[FEATURE] Adapt input/output file validator to read extensions from a…

… file.
seqan · Jul 11, 2019 · f3f4b52 · f3f4b52
1 parent 7c8d29f
commit f3f4b52
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Showing 2 changed files with 57 additions and 1 deletion.
diff --git a/include/seqan3/argument_parser/validators.hpp b/include/seqan3/argument_parser/validators.hpp
@@ -21,6 +21,7 @@
 #include <seqan3/core/detail/to_string.hpp>
 #include <seqan3/core/type_traits/basic.hpp>
 #include <seqan3/core/type_traits/pre.hpp>
+#include <seqan3/io/detail/misc.hpp>
 #include <seqan3/io/detail/safe_filesystem_entry.hpp>
 #include <seqan3/range/container/concept.hpp>
 #include <seqan3/range/view/drop.hpp>
@@ -412,6 +413,20 @@ class input_file_validator : public file_validator_base
     input_file_validator & operator=(input_file_validator &&) = default;      //!< Defaulted.
     virtual ~input_file_validator() = default;                                //!< Virtual destructor.
 
+    /*!\brief Constructs from a given file.
+     * \tparam    file_t The type of the file; must have a member type called `valid_formats` containing the formats.
+     * \param[in] file   The file to get the valid extensions for.
+     *
+     * \details
+     *
+     * Uses the extensions from the formats of the file to initialise the valid extensions.
+     */
+    template <typename file_t>
+        requires requires { typename file_t::valid_formats; }
+    explicit input_file_validator(file_t const & SEQAN3_DOXYGEN_ONLY(file)) :
+        file_validator_base{detail::valid_file_extensions<typename file_t::valid_formats>()}
+    {}
+
     // Import base class constructor.
     using file_validator_base::file_validator_base;
     //!\}
@@ -487,6 +502,20 @@ class output_file_validator : public file_validator_base
     output_file_validator & operator=(output_file_validator &&) = default;        //!< Defaulted.
     virtual ~output_file_validator() = default;                                   //!< Virtual Destructor.
 
+    /*!\brief Constructs from a given file.
+     * \tparam    file_t The type of the file; must have a member type called `valid_formats` containing the formats.
+     * \param[in] file   The file to get the valid extensions for.
+     *
+     * \details
+     *
+     * Uses the extensions from the formats of the file to initialise the valid extensions.
+     */
+    template <typename file_t>
+        requires requires { typename file_t::valid_formats; }
+    explicit output_file_validator(file_t const & SEQAN3_DOXYGEN_ONLY(file)) :
+        file_validator_base{detail::valid_file_extensions<typename file_t::valid_formats>()}
+    {}
+
     // Import base constructor.
     using file_validator_base::file_validator_base;
     //!\}

diff --git a/test/unit/argument_parser/format_parse_validators_test.cpp b/test/unit/argument_parser/format_parse_validators_test.cpp
@@ -21,6 +21,22 @@
 
 using namespace seqan3;
 
+struct dummy_file
+{
+
+    struct format1
+    {
+        static inline std::vector<std::string> file_extensions{ {"fa"}, {"fasta"}};
+    };
+
+    struct format2
+    {
+        static inline std::vector<std::string> file_extensions{ {"sam"}, {"bam"}};
+    };
+
+    using valid_formats = type_list<format1, format2>;
+};
+
 std::string const basic_options_str = "OPTIONS"
                                       "Basic options:"
                                       "-h, --help Prints the help page."
@@ -92,6 +108,12 @@ TEST(validator_test, input_file)
             EXPECT_THROW(my_validator(does_not_exist), parser_invalid_argument);
         }
 
+        {  // read from file
+            dummy_file df{};
+            input_file_validator my_validator{df};
+            EXPECT_NO_THROW(my_validator(tmp_name.get_path()));
+        }
+
         std::filesystem::path file_in_path;
 
         // option
@@ -166,7 +188,7 @@ TEST(validator_test, output_file)
 
         { // file has wrong format.
             output_file_validator my_validator{std::vector{std::string{"sam"}}};
-                EXPECT_THROW(my_validator(tmp_name.get_path()), parser_invalid_argument);
+            EXPECT_THROW(my_validator(tmp_name.get_path()), parser_invalid_argument);
         }
 
         { // file has no extension.
@@ -176,6 +198,11 @@ TEST(validator_test, output_file)
             EXPECT_THROW(my_validator(no_extension), parser_invalid_argument);
         }
 
+        {  // read from file
+            output_file_validator my_validator{dummy_file{}};
+            EXPECT_NO_THROW(my_validator(tmp_name.get_path()));
+        }
+
         std::filesystem::path file_out_path;
 
         // option