@Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
public String study;

@Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String id;

@Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1)
Expand All @@ -444,7 +444,7 @@ public class SearchInterpretationCommandOptions {
@Parameter(names = {"--analyst-id"}, description = "Analyst ID", required = false, arity = 1)
public String analystId;

@Parameter(names = {"--method-name"}, description = "Interpretation method name", required = false, arity = 1)
@Parameter(names = {"--method-name"}, description = "Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String methodName;

@Parameter(names = {"--panels"}, description = "Interpretation panels", required = false, arity = 1)
Expand Down Expand Up @@ -1488,7 +1488,7 @@ public class SearchCommandOptions {
@Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
public String study;

@Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String id;

@Parameter(names = {"--uuid"}, description = "Comma separated list of Clinical Analysis UUIDs up to a maximum of 100", required = false, arity = 1)
Expand All @@ -1497,7 +1497,7 @@ public class SearchCommandOptions {
@Parameter(names = {"--type"}, description = "Clinical Analysis type", required = false, arity = 1)
public String type;

@Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder", required = false, arity = 1)
@Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String disorder;

@Parameter(names = {"--files"}, description = "Clinical Analysis files", required = false, arity = 1)
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10 changes: 5 additions & 5 deletions opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java
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Expand Up @@ -242,10 +242,10 @@ public class DistinctCommandOptions {
@Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
public String study;

@Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String id;

@Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String name;

@Parameter(names = {"--uuid"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1)
Expand Down Expand Up @@ -334,7 +334,7 @@ public class GenerateCommandOptions {
@Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1)
public String status;

@Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1)
@Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String phenotypes;

@Parameter(names = {"--annotation"}, description = "Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0", required = false, arity = 1)
Expand Down Expand Up @@ -411,10 +411,10 @@ public class SearchCommandOptions {
@Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
public String study;

@Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String id;

@Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String name;

@Parameter(names = {"--uuid"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1)
Expand Down
32 changes: 16 additions & 16 deletions ...pp/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java
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Expand Up @@ -157,37 +157,37 @@ public class DistinctCommandOptions {
@Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
public String study;

@Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String id;

@Parameter(names = {"--uuid"}, description = "Comma separated list of panel UUIDs up to a maximum of 100", required = false, arity = 1)
public String uuid;

@Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String name;

@Parameter(names = {"--internal-status"}, description = "Filter by internal status", required = false, arity = 1)
public String internalStatus;

@Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1)
@Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String disorders;

@Parameter(names = {"--variants"}, description = "Comma separated list of variant ids", required = false, arity = 1)
@Parameter(names = {"--variants"}, description = "Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String variants;

@Parameter(names = {"--genes"}, description = "Comma separated list of gene ids", required = false, arity = 1)
@Parameter(names = {"--genes"}, description = "Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String genes;

@Parameter(names = {"--source"}, description = "Comma separated list of source ids or names.", required = false, arity = 1)
public String source;

@Parameter(names = {"--regions"}, description = "Comma separated list of regions", required = false, arity = 1)
@Parameter(names = {"--regions"}, description = "Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String regions;

@Parameter(names = {"--categories"}, description = "Comma separated list of category names", required = false, arity = 1)
@Parameter(names = {"--categories"}, description = "Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String categories;

@Parameter(names = {"--tags"}, description = "Panel tags", required = false, arity = 1)
@Parameter(names = {"--tags"}, description = "Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String tags;

@Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0)
Expand Down Expand Up @@ -275,37 +275,37 @@ public class SearchCommandOptions {
@Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
public String study;

@Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String id;

@Parameter(names = {"--uuid"}, description = "Comma separated list of panel UUIDs up to a maximum of 100", required = false, arity = 1)
public String uuid;

@Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100", required = false, arity = 1)
@Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String name;

@Parameter(names = {"--internal-status"}, description = "Filter by internal status", required = false, arity = 1)
public String internalStatus;

@Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1)
@Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String disorders;

@Parameter(names = {"--variants"}, description = "Comma separated list of variant ids", required = false, arity = 1)
@Parameter(names = {"--variants"}, description = "Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String variants;

@Parameter(names = {"--genes"}, description = "Comma separated list of gene ids", required = false, arity = 1)
@Parameter(names = {"--genes"}, description = "Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String genes;

@Parameter(names = {"--source"}, description = "Comma separated list of source ids or names.", required = false, arity = 1)
public String source;

@Parameter(names = {"--regions"}, description = "Comma separated list of regions", required = false, arity = 1)
@Parameter(names = {"--regions"}, description = "Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String regions;

@Parameter(names = {"--categories"}, description = "Comma separated list of category names", required = false, arity = 1)
@Parameter(names = {"--categories"}, description = "Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String categories;

@Parameter(names = {"--tags"}, description = "Panel tags", required = false, arity = 1)
@Parameter(names = {"--tags"}, description = "Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
public String tags;

@Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0)
Expand Down
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