/* *******************************************************************
 * The contents of this file are subject to the Mozilla Public License
 * Version 1.1 (the "License"); you may not use this file except in
 * compliance with the License. You may obtain a copy of the License at
 * http://www.mozilla.org/MPL/
 *
 * Software distributed under the License is distributed on an "AS IS"
 * basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See
 * the License for the specific language governing rights and
 * limitations under the License.
 *
 * The Original Code is the BioWarehouse.
 *
 * The Initial Developer of the Original Code is SRI International.
 * Portions created by SRI International are Copyright (C) 2004.
 * All Rights Reserved.
 ******************************************************************* */
/*
 * PGDB PUBS loader for the BioSpice Data Warehouse
 * Thomas J Lee, SRI International, August 2002
 */

#include "main.h"
#include "pubs-parse.h"
#ifdef ORACLE
#include <sqlca.h>
#endif

#define DEBUG 0

extern int dataset_wid;
extern int organism_wid;

void
pubs_load_entry(struct pubs_entry *entry) {

  int citation_wid;
  char *fulltext;                    /* Holds the citation proper, with all fields catenated */
  short error = 0;                   /* numeric conversion error */
  struct stringlist *sptr;           /* to iterate over synonyms */

  /* Set indicator variables for optional columns, and check string lengths, numeric formats etc. */
  short pubmed_id_ind;                /* is PUBMED-ID field present? */
  char *pubmed_id = string_column(entry->pubmed_id, 20, &pubmed_id_ind);

  if (DEBUG) printf("Loading pubs %s\n", entry->unique_id);
  
#ifdef ORACLE
  /* Try a WHENEVER to assist in debugging silent Oracle errors */
  EXEC SQL WHENEVER SQLERROR DO sql_error("Oracle error in pubs-load");
#endif

  /* Build the full text of the citation by concatenating the various fields together, separating with tabs */
  fulltext = strdup("");
  for (sptr=entry->authors; sptr; sptr=sptr->next) /* Add reversed list of Authors back to front */
    fulltext = string_concatenate(strdup(sptr->string), fulltext, (strlen(fulltext) > 0 ? 2 : 0));
  if (entry->title) fulltext = string_concatenate(fulltext, strdup(entry->title), 4); /* tab-separate */
  if (entry->source) fulltext = string_concatenate(fulltext, strdup(entry->source), 4); /* tab-separate */
  if (entry->year) fulltext = string_concatenate(fulltext, strdup(entry->year), 4); /* tab-separate */
  if (entry->url) fulltext = string_concatenate(fulltext, strdup(entry->url), 4); /* tab-separate */
  if (DEBUG) printf("fulltext=<%s>\n", fulltext);

  /*
    For a pub, we can see either the main entry, or a REFERENT-FRAME,
    or both in either order. We assure these frame IDs point map to the same WID.
    NOTE: Assumption is that citation attributes (fulltext) will not be split among
    the main frame and the referent frame. If they are, only the last
    rame's info will be loaded.
  */
  if (citation_wid = find_citation(entry->unique_id)) {
    // We've seen this UNIQUE-ID in a prior referent entry
    // UPDATE with any info specified in this entry
    wh_update_citation(citation_wid, fulltext,
		       pubmed_id, pubmed_id_ind);
  }
  else if (citation_wid = find_citation(entry->referent_frame)) {
    // We've seen this REFERENT-FRAME in a prior main entry
    // Remember ID & UPDATE with any additional info (typically this is a no-op)
    widtable_insert(citation_wids, citation_wid, entry->unique_id);
    //!! this if shouldn't be needed, but wh_update_citation seems to clobber-update
    if ((strlen(fulltext) > 0) || (pubmed_id_ind == INDICATE_NONNULL))
      wh_update_citation(citation_wid, fulltext,
                         pubmed_id, pubmed_id_ind);
  }
  else {
    // Haven't seen this pub before.
    // Remember ID & INSERT a new (possibly empty) Citation row
    citation_wid = wh_get_new_wid();
    widtable_insert(citation_wids, citation_wid, entry->unique_id); 
    wh_insert_citation(citation_wid, fulltext,
                       pubmed_id, pubmed_id_ind);

    /* Add DBID */
    if (!entry->unique_id)
      entry->load_error = 1;
    else
      wh_insert_dbid(citation_wid, entry->unique_id);
  
    /* Finally add Entry */
    wh_insert_entry(citation_wid, entry->load_error, 0, NULL);
  }
  free(fulltext);
  
  /* If this pub has a REFERENT-FRAME, associate that frame name with the assigned WID */
  if (entry->referent_frame)
    widtable_insert(citation_wids, citation_wid, entry->referent_frame);  /* remember wid-unique_id association */

  /* Add Medline crossreference if present */
  if (entry->medline_uid)
    wh_insert_crossreference(citation_wid, entry->medline_uid, "Medline");
  
  /* Add comments to CommentTable  */
  for (sptr=entry->comments; sptr; sptr=sptr->next)
    wh_insert_comment(citation_wid, sptr->string);
}