{"action":"created","comment":{"url":"https://api.github.com/repos/seqan/seqan3/pulls/comments/172239774","pull_request_review_id":101212001,"id":172239774,"diff_hunk":"@@ -0,0 +1,386 @@\n+// ============================================================================\n+//                 SeqAn - The Library for Sequence Analysis\n+// ============================================================================\n+//\n+// Copyright (c) 2006-2017, Knut Reinert & Freie Universitaet Berlin\n+// Copyright (c) 2016-2017, Knut Reinert & MPI Molekulare Genetik\n+// All rights reserved.\n+//\n+// Redistribution and use in source and binary forms, with or without\n+// modification, are permitted provided that the following conditions are met:\n+//\n+//     * Redistributions of source code must retain the above copyright\n+//       notice, this list of conditions and the following disclaimer.\n+//     * Redistributions in binary form must reproduce the above copyright\n+//       notice, this list of conditions and the following disclaimer in the\n+//       documentation and/or other materials provided with the distribution.\n+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of\n+//       its contributors may be used to endorse or promote products derived\n+//       from this software without specific prior written permission.\n+//\n+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE\n+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\n+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\n+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\n+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT\n+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY\n+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH\n+// DAMAGE.\n+//\n+// ============================================================================\n+\n+/*!\\file\n+ * \\ingroup argument_parser\n+ * \\author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>\n+ * \\brief Contains some standard validators for (positional) options.\n+ */\n+\n+#pragma once\n+\n+#include <sstream>\n+\n+#include <range/v3/all.hpp>\n+\n+#include <seqan3/core/detail/tokenization.hpp>\n+\n+namespace seqan3\n+{\n+\n+template <typename validator_type>\n+concept bool validator_concept = requires(validator_type validator,\n+                                          typename validator_type::value_type value,\n+                                          std::vector<typename validator_type::value_type> value_vector)\n+{\n+    typename validator_type::value_type;\n+    { validator(value) };\n+    { validator(value_vector) };\n+    { validator.get_help_page_message() } -> std::string;\n+};\n+\n+/*!\\brief A validator that checks whether a number is inside a given range.\n+ *\n+ * \\tparam option_value_type Must be a (container of) integral type(s).\n+ *\n+ * \\details\n+ * On construction, the validator must receive a maximum and a minimum number.\n+ * The struct than acts as a functor, that throws a seqan3::parser_invalid_argument\n+ * exception whenever a given value does not lie inside the given min/max range.\n+ *\n+ *```cpp\n+ *     int main(int argc, char ** argv)\n+ *     {\n+ *          seqan3::argument_parser myparser(argc, argv); // initialize\n+ *\n+ *          int myint;\n+ *          seqan3::range_validator my_validator{2, 10};\n+ *\n+ *          myparser.add_option(myint,'i',\"integer\",\"Give me a number.\",\n+ *                              seqan3::option_spec::DEFAULT, my_validator);\n+ *\n+ *          // an exception will be thrown if the user specifies an integer\n+ *          // that is not in range [2,10] (e.g. \"./test_app -i 15\")\n+ *          try\n+ *          {\n+ *               myparser.parse();\n+ *          }\n+ *          catch (seqan3::parser_invalid_argument const & ext) // the user did something wrong\n+ *          {\n+ *               std::cerr << \"[PARSER ERROR] \" << ext.what(); // customize your error message\n+ *               return -1;\n+ *          }\n+ *          catch (seqan3::parser_interruption const &) // expected behaviour on special requests (e.g. `--help`)\n+ *          {\n+ *               return 0;\n+ *          }\n+ *\n+ *          std::cout << \"integer given by user passed validation: \" << myint << endl;\n+ *          return 0;\n+ *     }\n+ *```\n+ */\n+template <typename option_value_type>\n+//!\\cond\n+    requires integral_concept<option_value_type> || integral_concept<typename option_value_type::value_type>\n+//!\\cond\n+class range_validator\n+{\n+public:\n+    using value_type = option_value_type; //! Type of values that are tested by validator\n+\n+    /*!\\brief The constructor.\n+     *\n+     * \\param min_ Minimum set for the range to test.\n+     * \\param max_ Maximum set for the range to test.\n+     */\n+    range_validator(option_value_type const min_, option_value_type const max_) :\n+        min{min_}, max{max_}\n+    {}\n+\n+    /*!\\brief Tests whether cmp lies inside [min,max].\n+     * \\throws parser_invalid_argument\n+     */\n+    void operator()(option_value_type const & cmp) const\n+    {\n+        if (!((cmp <= max) && (cmp >= min)))\n+            throw parser_invalid_argument(detail::paste(\"Validation Failed - Value \", cmp,\n+                                                        \" is not in range [\", min, \",\", max, \"].\"));\n+    }\n+\n+    //!\\brief Tests whether all values of v lie inside [min,max].\n+    template <typename container_type>\n+    //!\\cond\n+        requires container_concept<container_type> &&\n+                 std::is_same<typename container_type::value_type, option_value_type>::value\n+    //!\\endcond\n+    void operator()(container_type const & v) const\n+    {\n+        std::for_each(v.begin(), v.end(), [&] (auto cmp) { (*this)(cmp); });\n+    }\n+\n+    //!\\brief Returns a message that can be appended to the (positional) options help page info.\n+    std::string get_help_page_message() const\n+    {\n+        return detail::paste(\"Value must be in range [\", min, \",\", max, \"].\");\n+    }\n+\n+private:\n+    //! \\privatesection\n+\n+    //!\\brief Minimum of the range to test.\n+    option_value_type min;\n+\n+    //!\\brief Maximum of the range to test.\n+    option_value_type max;\n+\n+};\n+\n+/*!\\brief A validator that checks whether a value is inside a list of valid values.\n+ *\n+ * \\details\n+ * On construction, the validator must receive a list (vector) of valid values.\n+ * The struct than acts as a functor, that throws a seqan3::parser_invalid_argument\n+ * exception whenever a given value is not in the given list.\n+ *\n+ *```cpp\n+ *     int main(int argc, char ** argv)\n+ *     {\n+ *          seqan3::argument_parser myparser(argc, argv); // initialize\n+ *\n+ *          int myint;\n+ *          seqan3::value_list_validator my_validator{2,4,6,8,10};\n+ *\n+ *          myparser.add_option(myint,'i',\"integer\",\"Give me a number.\",\n+ *                              seqan3::option_spec::DEFAULT, my_validator);\n+ *\n+ *          // an exception will be thrown if the user specifies an integer\n+ *          // that is not one of [2,4,6,8,10] (e.g. \"./test_app -i 3\")\n+ *          try\n+ *          {\n+ *               myparser.parse();\n+ *          }\n+ *          catch (seqan3::parser_invalid_argument const & ext) // the user did something wrong\n+ *          {\n+ *               std::cerr << \"[PARSER ERROR] \" << ext.what(); // customize your error message\n+ *               return -1;\n+ *          }\n+ *          catch (seqan3::parser_interruption const &) // expected behaviour on special requests (e.g. `--help`)\n+ *          {\n+ *               return 0;\n+ *          }\n+ *\n+ *          std::cout << \"integer given by user passed validation: \" << myint << endl;\n+ *          return 0;\n+ *     }\n+ *```\n+ */\n+template <typename option_value_type>\n+class value_list_validator\n+{\n+public:\n+    using value_type = option_value_type; //! Type of values that are tested by validator\n+\n+    /*!\\brief Constructing from a vector.\n+     *\n+     * \\param v The vector of valid values to test.\n+     */\n+    value_list_validator(std::vector<option_value_type> const & v) :\n+        values{v}\n+    {}\n+\n+    /*!\\brief Constructing from an initializer_list.\n+     *\n+     * \\param v The initializer_list of valid values to test.\n+     */\n+    value_list_validator(std::initializer_list<option_value_type> const & v) :\n+        values{v}\n+    {}\n+\n+    /*!\\brief Tests whether cmp lies inside values.\n+     * \\throws parser_invalid_argument\n+     */\n+    void operator()(option_value_type const & cmp) const\n+    {\n+        if (!(std::find(values.begin(), values.end(), cmp) != values.end()))\n+            throw parser_invalid_argument(detail::paste(\"Value \", cmp, \" is not one of \", ranges::view::all(values), \".\"));\n+    }\n+\n+    //!\\brief Tests whether every value of v lies inside values.\n+    template <typename container_type>\n+    //!\\cond\n+        requires container_concept<container_type> &&\n+                 std::is_same<typename container_type::value_type, option_value_type>::value\n+    //!\\endcond\n+    void operator()(container_type const & v) const\n+    {\n+        std::for_each(v.begin(), v.end(), [&] (auto cmp) { (*this)(cmp); });\n+    }\n+\n+    //!\\brief Returns a message that can be appended to the (positional) options help page info.\n+    std::string get_help_page_message() const\n+    {\n+        return detail::paste(\"Value must be one of \", ranges::view::all(values), \".\");\n+    }\n+\n+private:\n+\n+    //!\\brief Minimum of the range to test.\n+    std::vector<option_value_type> values;\n+};\n+\n+//!\\brief Type deduction for const char * initializer list to be seen as string\n+value_list_validator(std::initializer_list<const char *> const & v) -> value_list_validator<std::string>;\n+\n+/*!\\brief A validator that checks if a filenames has one of the valid extensions.\n+ *\n+ * \\details\n+ * On construction, the validator must receive a list (vector) of valid file extensions.\n+ * The struct than acts as a functor, that throws a seqan3::parser_invalid_argument\n+ * exception whenever a given filename (string) is not in the given extension list.\n+ *\n+ *```cpp\n+ *     int main(int argc, char ** argv)\n+ *     {\n+ *          seqan3::argument_parser myparser(argc, argv); // initialize\n+ *\n+ *          std::string myfile;\n+ *          seqan3::file_ext_validator my_validator{\"fa\",\"fasta\"};\n+ *\n+ *          myparser.add_option(myfile,'f',\"file\",\"Give me a filename.\",\n+ *                              seqan3::option_spec::DEFAULT, my_validator);\n+ *\n+ *          // an exception will be thrown if the user specifies a filename\n+ *          // that does not have one of the extensions [\"fa\",\"fasta\"]\n+ *          try\n+ *          {\n+ *               myparser.parse();\n+ *          }\n+ *          catch (seqan3::parser_invalid_argument const & ext) // the user did something wrong\n+ *          {\n+ *               std::cerr << \"[PARSER ERROR] \" << ext.what(); // customize your error message\n+ *               return -1;\n+ *          }\n+ *          catch (seqan3::parser_interruption const &) // expected behaviour on special requests (e.g. `--help`)\n+ *          {\n+ *               return 0;\n+ *          }\n+ *\n+ *          std::cout << \"filename given by user passed validation: \" << myfile << endl;\n+ *          return 0;\n+ *     }\n+ *```\n+ */\n+class file_ext_validator // TODO check if file exists, also allow filepath\n+{\n+public:\n+    using value_type = std::string; //! Type of values that are tested by validator\n+\n+    /*!\\brief Constructing from a vector.\n+     *\n+     * \\param v The vector of valid file extensions to test (e.g. {\"fa\", \"fasta\"}).\n+     */\n+    file_ext_validator(std::vector<std::string> const & v) :\n+        extensions{v}\n+    {}\n+\n+    /*!\\brief Constructing from an initializer_list.\n+     *\n+     * \\param v The initializer_list of valid file extensions to test (e.g. {\"fa\", \"fasta\"}).\n+     */\n+    file_ext_validator(std::initializer_list<std::string> const & v) :\n+        extensions{v}\n+    {}\n+\n+    /*!\\brief Tests whether cmp lies inside extensions.\n+     * \\throws parser_invalid_argument\n+     */\n+    void operator()(std::string const & cmp) const\n+    {\n+        std::string ext{cmp.substr(cmp.find_last_of('.') + 1)};\n+\n+        if (!(std::find(extensions.begin(), extensions.end(), ext) != extensions.end()))\n+            throw parser_invalid_argument(detail::paste(\"Extension \", ext, \" is not one of \",\n+                                                        ranges::view::all(extensions), \".\"));\n+    }\n+\n+    //!\\brief Tests whether every value of v lies inside extensions.\n+    void operator()(std::vector<std::string> const & v) const\n+    {\n+        std::for_each(v.begin(), v.end(), [&] (auto cmp) { (*this)(cmp); });\n+    }\n+\n+    //!\\brief Returns a message that can be appended to the (positional) options help page info.\n+    std::string get_help_page_message() const\n+    {\n+        return detail::paste(\"File name extension must be one of \", ranges::view::all(extensions), \".\");\n+    }\n+\n+private:\n+    //!\\brief Stores valid file extensions.\n+    std::vector<std::string> extensions;\n+","path":"include/seqan3/argument_parser/validators.hpp","position":343,"original_position":343,"commit_id":"1ddd52d3c936e286d2d06060e699d6fe9dff6a36","original_commit_id":"1ddd52d3c936e286d2d06060e699d6fe9dff6a36","user":{"login":"h-2","id":2996863,"avatar_url":"https://avatars2.githubusercontent.com/u/2996863?v=4","gravatar_id":"","url":"https://api.github.com/users/h-2","html_url":"https://github.com/h-2","followers_url":"https://api.github.com/users/h-2/followers","following_url":"https://api.github.com/users/h-2/following{/other_user}","gists_url":"https://api.github.com/users/h-2/gists{/gist_id}","starred_url":"https://api.github.com/users/h-2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/h-2/subscriptions","organizations_url":"https://api.github.com/users/h-2/orgs","repos_url":"https://api.github.com/users/h-2/repos","events_url":"https://api.github.com/users/h-2/events{/privacy}","received_events_url":"https://api.github.com/users/h-2/received_events","type":"User","site_admin":false},"body":"remove empty line","created_at":"2018-03-05T16:12:28Z","updated_at":"2018-03-05T16:59:33Z","html_url":"https://github.com/seqan/seqan3/pull/88#discussion_r172239774","pull_request_url":"https://api.github.com/repos/seqan/seqan3/pulls/88","author_association":"OWNER","_links":{"self":{"href":"https://api.github.com/repos/seqan/seqan3/pulls/comments/172239774"},"html":{"href":"https://github.com/seqan/seqan3/pull/88#discussion_r172239774"},"pull_request":{"href":"https://api.github.com/repos/seqan/seqan3/pulls/88"}}},"pull_request":{"url":"https://api.github.com/repos/seqan/seqan3/pulls/88","id":131347807,"html_url":"https://github.com/seqan/seqan3/pull/88","diff_url":"https://github.com/seqan/seqan3/pull/88.diff","patch_url":"https://github.com/seqan/seqan3/pull/88.patch","issue_url":"https://api.github.com/repos/seqan/seqan3/issues/88","number":88,"state":"open","locked":false,"title":"[FEATURE] The Argument Parser","user":{"login":"smehringer","id":7955878,"avatar_url":"https://avatars3.githubusercontent.com/u/7955878?v=4","gravatar_id":"","url":"https://api.github.com/users/smehringer","html_url":"https://github.com/smehringer","followers_url":"https://api.github.com/users/smehringer/followers","following_url":"https://api.github.com/users/smehringer/following{/other_user}","gists_url":"https://api.github.com/users/smehringer/gists{/gist_id}","starred_url":"https://api.github.com/users/smehringer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/smehringer/subscriptions","organizations_url":"https://api.github.com/users/smehringer/orgs","repos_url":"https://api.github.com/users/smehringer/repos","events_url":"https://api.github.com/users/smehringer/events{/privacy}","received_events_url":"https://api.github.com/users/smehringer/received_events","type":"User","site_admin":false},"body":"Some TODOs are left but you can start attacking the code and documentation\r\n\r\nTODOs:\r\n- [ ] Version Checker\r\n- [ ] CTD format\r\n(maybe those can be put into separate issues since they do not collide with any basic functionality)\r\n- [ ] Tests","created_at":"2017-07-19T15:15:21Z","updated_at":"2018-03-05T16:59:34Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c31ac8acd30c2d728c4b5420fce9c05746a23b3a","assignee":null,"assignees":[],"requested_reviewers":[{"login":"rrahn","id":1529364,"avatar_url":"https://avatars2.githubusercontent.com/u/1529364?v=4","gravatar_id":"","url":"https://api.github.com/users/rrahn","html_url":"https://github.com/rrahn","followers_url":"https://api.github.com/users/rrahn/followers","following_url":"https://api.github.com/users/rrahn/following{/other_user}","gists_url":"https://api.github.com/users/rrahn/gists{/gist_id}","starred_url":"https://api.github.com/users/rrahn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rrahn/subscriptions","organizations_url":"https://api.github.com/users/rrahn/orgs","repos_url":"https://api.github.com/users/rrahn/repos","events_url":"https://api.github.com/users/rrahn/events{/privacy}","received_events_url":"https://api.github.com/users/rrahn/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[{"id":568314043,"url":"https://api.github.com/repos/seqan/seqan3/labels/feature/proposal","name":"feature/proposal","color":"0e8a16","default":false},{"id":581690505,"url":"https://api.github.com/repos/seqan/seqan3/labels/in%20progress","name":"in 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