NCBI NETWORK SERVICES FOR ENTREZ QUERIES AND SEQUENCE FETCHING

NCBI has new network services for Entrez (term lists, Boolean queries,
document summaries, neighbors and links) and PubMed and Sequence record
fetching.  These are all CGI-based, were written by the group that maintains
our web services, and have a lot of advantages over our older network
services.

The code is all in the ncbi/access folder, and is compiled into the ncbiobj
library, along with the object loaders and api functions.  This library is
always linked in with our applications, and does not depend upon netcli or
netentr libraries.  The network connection functions are in the ncbi and
ncbiconn libraries, also always linked in.  The header files are ent2api.h
for Entrez2 services and pmfapi.h for PubMed and sequence fetching.

These functions are now accessed as named services, so the underlying URL is
not present in the client code.  This allows us to redirect requests between
multiple servers for load balancing, and to change minor URL parameters as
needed without breaking the client.  The only parameters the client sends are
essential ones (e.g., gi number).  These services will thus be stable and
supported over time, regardless of what we do behind the scenes.

Another advantage is that the services can be called either synchronously or
asynchronously.  Synchronous queries wait for the reply before returning
control back to your program, and are easier to code.  For example:

  PubmedEntryPtr pep = PubMedSynchronousQuery (pmid);

  SeqEntryPtr sep = PubSeqSynchronousQuery (gi, 0, 0);

These do not automatically try to reconnect if the network request failed,
and the client can decide whether to put these calls in a small retry loop.

Asynchronous queries are slighly more complicated to code, but allow better
responsiveness, without the need for multi-threading in interactive programs.
Asynchronous calls send the request to the server, add a block of data with
the connection and your callback function to a queue, and immediately return
control to your program.  You are responsible for calling a queue checking
function every so often, typically on a timer.  When the results are ready,
the queue checker calls the callback you specified.  Your callback reads the
data, does whatever you want with it, and returns to the queue checker, which
cleans up the connection before returning to the timer event loop.

Some NCBI toolkit library functions require the ability to fetch sequences
from a registered service.  For this, you can call

  PubSeqFetchEnable ();

to enable access and

  PubSeqFetchDisable ();

to disable access.  The asn2gb -r flag (for remote access) works this way.

The demo/entrez2 application uses desktop/e2trmlst.c and desktop/e2docsum.c
to access the new servers.

Some examples of how to use the new functions are provided below.


/* standard startup */

#include <sqnutils.h>
#include <objall.h>
#include <objsub.h>
#include <objfdef.h>

static void StandardStartup (void)

{
  ErrSetFatalLevel (SEV_MAX);
  ErrClearOptFlags (EO_SHOW_USERSTR);
  UseLocalAsnloadDataAndErrMsg ();
  ErrPathReset ();

  AllObjLoad ();
  SubmitAsnLoad ();
  FeatDefSetLoad ();
  SeqCodeSetLoad ();
  GeneticCodeTableLoad ();
}

/* enabling automatic fetch of components from SeqFetch service */

#include <pmfapi.h>

static void OnStartup (void)

{
  PubSeqFetchEnable ();
}

static void OnShutdown (void)

{
  PubSeqFetchDisable ();
}

/* example of fetching PubMed record */

#include <pmfapi.h>
#include <tomedlin.h>

static void SavePubMedRecord (Int4 pmid, FILE *fp)

{
  PubmedEntryPtr  pep;

  pep = PubMedSynchronousQuery (pmid);
  if (pep == NULL) return;

  MedlineEntryToDataFile ((MedlineEntryPtr) pep->medent, fp);
  PubmedEntryFree (pep);
}

/* example of fetching sequence record */

#include <pmfapi.h>
#include <asn2gnbk.h>

static void SaveSeqRecord (Int4 gi, FILE *fp)

{
  SeqEntryPtr  sep;

  sep = PubSeqSynchronousQuery (gi, 0, 0);
  if (sep == NULL) return;

  SeqEntryToGnbk (sep, NULL, GENBANK_FMT, RELEASE_MODE, NORMAL_STYLE,
                  0, 0, 0, NULL, fp);
  SeqEntryFree (sep);
}

/* example of Entrez2 Boolean query */

#include <ent2api.h>

static void DoBooleanRequest (FILE *fp)

{
  Entrez2BooleanReplyPtr  e2br;
  Entrez2IdListPtr        e2id;
  Entrez2RequestPtr       e2rq;
  Entrez2ReplyPtr         e2ry;
  Int4                    i;
  Int4Ptr                 uids;

  e2rq = EntrezCreateBooleanRequest (TRUE, FALSE, "Nucleotide", NULL,
                                     0, 0, NULL, 0, 0);
  if (e2rq == NULL) return;

  EntrezAddToBooleanRequest (e2rq, NULL, 0, "ORGN", "Saccharomyces cerevisiae",
                             NULL, 0, 0, NULL, NULL, TRUE, TRUE);
  EntrezAddToBooleanRequest (e2rq, NULL, ENTREZ_OP_AND, NULL, NULL,
                             NULL, 0, 0, NULL, NULL, TRUE, TRUE);
  EntrezAddToBooleanRequest (e2rq, NULL, 0, "PROP", "biomol mrna",
                             NULL, 0, 0, NULL, NULL, TRUE, TRUE);

  e2ry = EntrezSynchronousQuery (e2rq);
  e2rq = Entrez2RequestFree (e2rq);
  if (e2ry == NULL) return;

  e2br = EntrezExtractBooleanReply (e2ry);
  if (e2br == NULL) return;

  if (e2br->count > 0) {
    e2id = e2br->uids;

    if (e2id != NULL && e2id->num > 0 && e2id->uids != NULL) {
      fprintf (fp, "count=%ld\n", (long) e2id->num);

      uids = (Int4Ptr) BSMerge (e2id->uids, NULL);
      if (uids != NULL) {
        for (i = 0; i < e2id->num; i++) {
          fprintf (fp, "pmid=%ld\n", (long) uids [i]);
        }
        MemFree (uids);
      }
    }
  }

  Entrez2BooleanReplyFree (e2br);
}

/* example of fetching Entrez2 document summary */

#include <ent2api.h>

static void DoDocsumRequest (Int4 pmid, FILE *fp)

{
  Entrez2DocsumDataPtr  e2ddp;
  Entrez2DocsumListPtr  e2dlp;
  Entrez2DocsumPtr      e2dp;
  Entrez2RequestPtr     e2rq;
  Entrez2ReplyPtr       e2ry;

  e2rq = EntrezCreateDocSumRequest ("PubMed", pmid, 0, NULL, NULL);
  if (e2rq == NULL) return;

  e2ry = EntrezSynchronousQuery (e2rq);
  e2rq = Entrez2RequestFree (e2rq);
  if (e2ry == NULL) return;

  e2dlp = EntrezExtractDocsumReply (e2ry);
  if (e2dlp == NULL) return;

  for (e2dp = e2dlp->list; e2dp != NULL; e2dp = e2dp->next) {
    for (e2ddp = e2dp->docsum_data; e2ddp != NULL; e2ddp = e2ddp->next) {
      if (StringHasNoText (e2ddp->field_name)) continue;
      if (StringHasNoText (e2ddp->field_value)) continue;
      fprintf (fp, "%s - %s\n", e2ddp->field_name, e2ddp->field_value);
    }
  }

  Entrez2DocsumListFree (e2dlp);
}