EXP_interface.cxx

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//  ==================================================================== //
//                                                                       //
//    File      : EXP_interface.cxx                                      //
//    Purpose   :                                                        //
//                                                                       //
//                                                                       //
//  Coded by Ralf Westram (coder@reallysoft.de) in September 2001        //
//  Copyright Department of Microbiology (Technical University Munich)   //
//                                                                       //
//  Visit our web site at: http://www.arb-home.de/                       //
//                                                                       //
//                                                                       //
//  ==================================================================== //

#include "EXP_local.hxx"
#include "GEN_local.hxx"

#include <db_query.h>
#include <db_scanner.hxx>
#include <dbui.h>
#include <item_sel_list.h>
#include <info_window.h>

#include <awt_prompt.hxx>
#include <awt_sel_boxes.hxx>

#include <aw_awar_defs.hxx>
#include <aw_root.hxx>
#include <aw_msg.hxx>
#include <aw_question.hxx>

using namespace std;

#define AD_F_ALL AWM_ALL

static GBDATA* get_current_experiment_data(GBDATA *gb_main) {
    GBDATA *gb_species         = GEN_get_current_organism(gb_main);
    GBDATA *gb_experiment_data = NULp;

    if (gb_species) gb_experiment_data = EXP_get_experiment_data(gb_species);

    return gb_experiment_data;
}

static void EXP_select_experiment(GBDATA* /* gb_main */, AW_root *aw_root, const char *item_name) {
    char *name  = ARB_strdup(item_name);
    char *slash = strchr(name, '/');

    if (slash) {
        slash[0] = 0;
        aw_root->awar(AWAR_ORGANISM_NAME)->write_string(name);
        aw_root->awar(AWAR_EXPERIMENT_NAME)->write_string(slash+1);
    }
    free(name);
}

static char *EXP_get_experiment_id(GBDATA * /* gb_main */, GBDATA *gb_experiment) {
    GBDATA *gb_species = GB_get_grandfather(gb_experiment);
    return GBS_global_string_copy("%s/%s", GBT_get_name_or_description(gb_species), GBT_get_name_or_description(gb_experiment));
}

static GBDATA *EXP_find_experiment_by_id(GBDATA *gb_main, const char *id) {
    char   *organism = ARB_strdup(id);
    char   *exp      = strchr(organism, '/');
    GBDATA *result   = NULp;

    if (exp) {
        *exp++ = 0;
        GBDATA *gb_organism = GEN_find_organism(gb_main, organism);
        if (gb_organism) {
            result = EXP_find_experiment(gb_organism, exp);
        }
    }

    free(organism);
    return result;
}

static char *old_species_marks = NULp; // configuration storing marked species

inline void exp_restore_old_species_marks(GBDATA *gb_main) {
    if (old_species_marks) {
        GBT_restore_marked_species(gb_main, old_species_marks);
        freenull(old_species_marks);
    }
}

static GBDATA *EXP_get_first_experiment_data(GBDATA *gb_main, AW_root *aw_root, QUERY_RANGE range) {
    GBDATA   *gb_organism = NULp;
    GB_ERROR  error       = NULp;

    gen_assert(!old_species_marks); // old_species_marks may be out of date (better call EXP_get_(first|next)_experiment_data until it returns NULp!)
    exp_restore_old_species_marks(gb_main);

    switch (range) {
        case QUERY_CURRENT_ITEM: {
            char *species_name = aw_root->awar(AWAR_ORGANISM_NAME)->read_string();
            gb_organism         = GBT_find_species(gb_main, species_name);
            free(species_name);
            break;
        }
        case QUERY_MARKED_ITEMS: {
            GBDATA *gb_pseudo = GEN_first_marked_pseudo_species(gb_main);

            if (gb_pseudo) {    // there are marked pseudo-species..
                old_species_marks = GBT_store_marked_species(gb_main, true); // store and unmark marked species
                error             = GBT_with_stored_species(gb_main, old_species_marks, GEN_mark_organism_or_corresponding_organism, NULp); // mark organisms related with stored

                if (!error) {
                    gb_organism = GEN_first_marked_organism(gb_main);
                    if (!gb_organism) exp_restore_old_species_marks(gb_main); // got all -> clean up
                }
            }
            else {
                gb_organism = GEN_first_marked_organism(gb_main);
            }
            break;
        }
        case QUERY_ALL_ITEMS: {
            gb_organism = GBT_first_species(gb_main);
            break;
        }
        default: {
            gen_assert(0);
            break;
        }
    }

    if (error) GB_export_error(error);
    return gb_organism ? EXP_get_experiment_data(gb_organism) : NULp;
}

static GBDATA *EXP_get_next_experiment_data(GBDATA *gb_experiment_data, QUERY_RANGE range) {
    GBDATA *gb_organism = NULp;
    switch (range) {
        case QUERY_CURRENT_ITEM: {
            break;
        }
        case QUERY_MARKED_ITEMS: {
            GBDATA *gb_last_species = GB_get_father(gb_experiment_data);
            gb_organism             = GEN_next_marked_organism(gb_last_species);

            if (!gb_organism) exp_restore_old_species_marks(GB_get_root(gb_experiment_data)); // got all -> clean up
            break;
        }
        case QUERY_ALL_ITEMS: {
            GBDATA *gb_last_species = GB_get_father(gb_experiment_data);
            gb_organism             = GBT_next_species(gb_last_species);
            break;
        }
        default: {
            gen_assert(0);
            break;
        }
    }

    return gb_organism ? EXP_get_experiment_data(gb_organism) : NULp;
}

static GBDATA *EXP_get_current_experiment(GBDATA *gb_main, AW_root *aw_root) {
    GBDATA *gb_organism   = GEN_get_current_organism(gb_main);
    GBDATA *gb_experiment = NULp;

    if (gb_organism) {
        char *experiment_name = aw_root->awar(AWAR_EXPERIMENT_NAME)->read_string();
        gb_experiment         = EXP_find_experiment(gb_organism, experiment_name);
        free(experiment_name);
    }

    return gb_experiment;
}

static void add_selected_experiment_changed_cb(AW_root *aw_root, const RootCallback& cb) {
    aw_root->awar(AWAR_EXPERIMENT_NAME)->add_callback(cb);
    ORGANISM_get_selector().add_selection_changed_cb(aw_root, cb);
}

static GBDATA *first_experiment_in_range(GBDATA *gb_experiment_data, QUERY_RANGE range) {
    GBDATA *gb_first = NULp;
    switch (range) {
        case QUERY_ALL_ITEMS:    gb_first = EXP_first_experiment_rel_exp_data(gb_experiment_data); break;
        case QUERY_MARKED_ITEMS: gb_first = GB_first_marked(gb_experiment_data, "experiment"); break;
        case QUERY_CURRENT_ITEM: gb_first = EXP_get_current_experiment(GB_get_root(gb_experiment_data), AW_root::SINGLETON); break;
    }
    return gb_first;
}
static GBDATA *next_experiment_in_range(GBDATA *gb_prev, QUERY_RANGE range) {
    GBDATA *gb_next = NULp;
    switch (range) {
        case QUERY_ALL_ITEMS:    gb_next = EXP_next_experiment(gb_prev); break;
        case QUERY_MARKED_ITEMS: gb_next = GB_next_marked(gb_prev, "experiment"); break;
        case QUERY_CURRENT_ITEM: gb_next = NULp; break;
    }
    return gb_next;
}

static void refresh_displayed_experiments() {} // nothing todo here

static struct MutableItemSelector EXP_item_selector = { // @@@ move to SL/ITEMS
    QUERY_ITEM_EXPERIMENTS,
    EXP_select_experiment,
    EXP_get_experiment_id,
    EXP_find_experiment_by_id,
    experiment_field_selection_list_update_cb,
    -1, // unknown
    CHANGE_KEY_PATH_EXPERIMENTS,
    "experiment",
    "experiments",
    "name",
    EXP_get_first_experiment_data,
    EXP_get_next_experiment_data,
    first_experiment_in_range,
    next_experiment_in_range,
    EXP_get_current_experiment,
    add_selected_experiment_changed_cb,
    &ORGANISM_get_selector(), GB_get_grandfather,
    refresh_displayed_experiments,
};

ItemSelector& EXP_get_selector() { return EXP_item_selector; }

static QUERY::DbQuery *GLOBAL_experiment_query = NULp;

AW_window *EXP_create_experiment_query_window(AW_root *aw_root, GBDATA *gb_main) { // @@@ move to SL/DB_UI
    static AW_window_simple_menu *aws = NULp;
    if (!aws) {
        aws = new AW_window_simple_menu;
        aws->init(aw_root, "EXPERIMENT_QUERY", "Experiment SEARCH and QUERY");
        aws->create_menu("More functions", "f");
        aws->load_xfig("ad_query.fig");

        QUERY::query_spec awtqs(EXP_get_selector());

        awtqs.gb_main              = gb_main;
        awtqs.species_name         = AWAR_SPECIES_NAME;
        awtqs.tree_name            = AWAR_TREE;
        awtqs.select_bit           = GB_USERFLAG_QUERY;
        awtqs.use_menu             = 1;
        awtqs.ere_pos_fig          = "ere3";
        awtqs.where_pos_fig        = "where3";
        awtqs.by_pos_fig           = "by3";
        awtqs.qbox_pos_fig         = "qbox";
        awtqs.key_pos_fig          = NULp;
        awtqs.query_pos_fig        = "content";
        awtqs.result_pos_fig       = "result";
        awtqs.count_pos_fig        = "count";
        awtqs.do_query_pos_fig     = "doquery";
        awtqs.config_pos_fig       = "doconfig";
        awtqs.do_mark_pos_fig      = "domark";
        awtqs.do_unmark_pos_fig    = "dounmark";
        awtqs.do_mark_nt_pos_fig   = "domark_nt";
        awtqs.do_unmark_nt_pos_fig = "dounmark_nt";
        awtqs.do_delete_pos_fig    = "dodelete";
        awtqs.do_set_pos_fig       = "doset";
        awtqs.do_refresh_pos_fig   = "dorefresh";
        awtqs.open_parser_pos_fig  = "openparser";
        awtqs.popup_info_window    = EXP_popup_experiment_window;

        QUERY::DbQuery *query   = create_query_box(aws, &awtqs, "exp");
        GLOBAL_experiment_query = query;

        aws->create_menu("More search",     "s");
        aws->insert_menu_topic("exp_search_equal_fields_within_db", "Search For Equal Fields and Mark Duplicates",              "E", "search_duplicates.hlp", AWM_ALL, makeWindowCallback(QUERY::search_duplicated_field_content, query, false));
        aws->insert_menu_topic("exp_search_equal_words_within_db", "Search For Equal Words Between Fields and Mark Duplicates", "W", "search_duplicates.hlp", AWM_ALL, makeWindowCallback(QUERY::search_duplicated_field_content, query, true));

        aws->button_length(7);

        aws->at("close");
        aws->callback(AW_POPDOWN);
        aws->create_button("CLOSE", "CLOSE", "C");

        aws->at("help");
        aws->callback(makeHelpCallback("experiment_search.hlp"));
        aws->create_button("HELP", "HELP", "H");
    }
    return aws;
}

static void experiment_delete_cb(AW_window *aww, GBDATA *gb_main) {
    if (aw_ask_sure("experiment_delete", "Are you sure to delete the experiment")) {
        GB_transaction  ta(gb_main);
        GBDATA         *gb_experiment = EXP_get_current_experiment(gb_main, aww->get_root());

        GB_ERROR error = gb_experiment ? GB_delete(gb_experiment) : "Please select a experiment first";
        if (error) {
            error = ta.close(error);
            aw_message(error);
        }
    }
}

static GB_ERROR experiment_create_handler(const char *dest, GBDATA *gb_main) {
    GB_ERROR error = GB_begin_transaction(gb_main);

    if (!error) {
        AW_root *aw_root            = AW_root::SINGLETON;
        GBDATA  *gb_experiment_data = get_current_experiment_data(gb_main);

        if (!gb_experiment_data) error = "Please select an organism";
        else {
            GBDATA *gb_dest = EXP_find_experiment_rel_exp_data(gb_experiment_data, dest);
            if (gb_dest) {
                error  = GBS_global_string("Experiment '%s' already exists", dest);
            }
            else {
                gb_dest             = EXP_find_or_create_experiment_rel_exp_data(gb_experiment_data, dest);
                if (!gb_dest) error = GB_await_error();
                else aw_root->awar(AWAR_EXPERIMENT_NAME)->write_string(dest);
            }
        }
    }

    error = GB_end_transaction(gb_main, error);
    return error;
}
static GB_ERROR experiment_rename_handler(const char *dest, GBDATA *gb_main) {
    AW_root    *awr    = AW_root::SINGLETON;
    const char *source = awr->awar(AWAR_EXPERIMENT_NAME)->read_char_pntr();
    GB_ERROR    error  = NULp;

    if (strcmp(source, dest) != 0) {
        error = GB_begin_transaction(gb_main);
        if (!error) {
            GBDATA *gb_experiment_data = get_current_experiment_data(gb_main);

            if (!gb_experiment_data) error = "Please select an organism";
            else {
                GBDATA *gb_source = EXP_find_experiment_rel_exp_data(gb_experiment_data, source);
                GBDATA *gb_dest   = EXP_find_experiment_rel_exp_data(gb_experiment_data, dest);

                if (!gb_source) error   = "Please select an experiment";
                else if (gb_dest) error = GB_export_errorf("Experiment '%s' already exists", dest);
                else {
                    GBDATA *gb_name     = GB_search(gb_source, "name", GB_STRING);
                    if (!gb_name) error = GB_await_error();
                    else {
                        error = GB_write_string(gb_name, dest);
                        if (!error) awr->awar(AWAR_EXPERIMENT_NAME)->write_string(dest);
                    }
                }
            }
        }
        error = GB_end_transaction(gb_main, error);
    }

    return error;
}
static GB_ERROR experiment_copy_handler(const char *dest, GBDATA *gb_main) {
    AW_root    *awr    = AW_root::SINGLETON;
    const char *source = awr->awar(AWAR_EXPERIMENT_NAME)->read_char_pntr();
    GB_ERROR    error  = GB_begin_transaction(gb_main);

    if (!error) {
        GBDATA *gb_experiment_data = get_current_experiment_data(gb_main);

        if (!gb_experiment_data) error = "Please select an organism";
        else {
            GBDATA *gb_source = EXP_find_experiment_rel_exp_data(gb_experiment_data, source);
            GBDATA *gb_dest   = EXP_find_experiment_rel_exp_data(gb_experiment_data, dest);

            if (!gb_source) error   = "Please select an experiment";
            else if (gb_dest) error = GB_export_errorf("Experiment '%s' already exists", dest);
            else {
                gb_dest             = GB_create_container(gb_experiment_data, "experiment");
                if (!gb_dest) error = GB_await_error();
                else error          = GB_copy_dropProtectMarksAndTempstate(gb_dest, gb_source);

                if (!error) {
                    error = GBT_write_string(gb_dest, "name", dest);
                    if (!error) awr->awar(AWAR_EXPERIMENT_NAME)->write_string(dest);
                }
            }
        }
    }

    error = GB_end_transaction(gb_main, error);
    return error;
}
static void experiment_create_cb(AW_window *aww, GBDATA *gb_main) {
    ResultHandler  handler = makeResultHandler(experiment_create_handler, gb_main);
    const char    *source  = aww->get_root()->awar(AWAR_EXPERIMENT_NAME)->read_char_pntr();
    AWT_activate_prompt("Create experiment", "Enter name of new experiment:", source, "Create", handler);
}
static void experiment_rename_cb(AW_window *aww, GBDATA *gb_main) {
    ResultHandler  handler = makeResultHandler(experiment_rename_handler, gb_main);
    const char    *source  = aww->get_root()->awar(AWAR_EXPERIMENT_NAME)->read_char_pntr();
    AWT_activate_prompt("Rename experiment", "Enter new experiment name:", source, "Rename", handler);
}
static void experiment_copy_cb(AW_window *aww, GBDATA *gb_main) {
    ResultHandler  handler = makeResultHandler(experiment_copy_handler, gb_main);
    const char    *source  = aww->get_root()->awar(AWAR_EXPERIMENT_NAME)->read_char_pntr();
    AWT_activate_prompt("Copy experiment", "Enter name of new experiment:", source, "Copy", handler);
}

static void EXP_create_field_items(AW_window *aws, GBDATA *gb_main) {
    static BoundItemSel *bis = new BoundItemSel(gb_main, EXP_get_selector());
    exp_assert(bis->gb_main == gb_main);

    aws->insert_menu_topic(aws->local_id("exp_reorder_fields"), "Reorder fields ...",    "R", "spaf_reorder.hlp", AD_F_ALL, makeCreateWindowCallback(DBUI::create_fields_reorder_window, bis));
    aws->insert_menu_topic(aws->local_id("exp_delete_field"),   "Delete/Hide Field ...", "D", "spaf_delete.hlp",  AD_F_ALL, makeCreateWindowCallback(DBUI::create_field_delete_window, bis));
    aws->insert_menu_topic(aws->local_id("exp_create_field"),   "Create fields ...",     "C", "spaf_create.hlp",  AD_F_ALL, makeCreateWindowCallback(DBUI::create_field_create_window, bis));
    aws->sep______________();
    aws->insert_menu_topic("exp_unhide_fields",  "Show all hidden fields", "S", "scandb.hlp", AD_F_ALL, makeWindowCallback(experiment_field_selection_list_unhide_all_cb, gb_main));
    aws->insert_menu_topic("exp_refresh_fields", "Refresh fields",         "f", "scandb.hlp", AD_F_ALL, makeWindowCallback(experiment_field_selection_list_update_cb,     gb_main));
}

static AW_window *popup_new_experiment_window(AW_root *aw_root, GBDATA *gb_main, int detach_id);

static void popup_detached_experiment_window(AW_window *aw_parent, const InfoWindow *infoWin) {
    const InfoWindow *reusable = InfoWindowRegistry::infowin.find_reusable_of_same_type_as(*infoWin);
    if (reusable) {
        reusable->reuse();
    }
    else { // create a new window if none is reusable
        popup_new_experiment_window(aw_parent->get_root(),
                                    infoWin->get_gbmain(),
                                    InfoWindowRegistry::infowin.allocate_detach_id(*infoWin));
    }
}

static AW_window *popup_new_experiment_window(AW_root *aw_root, GBDATA *gb_main, int detach_id) { // INFO_WINDOW_CREATOR
    AW_window_simple_menu *aws      = new AW_window_simple_menu;
    const ItemSelector&    itemType = EXP_get_selector();

    DBUI::init_info_window(aw_root, aws, itemType, detach_id);
    aws->load_xfig("ad_spec.fig");

    aws->button_length(8);

    aws->at("close");
    aws->callback(AW_POPDOWN);
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->at("search");
    aws->callback(makeCreateWindowCallback(EXP_create_experiment_query_window, gb_main));
    aws->create_button("SEARCH", "SEARCH", "S", "+");

    aws->at("help");
    aws->callback(makeHelpCallback("experiment_info.hlp"));
    aws->create_button("HELP", "HELP", "H");

    DbScanner *scanner = DbScanner::create(gb_main,
                                           InfoWindowRegistry::localize_scanner_id("experiment", detach_id),
                                           aws, "box", "field", "enable", DB_KEYVIEWER, "mark", itemType);

    const InfoWindow& infoWin = InfoWindowRegistry::infowin.registerInfoWindow(aws, scanner, detach_id);

    if (infoWin.is_maininfo()) {
        aws->create_menu("EXPERIMENT", "E", AD_F_ALL);
        aws->insert_menu_topic("experiment_delete", "Delete",     "D", "spa_delete.hlp", AD_F_ALL, makeWindowCallback(experiment_delete_cb, gb_main));
        aws->insert_menu_topic("experiment_rename", "Rename ...", "R", "spa_rename.hlp", AD_F_ALL, makeWindowCallback(experiment_rename_cb, gb_main));
        aws->insert_menu_topic("experiment_copy",   "Copy ...",   "y", "spa_copy.hlp",   AD_F_ALL, makeWindowCallback(experiment_copy_cb,   gb_main));
        aws->insert_menu_topic("experiment_create", "Create ...", "C", "spa_create.hlp", AD_F_ALL, makeWindowCallback(experiment_create_cb, gb_main));
    }

    aws->create_menu("FIELDS", "F", AD_F_ALL);
    EXP_create_field_items(aws, gb_main);

    aws->at("detach");
    infoWin.add_detach_area(popup_detached_experiment_window);

    aws->show();
    infoWin.attach_selected_item();

    return aws;
}

void EXP_popup_experiment_window(AW_root *aw_root, GBDATA *gb_main) { // @@@ move to SL/DB_UI
    static AW_window *aws = NULp;
    if (!aws) {
        aws = popup_new_experiment_window(aw_root, gb_main, InfoWindow::MAIN_WINDOW);
    }
    else {
        InfoWindowRegistry::reactivate(aws);
    }
}