コード例 #1
0
ファイル: web_files.cpp プロジェクト: xywei/texmacs
url
get_from_web (url name) {
    if (!is_rooted_web (name)) return url_none ();
    url res= get_cache (name);
    if (!is_none (res)) return res;

#ifdef OS_WIN32
    string urlString = as_string (name);
    url tmp = url_temp();

    if (starts (urlString, "www."))
        urlString = "http://" * urlString;
    else if (starts (urlString, "ftp."))
        urlString = "ftp://" * urlString;
    else if (starts (urlString, "ftp://"))
        urlPath = NULL;
    else if (starts (urlString, "http://"))
        urlPath = NULL;
    else
        urlString = "http://" * urlString;
    urlString= web_encode (urlString);

    c_string urlPath (urlString);
    c_string tempFilePath (as_string (tmp));

    if(!URL_Get(urlPath, tempFilePath))
        return url_none();
    else return set_cache (name, tmp);
#else
    string test= var_eval_system ("which wget");
    if (!ends (test, "wget")) return url_none ();
    url tmp= url_temp ();
    string tmp_s= escape_sh (concretize (tmp));
    string cmd= "wget --header='User-Agent: TeXmacs-" TEXMACS_VERSION "' -q";
    cmd << " -O " << tmp_s << " " << escape_sh (web_encode (as_string (name)));
    // cout << cmd << "\n";
    system (cmd);
    // cout << "got " << name << " as " << tmp << "\n";

    if (var_eval_system ("cat " * tmp_s * " 2> /dev/null") == "") {
        remove (tmp);
        return url_none ();
    }
    else return set_cache (name, tmp);
#endif
}
コード例 #2
0
ファイル: tf_misc.cpp プロジェクト: Tristor/ParselXBTT
std::string encode_field(const std::string& v, const std::string& local_domain_url)
{
	std::string r;
	r.reserve(v.length() << 1);
	for (size_t i = 0; i < v.length(); )
	{
		if (boost::istarts_with(v.c_str() + i, "ftp://")
			|| boost::istarts_with(v.c_str() + i, "http://")
			|| boost::istarts_with(v.c_str() + i, "https://")
			|| boost::istarts_with(v.c_str() + i, "mailto:"))
		{
			size_t p = i;
			while (p < v.length()
				&& !isspace(v[p] & 0xff)
				&& v[p] != '\"'
				&& v[p] != '<'
				&& v[p] != '>')
			{
				p++;
			}
			if (v[p - 1] == '!' || v[p - 1] == ',' || v[p - 1] == '.' || v[p - 1] == '?')
				p--;
			if (v[p - 1] == ')')
				p--;
			std::string url = web_encode(v.substr(i, p - i));
			if (boost::istarts_with(v.c_str() + i, "ftp."))
				r += web_link(url, "ftp://" + url, false);
			else if (boost::istarts_with(v.c_str() + i, "www."))
				r += web_link(url, "http://" + url, false);
			else
				r += web_link(boost::istarts_with(v.c_str() + i, "mailto:") ? url.substr(7) : encode_local_url(url, local_domain_url), url, false);
			i = p;
		}
		else
		{
			char c = v[i++];
			switch (c)
			{
			case '<':
				r += "&lt;";
				break;
			case '&':
				r += "&amp;";
				break;
			default:
				r += c;
			}
		}
	}
	return r;
}
コード例 #3
0
ファイル: tf_misc.cpp プロジェクト: nosmall/BitPark
static std::string web_link(str_ref title, str_ref link)
{
	return "<a href=\"" + web_encode(link) + "\">" + web_encode(title.empty() ? link : title) + "</a>";
}
コード例 #4
0
ファイル: tf_misc.cpp プロジェクト: Tristor/ParselXBTT
static std::string web_link(const std::string& link_title, const std::string& link, bool encode)
{
	return encode
		? web_link(web_encode(link_title), web_encode(link), false)
		: (boost::format("<a href=\"%s\">%s</a>") % link % (link_title.empty() ? link : link_title)).str();
}
コード例 #5
0
void do_url1(FILE *fp, const struct mngmsg *m_msp, const struct pstruct *ppst,
	     char *l_name, int n1,
	     const struct a_struct *aln_p, const char *annot_var_s,
	     const struct annot_str *q_annot_p,
	     const struct annot_str *l_annot_p )
{
  char my_q_name[200], my_l_name[200], json_l_name[200];
  char *db, *bp;
  char pgm[10], o_pgm[10], lib[MAX_LSTR];
  char *tmp_annot_s, *q_domain_s, *l_domain_s, *tmp_domain_s, *etmp_domain_s;
  int  n_tmp_annot_s, n_tmp_domain;
  long q_offset, l_offset;
  char *ref_url, *lbp=NULL;
  char *srch_url, *srch_url1, *dom_url;

  /* set the database */
  if (m_msp->ldb_info.ldnaseq==SEQT_DNA) db="nucleotide";
  else db="Protein";

  /* set the program type */
  if (strncmp(m_msp->f_id0,"rss",3)==0) {
    strncpy(pgm,"fa",sizeof(pgm));
  }
  else if (strncmp(m_msp->f_id0,"rfx",3)==0) {
    strncpy(pgm,"fx",sizeof(pgm));
  }
  else { strncpy(pgm,m_msp->f_id0,sizeof(pgm)); }

  SAFE_STRNCPY(o_pgm, pgm, sizeof(o_pgm));

  /* get a library name (probably does not work for %, + abbreviations */
  if (m_msp->lname[0]!='%') {
    SAFE_STRNCPY(lib,m_msp->lname,sizeof(lib));
  }
  else {
    SAFE_STRNCPY(lib,"%25",sizeof(lib));
    SAFE_STRNCAT(lib,&m_msp->lname[1],sizeof(lib));
  }
  lib[sizeof(lib)-1]='\0';

  if ((lbp = strchr(l_name,'|'))==NULL) {
    lbp = l_name;
  }
  else {
    lbp++;
  }

  SAFE_STRNCPY(my_q_name,m_msp->qtitle,sizeof(my_q_name));
  if ((bp=strchr(my_q_name,' '))!=NULL) *bp='\0';

  SAFE_STRNCPY(my_l_name,lbp,sizeof(my_l_name));

  if (pgm[0]=='t' || !strcmp(pgm,"fx") || !strcmp(pgm,"fy")==0 ) {
    if ((lbp=strchr(my_l_name,':'))!=NULL) *lbp='\0';
    lbp = &my_l_name[strlen(my_l_name)-2];
    if ( *lbp == '_' ) *lbp = '\0';
  }

  /* change the program name for fastx, tfastx, tfasta */
  /* fastx returns proteins */
  if (strcmp(pgm,"fx")==0 || strcmp(pgm,"fy")==0) {SAFE_STRNCPY(pgm,"fa",sizeof(pgm));}
  else if (strcmp(pgm,"ff")==0) {SAFE_STRNCPY(pgm,"fa",sizeof(pgm));}
  else if (pgm[0]=='t') {
    SAFE_STRNCPY(pgm,"fx",sizeof(pgm));
    SAFE_STRNCPY(lib,DEF_PROT_LIB,sizeof(lib));
  }

  fflush(fp);

  q_offset = aln_p->q_offset;
  l_offset = aln_p->l_offset;

  /* set up ref_url, srch_url, srch_url1, dom_url */

  fflush(fp);

  ref_url = getenv("REF_URL");
  srch_url = getenv("SRCH_URL");
  srch_url1 = getenv("SRCH_URL1");
  dom_url = NULL;
  dom_url = getenv("DOMAIN_PLOT_URL");

  if (ref_url || srch_url || srch_url1 || dom_url) {
    fprintf(fp,"<!-- LINK_START %s -->",l_name);

  /* REF_URL should provide */
  /* "<A HREF=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=%s&fcmd=Search&doptcmd1=DocSum&term=%s\">Entrez lookup</A>&nbsp;&nbsp;" */
  if (ref_url != NULL) {fprintf(fp,ref_url,db,my_l_name);}

  /* SRCH_URL should provide */
  /* "<A HREF=\"http://localhost/fasta_www2/searchfa.cgi?query=%s&db=fasta_www.cgi&lib=%s&pgm=%s&start=%ld&stop=%ld&n1=%d&o_pgm=%s\">Re-search database</A>&nbsp;&nbsp;" */
  if (srch_url != NULL) {
    fprintf(fp,srch_url,my_l_name,db,lib,pgm,
	    l_offset+aln_p->amin1+1,l_offset+aln_p->amax1,n1,m_msp->f_id0);
  }

  /* SRCH_URL1 should provide: */
  /*  "<A HREF=\"http://localhost/fasta_www2/searchxf.cgi?query=%s&db=%s&lib=%s&pgm=%s&start=%ld&stop=%ld&n1=%d&o_pgm=%s\">General re-search</A>\n" */

  if (srch_url1 != NULL) {
    fprintf(fp,srch_url1,my_l_name,db,lib,pgm,
	    l_offset+aln_p->amin1+1,l_offset+aln_p->amax1,n1,m_msp->f_id0);
  }
  
  if (dom_url!=NULL) {
    if (annot_var_s && annot_var_s[0]) {
      tmp_annot_s = web_encode(annot_var_s);
    }
    else tmp_annot_s = "";

    q_domain_s = l_domain_s = NULL;

    if (q_annot_p && q_annot_p->n_domains > 0 && 
	(q_domain_s = display_domains('q',q_annot_p->s_annot_arr_p, q_annot_p->n_annot))!=NULL) {
    }
    if (l_annot_p && l_annot_p->n_domains > 0 && 
	(l_domain_s = display_domains('l',l_annot_p->s_annot_arr_p, l_annot_p->n_annot))!=NULL) {
    }

    /* combine domain strings */
    n_tmp_domain = 0;
    if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1;
    if (l_domain_s) n_tmp_domain += strlen(l_domain_s)+1;
    etmp_domain_s = "";
    if (n_tmp_domain > 0) {
      if ((tmp_domain_s=(char *)calloc(n_tmp_domain,sizeof(char)))==NULL) {
	fprintf(stderr,"*** error [%s:%d] *** cannot allocate tmp_domain_s[%d]\n",
		__FILE__, __LINE__,n_tmp_domain);
      }
      else {
	tmp_domain_s[0] = '\0';
	if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain);
	if (l_domain_s) SAFE_STRNCAT(tmp_domain_s, l_domain_s, n_tmp_domain);
	etmp_domain_s = web_encode(tmp_domain_s);
      }
    }

    /* appropriate format string: */
    /* 
       pgm=%s	    -- program abbrev that created alignment
       q_name=%s     -- query info
       q_cstart=%ld
       q_cstop=%ld
       q_astart=%ld
       q_astop=%ld
       l_name=%s     -- library info
       l_cstart=%ld
       l_cstop=%ld
       l_astart=%ld
       l_astop=%ld
       region=%s       -- aligned domain and variant information
       doms=%s

       DOMAIN_PLOT_URL = "pgm=%s;q_name=%s;q_cstart=%ld;q_cstop=%ld&q_astart=%ld&q_astop=%ld&l_name=%s&l_cstart=%ld&l_cstop=%ld&l_astart=%ld&l_astop=%ld&regions=%s&doms=%s"
    */

    /* think about the alternative of running a script
       rather than embedding it */

    fprintf(fp,dom_url,o_pgm,
	    my_q_name, q_offset+seq_pos(1,aln_p->qlrev,2),q_offset+seq_pos(m_msp->n0,aln_p->qlrev,2),
	    q_offset+seq_pos(aln_p->amin0+1,aln_p->qlrev,1), q_offset+seq_pos(aln_p->amax0, aln_p->qlrev,2),
	    my_l_name, l_offset+seq_pos(1,aln_p->llrev,2), l_offset+seq_pos(n1,aln_p->llrev,2),
	    l_offset+seq_pos(aln_p->amin1+1,aln_p->llrev,1),l_offset+seq_pos(aln_p->amax1,aln_p->llrev,2),
	    tmp_annot_s, etmp_domain_s);

    if (n_tmp_domain>0 && tmp_domain_s) {
      free(tmp_domain_s);
      free(etmp_domain_s);
    }
    if (l_annot_p && l_annot_p->n_domains && l_domain_s) {
      free(l_domain_s);
    }
    if (q_annot_p && q_annot_p->n_domains && q_domain_s) {
      free(q_domain_s);
    }
    if (annot_var_s && annot_var_s[0] && tmp_annot_s) free(tmp_annot_s);
  }

  fprintf(fp,"\n<!-- LINK_STOP -->");
  fflush(fp);
  }

  /*
    if ((srch_url2 = getenv("SRCH_URL2"))==NULL)
    fprintf(fp,"<A HREF=\"http://fasta.bioch.virginia.edu/fasta/cgi/lalignx.cgi?seq1=\"%s\"&in_seq1=\"FASTA\"&seq2=\"%s\"&in_seq2=\"Accession\"&ssr2=%ld:%ld\">lalign</A>\n<p>\n",my_l_name,db,lib,pgm,l_offset+aln_p->amin1+1,l_offset+aln_p->amax1,n1);
    else 
    fprintf(fp,srch_url1,my_l_name,db,lib,pgm,
    l_offset+aln_p->amin1+1,l_offset+aln_p->amax1,n1);
  */


  if (getenv("JSON_HTML")) {

    /* replace '|' with '_' */
    SAFE_STRNCPY(json_l_name, l_name, sizeof(json_l_name));
    for (bp=strchr(json_l_name,'|'); bp; bp=strchr(bp+1,'|')) { *bp = '_'; }

    /* replace '.' with '_' */
    for (bp=strchr(json_l_name,'.'); bp; bp=strchr(bp+1,'.')) { *bp = '_'; }

    fprintf(fp,"\n<script type=\"text/javascript\">\n//<![CDATA[\n var json_%s = {\n",json_l_name);
    encode_json_str(fp, "db", db, 1);
    encode_json_str(fp, "l_acc", l_name, 0);
    encode_json_str(fp, "acc", my_l_name, 0);
    encode_json_str(fp, "lib", lib, 0);
    encode_json_str(fp, "pgm", pgm, 0);
    encode_json_str(fp, "o_pgm", m_msp->f_id0, 0);
    encode_json_aln(fp, aln_p, q_offset, l_offset, 0);
    if (annot_var_s && annot_var_s[0]) { encode_json_lines(fp, "annot", annot_var_s, 0); }
    if (q_annot_p && q_annot_p->n_domains > 0) { encode_json_domains(fp, "q_domains", q_annot_p, 0); }
    if (l_annot_p && l_annot_p->n_domains > 0) { encode_json_domains(fp, "l_domains", l_annot_p, 0); }

    fprintf(fp, "\n}\n//]]>\n</script>");
    fflush(fp);
  }
}