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move code from include/gemmi/json.hpp to src/json.cpp
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,113 @@ | ||
| // Copyright Global Phasing Ltd. | ||
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| #include <gemmi/json.hpp> | ||
| #include <algorithm> // for move | ||
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| #define SAJSON_UNSORTED_OBJECT_KEYS | ||
| #define SAJSON_NUMBERS_AS_STRINGS | ||
| #include "../third_party/sajson.h" | ||
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| namespace gemmi { | ||
| namespace cif { | ||
| using std::size_t; | ||
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| static std::string json_type_as_string(sajson::type t) { | ||
| switch (t) { | ||
| case sajson::TYPE_INTEGER: return "<integer>"; | ||
| case sajson::TYPE_DOUBLE: return "<double>"; | ||
| case sajson::TYPE_NULL: return "<null>"; | ||
| case sajson::TYPE_FALSE: return "<false>"; | ||
| case sajson::TYPE_TRUE: return "<true>"; | ||
| case sajson::TYPE_STRING: return "<string>"; | ||
| case sajson::TYPE_ARRAY: return "<array>"; | ||
| case sajson::TYPE_OBJECT: return "<object>"; | ||
| default: return "<unknown type>"; | ||
| } | ||
| } | ||
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| static std::string as_cif_value(const sajson::value& val) { | ||
| switch (val.get_type()) { | ||
| case sajson::TYPE_DOUBLE: | ||
| return val.as_string(); | ||
| case sajson::TYPE_NULL: | ||
| return "?"; | ||
| // mmJSON files from PDBj (this format has no spec) have special support | ||
| // for boolean YES|NO, which is used only in category _em_specimen. | ||
| // IMO it's a bad idea, but we must handle it if we want to read mmJSON. | ||
| case sajson::TYPE_FALSE: | ||
| return "NO"; // "." in CIF-JSON | ||
| case sajson::TYPE_TRUE: | ||
| return "YES"; | ||
| case sajson::TYPE_STRING: | ||
| return quote(val.as_string()); | ||
| default: | ||
| fail("Unexpected ", json_type_as_string(val.get_type()), " in JSON."); | ||
| return ""; | ||
| } | ||
| } | ||
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| static void fill_document_from_sajson(Document& d, const sajson::document& s) { | ||
| // assuming mmJSON here, we'll add handling of CIF-JSON later on | ||
| sajson::value root = s.get_root(); | ||
| if (root.get_type() != sajson::TYPE_OBJECT || root.get_length() != 1) | ||
| fail("not mmJSON"); | ||
| std::string block_name = root.get_object_key(0).as_string(); | ||
| if (!starts_with(block_name, "data_")) | ||
| fail("not mmJSON - top level key should start with data_\n" | ||
| "(if you use gemmi-cif2json to write JSON, use -m for mmJSON)"); | ||
| d.blocks.emplace_back(block_name.substr(5)); | ||
| std::vector<Item>& items = d.blocks[0].items; | ||
| sajson::value top = root.get_object_value(0); | ||
| if (top.get_type() != sajson::TYPE_OBJECT) | ||
| fail(""); | ||
| for (size_t i = 0; i != top.get_length(); ++i) { | ||
| std::string category_name = "_" + top.get_object_key(i).as_string() + "."; | ||
| sajson::value category = top.get_object_value(i); | ||
| if (category.get_type() != sajson::TYPE_OBJECT || | ||
| category.get_length() == 0 || | ||
| category.get_object_value(0).get_type() != sajson::TYPE_ARRAY) | ||
| fail(""); | ||
| size_t cif_cols = category.get_length(); | ||
| size_t cif_rows = category.get_object_value(0).get_length(); | ||
| if (cif_rows > 1) { | ||
| items.emplace_back(LoopArg{}); | ||
| Loop& loop = items.back().loop; | ||
| loop.tags.reserve(cif_cols); | ||
| loop.values.resize(cif_cols * cif_rows); | ||
| } | ||
| for (size_t j = 0; j != cif_cols; ++j) { | ||
| std::string tag = category_name + category.get_object_key(j).as_string(); | ||
| sajson::value arr = category.get_object_value(j); | ||
| if (arr.get_type() != sajson::TYPE_ARRAY) | ||
| fail("Expected array, got " + json_type_as_string(arr.get_type())); | ||
| if (arr.get_length() != cif_rows) | ||
| fail("Expected array of length ", std::to_string(cif_rows), " not ", | ||
| std::to_string(arr.get_length())); | ||
| if (cif_rows == 1) { | ||
| items.emplace_back(tag, as_cif_value(arr.get_array_element(0))); | ||
| } else { | ||
| Loop& loop = items.back().loop; | ||
| loop.tags.emplace_back(std::move(tag)); | ||
| for (size_t k = 0; k != cif_rows; ++k) | ||
| loop.values[j + k*cif_cols] = as_cif_value(arr.get_array_element(k)); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| Document read_mmjson_insitu(char* buffer, size_t size, const std::string& name) { | ||
| Document doc; | ||
| sajson::document json = sajson::parse(sajson::dynamic_allocation(), | ||
| sajson::mutable_string_view(size, buffer)); | ||
| if (!json.is_valid()) | ||
| fail(name + ":", std::to_string(json.get_error_line()), " error: ", | ||
| json.get_error_message_as_string()); | ||
| fill_document_from_sajson(doc, json); | ||
| doc.source = name; | ||
| return doc; | ||
| } | ||
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| } // namespace cif | ||
| } // namespace gemmi |
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