206 lines
7.6 KiB
Plaintext
206 lines
7.6 KiB
Plaintext
/* =========================================================================
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*
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* Nanite Systems Advanced Research Encapsulation System
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*
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* Copyright (c) 2022–2025 Nanite Systems Corporation
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*
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* =========================================================================
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*
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* Scientific Database Lookup Utility
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*
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* This program is covered under the terms of the ARES Software Copyright
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* License, Section 2 (ASCL-ii). Although it appears in ARES as part of
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* commercial software, it may be used as the basis of derivative,
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* non-profit works that retain a compatible license. Derivative works of
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* ASCL-ii software must retain proper attribution in documentation and
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* source files as described in the terms of the ASCL. Furthermore, they
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* must be distributed free of charge and provided with complete, legible
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* source code included in the package.
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*
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* To see the full text of the ASCL, type 'help license' on any standard
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* ARES distribution, or visit http://nanite-systems.com/ASCL for the
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* current version.
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*
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* DISCLAIMER
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 'AS
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* IS' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
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* TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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* PARTICULAR PURPOSE ARE DISCLAIMED.
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*
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* IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY
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* DAMAGES HOWEVER CAUSED ON ANY THEORY OF LIABILITY ARISING IN ANY WAY OUT
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* OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
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* DAMAGE.
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*
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* =========================================================================
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*
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*/
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#include <ARES/a>
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#define CLIENT_VERSION "0.2.2"
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#define CLIENT_VERSION_TAGS "alpha"
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string DEFAULT_DOMAIN = "eutils.ncbi.nlm.nih.gov";
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string DEFAULT_DB = "pubmed";
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string DEFAULT_QUERY_KEY = "1";
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#define SEARCH_STRING(DB, Q) "/entrez/eutils/esearch.fcgi?usehistory=y&db=" + llEscapeURL(DB) + "&term=" + llEscapeURL(Q)
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#define POST_STRING(DB, Q) "/entrez/eutils/epost.fcgi?usehistory=y&db=" + llEscapeURL(DB) + "&id=" + llEscapeURL(Q)
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#define SUMMARY_STRING(DB, Q, ENV) "/entrez/eutils/esummary.fcgi?usehistory=y&db=" + llEscapeURL(DB) + "&query_key=" + llEscapeURL(Q) + "&WebEnv=" + llEscapeURL(ENV)
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#define ABSTRACT_STRING(DB, Q, ENV) "/entrez/eutils/efetch.fcgi?usehistory=y&db=" + llEscapeURL(DB) + "&query_key=" + llEscapeURL(Q) + "&WebEnv=" + llEscapeURL(ENV) + "&rettype=abstract&retmode=text"
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#define FASTA_STRING(DB, Q, ENV) "/entrez/eutils/efetch.fcgi?usehistory=y&db=" + llEscapeURL(DB) + "&query_key=" + llEscapeURL(Q) + "&WebEnv=" + llEscapeURL(ENV) + "&rettype=fasta&retmode=text"
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key scidb_receive_pipe;
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string waiting_queries = "{}";
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string queries_in_progress = "{}";
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#define MODE_SEARCH 0
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#define MODE_SUMMARY 1
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#define MODE_ABSTRACT 2
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#define MODE_FASTA 3
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send_query(string query, key handle) {
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string domain = getjs(query, [4]);
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string database = getjs(query, [5]);
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string question = getjs(query, [6]);
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integer mode = (integer)getjs(query, [7]);
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string query_key = getjs(query, [8]);
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queries_in_progress = setjs(queries_in_progress, [(string)handle], query);
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string url;
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if(mode == MODE_SEARCH)
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url = domain + SEARCH_STRING(database, question);
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else if(mode == MODE_SEARCH)
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url = domain + POST_STRING(database, question);
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else if(mode == MODE_SUMMARY)
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url = domain + SUMMARY_STRING(database, query_key, question);
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else if(mode == MODE_ABSTRACT)
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url = domain + ABSTRACT_STRING(database, query_key, question);
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else if(mode == MODE_FASTA)
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url = domain + FASTA_STRING(database, query_key, question);
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http_get(url, scidb_receive_pipe, handle);
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}
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main(integer src, integer n, string m, key outs, key ins, key user) {
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if(n == SIGNAL_INVOKE) {
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list argv = split(m, " ");
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integer argc = count(argv);
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string msg = "";
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if(argc == 1) {
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msg = "Syntax: " + PROGRAM_NAME + " [-d <database> -m <domain> -q <querykey> -s|-f|-a-p] <query>\n\nLooks up <query> on the specified [https://www.ncbi.nlm.nih.gov/ NCBI Entrez] database at <domain> (default: " + DEFAULT_DB + " at " + DEFAULT_DOMAIN + "). -s will retrieve summaries from a matching WebEnv query. -q will set the query key (default: 1) -p will post queries to sequence databases. -a will fetch abstracts. -f will fetch FASTA sequences.";
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} else {
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string domain = DEFAULT_DOMAIN;
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string database = DEFAULT_DB;
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integer mode = MODE_SEARCH;
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string query_key = DEFAULT_QUERY_KEY;
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string a1;
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integer a1i;
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while(~(a1i = llListFindList(["-m", "-d", "-s", "-f", "-a", "-q"], [a1 = gets(argv, 1)]))) {
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if(a1i == 0) { // -m
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domain = gets(argv, 2);
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argv = delrange(argv, 1, 2);
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} else if(a1i == 1) { // -d
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database = gets(argv, 2);
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argv = delrange(argv, 1, 2);
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} else if(a1i == 5) { // -q
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query_key = gets(argv, 2);
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argv = delrange(argv, 1, 2);
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} else if(a1i == 2) { // -s
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mode = MODE_SUMMARY;
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argv = delrange(argv, 1, 1);
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} else if(a1i == 3) { // -f
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mode = MODE_FASTA;
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argv = delrange(argv, 1, 1);
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} else if(a1i == 4) { // -a
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mode = MODE_ABSTRACT;
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argv = delrange(argv, 1, 1);
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}
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}
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string question = concat(delitem(argv, 0), " ");
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if(!~strpos(domain, "://"))
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domain = "https://" + domain;
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key handle = llGenerateKey();
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string query = jsarray([outs, ins, user, _resolved, domain, database, question, mode, query_key]);
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_resolved = 0;
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llSetMemoryLimit(0x10000);
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if(scidb_receive_pipe) {
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queries_in_progress = setjs(queries_in_progress, [handle], query);
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send_query(query, handle);
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} else {
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scidb_receive_pipe = llGenerateKey();
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waiting_queries = setjs(waiting_queries, [handle], query);
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pipe_open(["p:"+(string)scidb_receive_pipe + " notify " + PROGRAM_NAME + " response"]);
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}
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}
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if(msg != "")
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print(outs, user, msg);
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} else if(n == SIGNAL_NOTIFY) {
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list argv = split(m, " ");
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string cmd = gets(argv, 1);
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if(cmd == "pipe") {
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list queries = jskeys(waiting_queries);
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integer qi = 0;
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integer qmax = count(queries);
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while(qi < qmax) {
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key handle = gets(queries, qi);
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string query = getjs(waiting_queries, [(string)handle]);
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waiting_queries = setjs(waiting_queries, [(string)handle], JSON_DELETE);
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send_query(query, handle);
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++qi;
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}
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} else if(cmd == "response") {
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string query = getjs(queries_in_progress, [(string)user]);
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if(query != JSON_INVALID) {
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key o_outs = getjs(query, [0]);
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key o_ins = getjs(query, [1]);
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key o_user = getjs(query, [2]);
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integer o_rc = (integer)getjs(query, [3]);
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string buffer;
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pipe_read(ins, buffer);
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/* string fieldset = getjs(buffer, ["query", "pages", 0]);
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string field;
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if(fieldset != JSON_INVALID) {
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if(getjs(fieldset, ["missing"]) == JSON_TRUE) {
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field = getjs(fieldset, ["title"]) + " does not exist (" + getjs(query, [0]) + "/)";
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} else {
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field = getjs(fieldset, ["extract"]);
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}
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} else {
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field = buffer;
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} */
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print(o_outs, o_user, buffer);
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// resolve_io(o_rc, o_outs, o_ins);
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queries_in_progress = setjs(queries_in_progress, [(string)user], JSON_DELETE);
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resolve_i(o_rc, o_ins);
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}
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if(queries_in_progress == "{}") {
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pipe_close(scidb_receive_pipe);
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scidb_receive_pipe = "";
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llSetMemoryLimit(0x2000);
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}
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}
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} else if(n == SIGNAL_INIT) {
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#ifdef DEBUG
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echo("[" + PROGRAM_NAME + "] init event");
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#endif
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llSetMemoryLimit(0x2000);
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} else if(n == SIGNAL_UNKNOWN_SCRIPT) {
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echo("[" + PROGRAM_NAME + "] failed to run '" + m + "' (kernel could not find the program specified)");
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} else {
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echo("[" + PROGRAM_NAME + "] unimplemented signal " + (string)n + ": " + m);
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}
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}
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#include <ARES/program>
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