Merge pull request #237 from eseiler/fix/format_tdl

[FIX] CWL: positional options
seqan · Feb 14, 2024 · 4b75957 · 4b75957
2 parents 3b55514 + fb246f5
commit 4b75957
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Showing 10 changed files with 89 additions and 24 deletions.
diff --git a/include/sharg/detail/format_tdl.hpp b/include/sharg/detail/format_tdl.hpp
@@ -298,15 +298,18 @@ class format_tdl : format_base
                 ++positional_option_count;
                 auto description = config.description + default_message + validator_message;
 
-                parameters.push_back(tdl::Node{
-                    .name = id,
-                    .description = description,
-                    .tags = {},
-                    .value = tdl::StringValue{},
-                });
-                if (!config.long_id.empty())
+                parameters.push_back(tdl::Node{.name = id, .description = description});
+
+                auto & node = parameters.back();
+
+                if constexpr (detail::is_container_option<option_type>)
                 {
-                    info.cliMapping.emplace_back("--" + config.long_id, config.long_id);
+                    node.value = tdl::StringValueList{};
+                }
+                else
+                {
+                    node.value = tdl::StringValue{};
+                    node.tags.insert("required");
                 }
             });
     }

diff --git a/test/api_stability/1.1.1/0001-API-Update-TDL.patch b/test/api_stability/1.1.1/0001-API-Update-TDL.patch
@@ -1,7 +1,7 @@
-From ace25c7fffccdac9ccaf81329ada87f60021b5f9 Mon Sep 17 00:00:00 2001
+From 769620513bcc59d257119aacfa06020df7ca45a6 Mon Sep 17 00:00:00 2001
 From: Simon Gene Gottlieb <[email protected]>
 Date: Thu, 5 Oct 2023 13:43:30 +0200
-Subject: [PATCH 1/5] [API] Update TDL
+Subject: [PATCH 1/6] [API] Update TDL
 
 ---
  test/unit/detail/format_ctd_test.cpp |  2 +-

diff --git a/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch b/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch
@@ -1,7 +1,7 @@
-From 7bf847b4991636a59f26ca89977e94f51edfbf11 Mon Sep 17 00:00:00 2001
+From 9d8035baa8b0ff4accd6ba2e60a22f779986483d Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Mon, 5 Feb 2024 16:02:03 +0100
-Subject: [PATCH 2/5] [API] Quoted strings and paths
+Subject: [PATCH 2/6] [API] Quoted strings and paths
 
 ---
  test/snippet/readme_sneak_peek.out            |  6 ++---

diff --git a/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch b/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch
@@ -1,7 +1,7 @@
-From f02ddb2f31a47da16742dbf612d780b328e7602b Mon Sep 17 00:00:00 2001
+From a4fffdf64380b018822b13a9ad72586f0564385f Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Wed, 7 Feb 2024 13:31:22 +0100
-Subject: [PATCH 3/5] [NOAPI] Update copyright
+Subject: [PATCH 3/6] [NOAPI] Update copyright
 
 ---
  test/unit/detail/format_help_test.cpp | 10 +++++-----

diff --git a/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch b/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch
@@ -1,7 +1,7 @@
-From 9f040f8ccb8d304841d24d8ac4d67db0d06c370f Mon Sep 17 00:00:00 2001
+From 1481f5dfdc68d2d5e04cb5abbec45fab7f15fbcd Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Fri, 9 Feb 2024 16:17:21 +0100
-Subject: [PATCH 4/5] [INFRA] Update TDL
+Subject: [PATCH 4/6] [INFRA] Update TDL
 
 ---
  test/unit/detail/format_cwl_test.cpp | 28 +++++++++++++++++++++++++++-

diff --git a/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch b/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch
@@ -1,7 +1,7 @@
-From 3a7dfd8103806e97af6376e9173d686b67fb5b52 Mon Sep 17 00:00:00 2001
+From 085bc1fd63f3c48999610e0a9a916895a7cf9207 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Fri, 9 Feb 2024 18:13:36 +0100
-Subject: [PATCH 5/5] [INFRA] Use seqan3 main branch
+Subject: [PATCH 5/6] [INFRA] Use seqan3 main branch
 
 ---
  test/unit/detail/CMakeLists.txt | 2 +-

diff --git a/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch b/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch
@@ -0,0 +1,59 @@
+From c84f8aeeba0895677c64d9740f4df908674cd0be Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <[email protected]>
+Date: Wed, 14 Feb 2024 12:34:40 +0100
+Subject: [PATCH 6/6] [API][FIX] positional options in CWL/CTD
+
+---
+ test/unit/detail/format_ctd_test.cpp | 4 ++--
+ test/unit/detail/format_cwl_test.cpp | 8 ++++----
+ 2 files changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/test/unit/detail/format_ctd_test.cpp b/test/unit/detail/format_ctd_test.cpp
+index eb14047..4e9261a 100644
+--- a/test/unit/detail/format_ctd_test.cpp
++++ b/test/unit/detail/format_ctd_test.cpp
+@@ -42,9 +42,9 @@ struct format_ctd_test : public ::testing::Test
+         "\n"
+         R"del(    <PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">)del"
+         "\n"
+-        R"del(        <ITEM name="positional_0" value="" type="string" description="this is a positional option." required="false" advanced="false" />)del"
++        R"del(        <ITEM name="positional_0" value="" type="string" description="this is a positional option." required="true" advanced="false" />)del"
+         "\n"
+-        R"del(        <ITEM name="positional_1" value="" type="string" description="this is a positional option. Default: []" required="false" advanced="false" />)del"
++        R"del(        <ITEMLIST name="positional_1" type="string" description="this is a positional option. Default: []" required="false" advanced="false" />)del"
+         "\n"
+         R"del(        <ITEM name="int" value="5" type="int" description="this is a int option. Default: 5" required="false" advanced="false" />)del"
+         "\n"
+diff --git a/test/unit/detail/format_cwl_test.cpp b/test/unit/detail/format_cwl_test.cpp
+index eaf0cad..52079db 100644
+--- a/test/unit/detail/format_cwl_test.cpp
++++ b/test/unit/detail/format_cwl_test.cpp
+@@ -82,10 +82,10 @@ TEST(format_cwl_test, full_information)
+                                  "inputs:\n"
+                                  "  positional_0:\n"
+                                  "    doc: this is a positional option.\n"
+-                                 "    type: string?\n"
++                                 "    type: string\n"
+                                  "  positional_1:\n"
+                                  "    doc: \"this is a positional option. Default: []\"\n"
+-                                 "    type: string?\n"
++                                 "    type: string[]?\n"
+                                  "  int:\n"
+                                  "    doc: \"this is a int option. Default: 5\"\n"
+                                  "    type: long?\n"
+@@ -212,10 +212,10 @@ TEST(format_cwl_test, subparser)
+         "inputs:\n"
+         "  positional_0:\n"
+         "    doc: this is a positional option.\n"
+-        "    type: string?\n"
++        "    type: string\n"
+         "  positional_1:\n"
+         "    doc: \"this is a positional option. Default: []\"\n"
+-        "    type: string?\n"
++        "    type: string[]?\n"
+         "  int:\n"
+         "    doc: \"this is a int option. Default: 5\"\n"
+         "    type: long?\n"
+-- 
+2.43.0
+
diff --git a/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch.license b/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+SPDX-License-Identifier: BSD-3-Clause
diff --git a/test/unit/detail/format_ctd_test.cpp b/test/unit/detail/format_ctd_test.cpp
@@ -45,9 +45,9 @@ struct format_ctd_test : public ::testing::Test
         "\n"
         R"del(    <PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">)del"
         "\n"
-        R"del(        <ITEM name="positional_0" value="" type="string" description="this is a positional option." required="false" advanced="false" />)del"
+        R"del(        <ITEM name="positional_0" value="" type="string" description="this is a positional option." required="true" advanced="false" />)del"
         "\n"
-        R"del(        <ITEM name="positional_1" value="" type="string" description="this is a positional option. Default: []" required="false" advanced="false" />)del"
+        R"del(        <ITEMLIST name="positional_1" type="string" description="this is a positional option. Default: []" required="false" advanced="false" />)del"
         "\n"
         R"del(        <ITEM name="int" value="5" type="int" description="this is a int option. Default: 5" required="false" advanced="false" />)del"
         "\n"

diff --git a/test/unit/detail/format_cwl_test.cpp b/test/unit/detail/format_cwl_test.cpp
@@ -85,10 +85,10 @@ TEST(format_cwl_test, full_information)
                                  "inputs:\n"
                                  "  positional_0:\n"
                                  "    doc: this is a positional option.\n"
-                                 "    type: string?\n"
+                                 "    type: string\n"
                                  "  positional_1:\n"
                                  "    doc: \"this is a positional option. Default: []\"\n"
-                                 "    type: string?\n"
+                                 "    type: string[]?\n"
                                  "  int:\n"
                                  "    doc: \"this is a int option. Default: 5\"\n"
                                  "    type: long?\n"
@@ -215,10 +215,10 @@ TEST(format_cwl_test, subparser)
         "inputs:\n"
         "  positional_0:\n"
         "    doc: this is a positional option.\n"
-        "    type: string?\n"
+        "    type: string\n"
         "  positional_1:\n"
         "    doc: \"this is a positional option. Default: []\"\n"
-        "    type: string?\n"
+        "    type: string[]?\n"
         "  int:\n"
         "    doc: \"this is a int option. Default: 5\"\n"
         "    type: long?\n"