1:- module( pub_graph,
    2               [ 
    3                    pub_graph_abstracts/2,
    4                    pub_graph_cited_by/2, pub_graph_cited_by/3,
    5                    pub_graph_cites/2, pub_graph_cites/3,
    6                    pub_graph_cache_open/5,
    7                    pub_graph_cache_save/4,
    8                    pub_graph_cited_by_graph/3,
    9                    pub_graph_cited_by_treadmill/3,
   10                    pub_graph_summary_info/3,
   11                    pub_graph_search/2, pub_graph_search/3,
   12                    pub_graph_summary_display/1, pub_graph_summary_display/2,
   13                    pub_graph_summary_display/3,
   14                    pub_graph_summary_display_info/2,
   15                    pub_graph_table/3,
   16                    pub_graph_id/2,
   17                    pub_graph_version/2
   18                   ]
   19         ).   20
   21:- use_module(library(sgml)).   22:- use_module(library(apply)).   23:- use_module(library(debug)).   24:- use_module(library(lists)).   25:- use_module(library(ordsets)).          % ord_add_element/3.
   26:- use_module(library(http/http_open)).   % http_open/3
   27:- use_module(library(http/json)).        % json_read/2,3
   28:- use_module(library(http/html_write) ).   29
   30% stoics.org.uk  libs:
   31:- use_module( library(options) ).   32
   33:- dynamic pub_graph_cache:cited_by/3.   34:- dynamic pub_graph_cache:info/4.   35:- dynamic pub_graph_cache:info_date/2.

    ?- debug(pub_graph).

    ?- pack_install(pub_graph).
    % and load with
    ?- use_module(library(pub_graph)).

   85% This does (no longer ?) work: [try abs_fname/n]
   86:- ( catch(use_module(library(prosqlite)),_,fail) -> true
   87     ;  
   88     debug(pub_graph, 'proSQLite not available. Caching through prosqlite disabled', [] ) 
   89   ).   90
   91:- ( catch(use_module(library(odbc)),_,fail) -> true
   92     ;  
   93     debug(pub_graph, 'proSQLite not available. Caching through odbc disabled', [] ) 
   94   ).   95:- ( catch(use_module(library(db_facts)),_,fail) -> true
   96     ;  
   97     debug(pub_graph, 'pack(db_facts) not available. Caching is disabled', [] ) 
   98   ).   99
  100% Section: defaults, shortcuts.
  101
  102file_type_extension(csv, csv).
  103file_type_extension(prolog, pl).
  104file_type_extension(sqlite, sqlite).
  105
  106url_eutils('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/').
  107url_efetch_pubmed('efetch.fcgi?db=pubmed').
  108
  109url_semscholar('http://api.semanticscholar.org/v1/paper/').
  110
  111default_names( Names ) :- 
  112    default_names( ncbi, Names ).
  113default_names( semscholar, Names ) :-
  114    Names = [arxivId,authors,doi,title,topics,venue,year].
  115    % citationVelocity, citations, influentialCitationCount, paperId, references, url
  116default_names( ncbi, Names ) :-
  117     Names = ['Author','Title','Source','Pages','PubDate',
  118              'Volume','Issue','ISSN','PmcRefCount',
  119              'PubType','FullJournalName'].
  120
  121pub_graph_graph(true).  % needed for options_append/3
  122pub_graph_graph_defaults( [depth(0),verbose(false),update(true),date(AgesAgo),flat(false)] ) :-
  123     a_month_ago( AgesAgo ).

 pub_graph_id(+Id, -IdType)

True if Id corresponds to a paper identifier from server typed by IdType.
Currently ncbi (https://www.ncbi.nlm.nih.gov/pubmed/) and semscholar (http://semanticscholar.org/) are the known IdTypes.

The predicate does not connect to the server, it only type checks the shape of Id.
If Id is an integer or an atom that can be turned to an integer, then IdType is instantiated to ncbi.
There are three term forms for semscholar.

hex

such as cbd251a03b1a29a94f7348f4f5c2f830ab80a909

doi

presented as, doi:'10.1109/TITB.2002.1006298' (doi is stripped before request is posted)

arXiv

as, arXiv:1705.10311 (arXiv forms part of the semanticscholar.org request)

The following two ids correspond to the same paper.

?-
    pub_graph_id( 12075665, Type ).

Type = ncbi.

?-
    pub_graph_id( cbd251a03b1a29a94f7348f4f5c2f830ab80a909, Type ).

Type = semscholar.

author

- nicos angelopoulos

version

- 0.1 2018/9/11

See also

- https://www.ncbi.nlm.nih.gov/pubmed/

- http://semanticscholar.org

*/

  161pub_graph_id( Id, IdType ) :-
  162    ( integer(Id) ; (catch(atom_number(Id,Numb),_,fail),integer(Numb)) ),
  163    !,
  164    IdType = ncbi.
  165pub_graph_id( Term, IdType ) :-
  166    (
  167        catch( hex_bytes(Term,_Bytes), _, fail )
  168        ;
  169        Term = doi:_
  170        ;
  171        Term = arXiv
  172    ),
  173    !,
  174    IdType = semscholar.
  175
  176% Section: interface predicates

 pub_graph_version(+Version, +Date)

Get version information and date of publication.

?-
    pub_graph_version(V,D).

V = 1:2:0,
D = date(2023, 9, 20).

*/

  191pub_graph_version( 1:2:0, date(2023,9,20) ).
  192% pub_graph_version( 1:1:0, date(2018,9,23) ).
  193% pub_graph_version( 1:0:0, date(2018,9,22) ).
  194% pub_graph_version( 0:0:3, date(2012,08,15) ).
  195
  196pub_graph_search_defaults( Defs ) :- 
  197               Defs = [
  198                        gap(0),
  199                        retmax(100),
  200                        quote_value(true),
  201                        tmp_keep(false),
  202                        verbose(false)
  203                        ].

 pub_graph_search(+STerm, -Ids)

 pub_graph_search(+STerm, -Ids, +Options)

This is currently only implemented for ncbi ids as there is no means for searching in the semantic scholar API.

Search in pub_graph for terms in the search term STerm. In this, conjunction is marked by , (comma) and disjunction by ; (semi-column). '-' pair terms are considered as Key-Value and interpreted as Value[Key] in the query. List are thought to be flat conjoint search terms with no pair values in them which are interpreted by pub_graph also as OR operations. (See example below.) Known keys are : journal, pdat. au, All Fields The predicate constructs a query that is posted via the http API provided by NCBI (http://www.ncbi.nlm.nih.gov/books/NBK25500/).

Options should be a term or list of terms from:

gap(Gap=0)

Gap allowed for approximate reasoning in ncbi terms: Title, Title/Abstract and Affiliation. The higher the number the looser the match. The default allows for no intervening words, so only exact sub-matches will be returned (see example: fixme below) see: https://pubmed.ncbi.nlm.nih.gov/help/#proximity-searching

maxdate(Xdat)

see mindate Option For instance, taking an example from the url we show how to find all breast cancer articles that were published in Science in 2008.

mindate(Ndat)

Date range used to limit a link operation by the date specified by datetype. These two parameters (mindate, maxdate) must be used together to specify an arbitrary date range. The general date format is YYYY/MM/DD, and these variants are also allowed: YYYY, YYYY/MM.

qtranslation(QTrans)

return in QTrans the actual query ran on the the pub_graph server.

quote_value(Qv=true)

whether to quote values of K=V search terms

reldate(Rdat)

When reldate is set to an integer n, ELink returns only those items that have a date specified by datetype within the last n days.

retmax(RetMax)

the maximum number of records that will be returned def: 100

tmp_file(Tmp)

file to use, or when Tmp is variable the file that was used to receive the results from pub_graph.

tmp_keep(Keep)

keep the file with the xml result iff Keep==true

verbose(Verbose)

if Verbose == true then the predicate is verbose about its progress by, for instance, requesting query is printed on current output stream.

?-
    St = (journal=science,[breast,cancer],pdat=2008),
    pub_graph_search( St, Ids, [verbose(true),qtranslation(QTrans)] ),
    length( Ids, Len ), write( number_of:Len ), nl,
    pub_graph_summary_display( Ids, _, display(all) ).

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=100&term=science[journal]+AND+breast+cancer+AND+2008[pdat]
tmp_file(/tmp/swipl_3884_9)
number_of:6
----
1:19008416
        Author=[Varambally S,Cao Q,Mani RS,Shankar S,Wang X,Ateeq B,Laxman B,Cao X,Jing X,Ramnarayanan K,Brenner JC,Yu J,Kim JH,Han B,Tan P,Kumar-Sinha C,Lonigro RJ,Palanisamy N,Maher CA,Chinnaiyan AM]
        Title=Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer.
        Source=Science
        Pages=1695-9
        PubDate=2008 Dec 12
        Volume=322
        Issue=5908
        ISSN=0036-8075
        PmcRefCount=352
        PubType=Journal Article
        FullJournalName=Science (New York, N.Y.)
----
2:18927361
        Author=Couzin J
        Title=Genetics. DNA test for breast cancer risk draws criticism.
        Source=Science
...
...
...
6:18239125
        Author=[Silva JM,Marran K,Parker JS,Silva J,Golding M,Schlabach MR,Elledge SJ,Hannon GJ,Chang K]
        Title=Profiling essential genes in human mammary cells by multiplex RNAi screening.
        Source=Science
        Pages=617-20
        PubDate=2008 Feb 1
        Volume=319
        Issue=5863
        ISSN=0036-8075
        PmcRefCount=132
        PubType=Journal Article
        FullJournalName=Science (New York, N.Y.)
----
St =  (journal=science, [breast, cancer], pdat=2008),
Ids = ['19008416', '18927361', '18787170', '18487186', '18239126', '18239125'],
QTrans = ['("Science"[Journal] OR "Science (80- )"[Journal] OR "J Zhejiang Univ Sci"[Journal]) AND ("breast neoplasms"[MeSH Terms] OR ("breast"[All Fields] AND "neoplasms"[All Fields]) OR "breast neoplasms"[All Fields] OR ("breast"[All Fields] AND "cancer"[All Fields]) OR "breast cancer"[All Fields]) AND 2008[pdat]'],
Len = 6.

?-
     date(Date),
     St = (author='Borst Piet'),
     pub_graph_search( St, Ids, verbose(true) ),
     length( Ids, Len ), write( number_of:Len ), nl.

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=100&term=Borst%20Piet\[author\]
tmp_file(/tmp/swipl_18703_0)
number_of:83
Date = date(2018, 9, 22),
St =  (author='Borst Piet'),
Ids = ['29894693', '29256493', '28821557', '27021571', '26774285', '26530471', '26515061', '25799992', '25662217'|...],
Len = 83.

?-
    date(Date), pub_graph_search( prolog, Ids ),
    length( Ids, Len ), write( number_of:Len ), nl.

number_of:100
Date = date(2018, 9, 22),
Ids = ['30089663', '28647861', '28486579', '27684214', '27142769', '25509153', '24995073', '22586414', '22462194'|...],
Len = 100.

?-
    date(Date), pub_graph_search( prolog, Ids, retmax(200) ),
    length( Ids, Len ), write( number_of:Len ), nl.

number_of:127
Date = date(2018, 9, 22),
Ids = ['30089663', '28647861', '28486579', '27684214', '27142769', '25509153', '24995073', '22586414', '22462194'|...],
Len = 127.

?-
   St = ('breast','cancer','Publication Type'='Review'),
   date(Date), pub_graph_search( St, Ids, reldate(30) ),
   length( Ids, Len ).

Date = date(2018, 9, 22),
Ids = ['30240898', '30240537', '30240152', '30238542', '30238005', '30237735', '30236642', '30236594', '30234119'|...],
Len = 100.

?-
    pub_graph_summary_display( 30243159, _, true ).
----
1:30243159
        Author=[Wang K,Yee C,Tam S,Drost L,Chan S,Zaki P,Rico V,Ariello K,Dasios M,Lam H,DeAngelis C,Chow E]
        Title=Prevalence of pain in patients with breast cancer post-treatment: A systematic review.
----
true.

Version 0:3 (pub_graph_version(1:2:0,_D)).

?-
     date(Date), pub_graph_search(title='Bayesian networks elucidate', Ids, true), length(Ids,Len).
Date = date(2023, 9, 20),
Ids = ['35379892'],
Len = 1.

?-
     date(Date), pub_graph_search(title='Bayesian elucidate', Ids, true), length(Ids,Len).

Date = date(2023, 9, 20),
Ids = [],
Len = 0.

?-
     date(Date), pub_graph_search(title='Bayesian elucidate', Ids, gap(1)), length(Ids, Len),  pub_graph_summary_display(Ids, _, true).

----
1:35379892
        Author=[Angelopoulos N,Chatzipli A,Nangalia J,Maura F,Campbell PJ]
        Title=Bayesian networks elucidate complex genomic landscapes in cancer.
----
Date = date(2023, 9, 20),
Ids = ['35379892'],
Len = 1.

?-
     date(D),
     write('Appears in abstract: "explainable Artificial Intelligence models"'), nl,
     pub_graph_search('Title/Abstract'='explainable Artificial Intelligence models', Ids, true),
     pub_graph_summary_display(Ids).

1
...
10:32417928
        Author=[Payrovnaziri SN,Chen Z,Rengifo-Moreno P,Miller T,Bian J,Chen JH,Liu X,He Z]
        Title=Explainable artificial intelligence models using real-world electronic health record data: a systematic scoping review.

?-
     date(D), pub_graph_search('Title/Abstract'='explainable Intelligence models', Ids, true).

D = date(2023, 9, 20),
Ids = [].

?-
     date(D), pub_graph_search((tiab='explainable Intelligence models',affiliation=sanger), Ids, gap(1)).

D = date(2023, 9, 20),
Ids = ['35379892'].

Also 0:3 added quote_value(Qv). Compare:

?- date(Date), pub_graph_search(title='Bayesian networks elucidate', Ids, true), length(Ids,Len).
Date = date(2023, 9, 20),
Ids = ['35379892'],
Len = 1.

?- date(Date), pub_graph_search(title='Bayesian networks elucidate', Ids, quote_value(false)), length(Ids,Len).
Date = date(2023, 9, 20),
Ids = ['35923659', '35379892', '32609725', '29055062', '27303742', '26362267'],
Len = 6.

author

- nicos angelopoulos

version

- 0:1 2012/07/15

- 0:2 2018/09/22, small update on \ escape on eutils, ncbi, queries

- 0:3 2023/09/20, added Gap, much better search for title + affiliation + title/abstract

*/

  427pub_graph_search( STerm, Ids ) :-
  428     pub_graph_search( STerm, Ids, [] ).
  429
  430pub_graph_search( Sterm, Ids, Args ) :-
  431    options_append( pub_graph_search, Args, Opts ),
  432    url_eutils( Eutils ),
  433    ( ground(Sterm) -> true; type_error(ground,Sterm) ),
  434    options( gap(Gap), Opts ),
  435    options( quote_value(Qv), Opts ),
  436    search_term_to_query( Sterm, Gap, Qv, Query ),
  437    memberchk( retmax(Ret), Opts ), 
  438    pub_graph_search_period_opts( '', Period, Opts ),
  439    atomic_list_concat( [Eutils,'esearch.fcgi?db=pubmed&retmax=',Ret,Period,'&term=',Query], Url ),
  440    memberchk_optional( tmp_file(Tmp), Opts ),
  441    memberchk( verbose(Verb), Opts ),
  442    true_writes( Verb, Url ),
  443    debug( pub_graph, 'Get url is: ~w', Url ),
  444    get_url_in_file( Url, Verb, Tmp ),
  445    true_writes( Verb, tmp_file(Tmp) ),
  446    load_xml_file( Tmp, Xml ),
  447    ( (memberchk(qtranslation(QTrans),Opts),
  448        QT = 'QueryTranslation',
  449        search_element_in_list(Xml,QT,[],element(_,_,QTrans))) -> true; true
  450    ),
  451    all_subs_in_xml_single( Xml, 'IdList', 'Id', NastyIds ),
  452    flatten( NastyIds, Ids ),
  453    memberchk_optional( tmp_keep(Keep), Opts ),
  454    true_atom_keeps_file( Keep, Tmp ).

 pub_graph_summary_display(+Ids)

Short for pub_graph_summary_display( Ids, _Summary, [] ).

*/

  461pub_graph_summary_display( Ids ) :-
  462     pub_graph_summary_display( Ids, _Summary, [] ).

 pub_graph_summary_display(+Ids, -Summary)

Short for pub_graph_summary_display( Ids, Summary, [] ). */

  468pub_graph_summary_display( Ids, Summary ) :-
  469     pub_graph_summary_display( Ids, Summary, [] ).
  470
  471% pub_graph_summary_display_defaults( [display(['Title','Author']),names(Names)] ) :-
  472%     default_names( Names ).
  473pub_graph_summary_display_defaults( [display([title,'Title',authors,'Author'])] ).

 pub_graph_summary_display(+IdS, -Summaries, +Opts)

A wrapper around pub_graph_summary_info/3. It call this predicate with same arguments before displaying the Summary information. Opts can be a single term option or a list of such terms. In addition to pub_graph_summary_info/3 options this wrapper also recognises the term:

Opts

display(Disp)

a list of article information keys that will displayed one on a line for each Id in Ids. Disp values of var(Disp), '*' and 'all', list all available values.

?-
    date(Date),
    pub_graph_search((programming,'Prolog'), Ids),
    length( Ids, Len),
    Ids = [A,B,C|_], pub_graph_summary_display( [A,B,C] ).

----
1:28486579
    Author=[Holmes IH,Mungall CJ]
    Title=BioMake: a GNU make-compatible utility for declarative workflow management.
----
2:24995073
    Author=[Melioli G,Spenser C,Reggiardo G,Passalacqua G,Compalati E,Rogkakou A,Riccio AM,Di Leo E,Nettis E,Canonica GW]
    Title=Allergenius, an expert system for the interpretation of allergen microarray results.
----
3:22215819
    Author=[Mørk S,Holmes I]
    Title=Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.
----
Date = date(2018, 9, 22),
Ids = ['28486579', '24995073', '22215819', '21980276', '15360781', '11809317', '9783213', '9293715', '9390313'|...],
Len = 43.
A = '28486579',
B = '24995073',
C = '22215819'.

?-
    pub_graph_summary_display( 30235570, _, display(*) ).

----
1:30235570
    Author=[Morgan CC,Huyck S,Jenkins M,Chen L,Bedding A,Coffey CS,Gaydos B,Wathen JK]
    Title=Adaptive Design: Results of 2012 Survey on Perception and Use.
    Source=Ther Innov Regul Sci
    Pages=473-481
    PubDate=2014 Jul
    Volume=48
    Issue=4
    ISSN=2168-4790
    PmcRefCount=0
    PubType=Journal Article
    FullJournalName=Therapeutic innovation & regulatory science
----

?-
     pub_graph_cited_by( 20195494, These ),
     pub_graph_summary_display( These, _, [display(['Title','Author','PubDate'])] ).

----
1:29975690
    Author=[Tang K,Boudreau CG,Brown CM,Khadra A]
    Title=Paxillin phosphorylation at serine 273 and its effects on Rac, Rho and adhesion dynamics.
    PubDate=2018 Jul
----
2:29694862
    Author=[McKenzie M,Ha SM,Rammohan A,Radhakrishnan R,Ramakrishnan N]
    Title=Multivalent Binding of a Ligand-Coated Particle: Role of Shape, Size, and Ligand Heterogeneity.
    PubDate=2018 Apr 24
----
3:29669897
    Author=[Padmanabhan P,Goodhill GJ]
    Title=Axon growth regulation by a bistable molecular switch.
    PubDate=2018 Apr 25
...
...
26:20473365
    Author=[Welf ES,Haugh JM]
    Title=Stochastic Dynamics of Membrane Protrusion Mediated by the DOCK180/Rac Pathway in Migrating Cells.
    PubDate=2010 Mar 1
----
These = [29975690, 29694862, 29669897, 28752950, 27939309, 27588610, 27276271, 25969948, 25904526|...].


?-
    pub_graph_summary_display( 20195494, _Res, true ).

----
1:20195494
    Author=[Cirit M,Krajcovic M,Choi CK,Welf ES,Horwitz AF,Haugh JM]
    Title=Stochastic model of integrin-mediated signaling and adhesion dynamics at the leading edges of migrating cells.
----
true.

?-
    pub_graph_summary_display( cbd251a03b1a29a94f7348f4f5c2f830ab80a909, _, display(all) ).

----
1:cbd251a03b1a29a94f7348f4f5c2f830ab80a909
        arxivId=[]
        authors=[Graham J. L. Kemp,Nicos Angelopoulos,Peter M. D. Gray]
        doi=10.1109/TITB.2002.1006298
        title=Architecture of a mediator for a bioinformatics database federation
        topics=[]
        venue=IEEE Transactions on Information Technology in Biomedicine
        year=2002
----
true.

*/

  593pub_graph_summary_display( IdS, Summary, Args ) :-
  594    % pub_graph_summary_display_defaults( Defs ),
  595    % options_append( Opts, Defs, All ),
  596    non_var_list( IdS, Ids ),
  597    options_append( pub_graph_summary_display, Args, Opts ),
  598    options( display(Disp), Opts ),
  599    pub_graph_summary_info( Ids, Summary, Opts ),
  600    pub_graph_summary_display_info( Summary, Disp ).

 pub_graph_summary_display_info(+Summaries, +Entries)

Display the Entries information for Summaries, which should be a list of summaries. If Entries is a variable all info will be printed.

  607pub_graph_summary_display_info( SummaryIn, Disp ) :-
  608     pg_en_list( SummaryIn, Summary ),
  609     write( '----' ), nl,
  610     nth1( N, Summary, Id-Rec ),
  611     write( N:Id ), nl,
  612     findall( _, (member(D-Val,Rec),once((var(Disp);Disp=all;Disp='*';member(D,Disp))),put(0'\t), write(D=Val),nl), _ ), 
  613     write( '----' ), nl, fail.
  614pub_graph_summary_display_info( _Summary, _Disp ).
  615
  616%
  617% Redirects to pub_graph_cited_by( Id, Ids, [] ).
  618%
  619pub_graph_cited_by( Id, Ids) :-
  620     pub_graph_cited_by( Id, Ids, [] ).

 pub_graph_cited_by(+Id, -Ids)

 pub_graph_cited_by(+Id, -Ids, +Options)

Ids is the list of pub_graph ids that cite Id.

Options is a term option or list of terms from the following;

verbose(Verb=false)

be verbose

cache(Type, Handle, Date, Update)

use cache with Handle and Type, cutting off cached items that are (strictly) older than Date. For Update = true update the cache if you do an explicit retrieval.

?-
     date(D), pub_graph_cited_by( 12075665, By ), length( By, Len ).

D = date(2018, 9, 22),
By = [25825659, 19497389, 19458771],
Len = 3.

?-
    date(D), pub_graph_cited_by( cbd251a03b1a29a94f7348f4f5c2f830ab80a909, By ), length( By, Len ).

D = date(2018, 9, 22),
By = ['2e1f686c2357cead711c8db034ff9aa2b7509621', '6f125881788967e1eec87e78b3d2db61d1a8d0ac'|...],
Len = 12.

*/

  654pub_graph_cited_by( Id, Ids, Args ) :-
  655     options_append( pub_graph_graph, Args, Opts ),
  656     pub_graph_cited_by_1( Id, Ids, Opts ).
  657
  658pub_graph_cited_by_1( Id, Ids, Opts ) :-
  659     ( ( memberchk(cache(Type,Handle,Date,_Upd), Opts),
  660         pub_graph_date_cached(Type,Handle,cited_by,Date,Id,Ids) ) ->
  661          ( memberchk(verbose(true),Opts) ->
  662               write( got_from_cache(Id,Ids) ), nl
  663               ;
  664               true
  665          )
  666          ;
  667          pub_graph_cited_by_uncached( Id, Ids, Opts ),
  668          ( (memberchk(cache(Type,Handle,_Date,Upd),Opts),Upd==true) ->
  669               pub_graph_update_cache( Type, Handle, cited_by, Id, Ids )
  670               ;
  671               true
  672          )
  673     ).
  674
  675pub_graph_cited_by_uncached( Id, Ids, Opts ) :-
  676    pub_graph_id( Id, IdType ),
  677    pub_graph_cited_by_uncached( IdType, Id, Ids, Opts ).
  678
  679pub_graph_cited_by_uncached( semscholar, Id, Ids, _Verb ) :-
  680    semscholar_id_json( Id, Json ),
  681    memberchk( citations=Citations, Json ),
  682    findall( ACit, (    member(json(Sub),Citations),
  683                        member(paperId=ACit,Sub),
  684                        ACit \== ''
  685                   ),
  686                        Ids ).
  687pub_graph_cited_by_uncached( ncbi, Id, Ids, Opts ) :-
  688     ( memberchk(verbose(Verb),Opts) -> true; Verb = false ),
  689     url_eutils( Eutils ),
  690     Query = 'elink.fcgi?report=xml&mode=text&tool=curl&db=pubmed&cmd=neighbor&linkname=pubmed_pubmed_citedin&id=',
  691     atomic_list_concat( [Eutils,Query,Id], Url ),
  692     get_url_in_file( Url, Verb, Tmp ),
  693     ( pub_graph_cited_by_parse_file(Tmp, Ids) -> 
  694          true
  695          ;
  696          Ids = []
  697     ),
  698     delete_file( Tmp ).

 pub_graph_id_journal(+Id, +Provisional, -Journal)

Allows for "correcting" Journal entries of Id. Journal is Provisional, except if id_has_journal/2 exists and id_has_journal( Id, Jounal ) succeeds (det.)

  706pub_graph_id_journal( IdPrv, _Provisional, Journal ) :-
  707    current_predicate( user:id_has_journal/2 ),
  708    to_number( IdPrv, Id ),
  709    user:id_has_journal( Id, Journal ),
  710    !.
  711pub_graph_id_journal( _Id, Journal, Journal ).
  712
  713%
  714% Redirects to pub_graph_cites( Id, Ids, [] ).
  715%
  716pub_graph_cites( Id, Ids ) :-
  717     pub_graph_cites( Id, Ids, [] ).

 pub_graph_cites(+Id, -Ids)

 pub_graph_cites(+Id, -Ids, +Options)

Ids is the list of pub_graph Ids (pub_graph_id/2) that are cited by Id.

Options is a term option or list of terms from the following;

verbose(Verb)

be verbose

?-
    date(D),
    pub_graph_cites( 20195494, Ids ),
    length( Ids, Len ), write( D:Len ), nl.

date(2018,9,22):38
D = date(2018, 9, 22),
Ids = ['19160484', '19118212', '18955554', '18800171', '18586481'|...],
Len = 38.

% pubmed does not have references cited by the following paper:

?-
    date(D),
    pub_graph_cites( 12075665, Ids ),
    length( Ids, Len ), write( D:Len ), nl.

false.

% whereas, semanticscholar.org finds 17 (non '') of the 21:
?-
    date(D),
    pub_graph_cites( cbd251a03b1a29a94f7348f4f5c2f830ab80a909, Ids ),
    length( Ids, Len ), write( D:Len ), nl.

date(2018,9,22):17
D = date(2018, 9, 22),
Ids = ['6477792829dd059c7d318927858d307347c54c2e', '1448901572d1afd0019c86c42288108a94f1fb25', |...],
Len = 17.

?-
    pub_graph_summary_display( 12075665, Results, true ).

----
1:12075665
    Author=[Kemp GJ,Angelopoulos N,Gray PM]
    Title=Architecture of a mediator for a bioinformatics database federation.
----
Results = [12075665-['Author'-['Kemp GJ', 'Angelopoulos N', 'Gray PM'], ... - ...|...]].

author

- nicos angelopoulos

version

- 0:1 2018/9/22

See also

- pub_graph_id/2

*/

  775pub_graph_cites( Id, Ids, OptsIn ) :-
  776    non_var_list( OptsIn, Opts ),
  777    pub_graph_id( Id, IdType ),
  778    ( memberchk(verbose(Verb),Opts) -> true; Verb = false ),
  779    pub_graph_id_type_cites( IdType, Id, Ids, Verb ).
  780
  781pub_graph_id_type_cites( ncbi, Id, Ids, Verb ) :-
  782     url_eutils( Eutils ),
  783     % Query = 'elink.fcgi?report=xml&mode=text&tool=curl&db=pmc&DbFrom=pubmed&Cmd=link&linkname=pubmed_pmc_refs&id=',
  784     Query = 'elink.fcgi?report=xml&mode=text&tool=curl&db=pubmed&Cmd=neighbor&linkname=pubmed_pubmed_refs&id=',
  785     atomic_list_concat( [Eutils,Query,Id], Url ),
  786     get_url_in_file( Url, Verb, Tmp ),
  787     load_xml_file( Tmp, Xml ),
  788     once( search_element_in_list( Xml, 'LinkSetDb', [], element(_,_,LXml) ) ),
  789     findall( CId, search_element_in_list(LXml,'Id',[],element(_,_,[CId])),Ids ),
  790     delete_file( Tmp ).
  791pub_graph_id_type_cites( semscholar, Id, Ids, _Verb ) :-
  792    semscholar_id_json( Id, Json ),
  793    memberchk( references=Citations, Json ),
  794    findall( ACit, (    member(json(Sub),Citations),
  795                        member(paperId=ACit,Sub),
  796                        ACit \== ''
  797                   ),
  798                        Ids ).
  799
  800pub_graph_table_defaults( Defs ) :-
  801    NoSearch = 'No search term available',
  802    Defs = [ include_if(false), output(csv), stem([]), spy([]), search(NoSearch) ].

 pub_graph_table(+Ids, -Rows, +Opts)

Create a table of information relating to IDs.

Can include journal impact factor if jif/6 is provided.

Output rows contain #citing, [IF ,] Date, Journal, Title, Author, (Title urled to pubmed/$id)

Opts

include_if(IF=false)

whether to include Impact Factor (IF) column (if true requires jif/6)

missing_if(MIF=throw)

what to do when a journal has no impact factor: [throw,has(Val),quite(Val)]

output(Type=html)

type of output, if file is expected (see stem), in [csv,?pdf?,html]

search(Search=No search term available)

search term corresponding to the Ids

spy Spy=[]

A number of ids to spy (list of atoms)

stem(Stem)

when present a file <Stem>.<Type> is created

     ?-
     pub_graph_table

author

- nicos angelopoulos

version

- 0:1 2018/9/20

*/

  840pub_graph_table( Ids, Rows, Args ) :-
  841    options_append( pub_graph_table, Args, Opts ),
  842    OTerms = [include_if(Iif),missing_if(Mif),output(Form),stem(Stem),spy(SpY)],
  843    options( OTerms, Opts ),
  844    pg_en_list( SpY, Spy ),
  845    % ground( Iif ), % i think options checks.
  846    maplist( pub_graph_table_id_row(Iif,Mif,Spy), Ids, Rows ),
  847    options( search(Search), Opts ),
  848    pub_graph_table_output( Stem, Form, Iif, Search, Rows ).
  849
  850pub_graph_table_id_row( Iif, Mif, Spy, Id, Row ) :-
  851    ( memberchk(Id,Spy) -> trace; true ),
  852    pub_graph_table_id_main_args( Id, Journal, Args ), 
  853    pub_graph_table_iif( Iif, Mif, Args, Journal, Irgs ),
  854    Row =.. [row|Irgs].
  855
  856pub_graph_table_id_main_args( Id, Journal, Args ) :-
  857    pub_graph_table_id_main_args_all( Id, Journal, Args ),
  858    !.
  859pub_graph_table_id_main_args( Id, Journal, Args ) :-
  860    throw( could_not_find_all_info_for_table_row_of(Id,Journal,Args) ).
  861
  862pub_graph_table_id_main_args_all( Id, Journal, Args ) :-
  863    pub_graph_summary_info( Id, Summ, [] ),
  864    memberchk( 'PmcRefCount'-PRCount, Summ ),
  865    memberchk( 'FullJournalName'-JournalPrv, Summ ),
  866    memberchk( 'Title'-Title, Summ ),
  867    memberchk( 'Author'-AuthorS, Summ ),
  868    pg_en_list( AuthorS, Authors ),
  869    atomic_list_concat( Authors, ', ', Author ),
  870    memberchk( 'PubDate'-Pdate, Summ ),
  871    pub_graph_id_journal( Id, JournalPrv, JournalPrv2 ),
  872    ( pub_graph_journal_synonym(JournalPrv2,Journal) -> true; Journal = JournalPrv2 ),
  873    Args = [PRCount,Pdate,Journal,Title,Author,Id].
  874
  875pub_graph_table_iif( false, _Mif, Args, _J, Args ).
  876pub_graph_table_iif( true, Mif, [A|Rgs], J, [A,Jif|Rgs] ) :-
  877    downcase_atom( J, DownJ ),
  878    pub_graph_table_jif( DownJ, J, Mif, Jif ).
  879
  880pub_graph_table_jif( DownJ, _J, _Mif, Jif ) :-
  881    user:jif( _, DownJ, _, JifGot, _, _ ),
  882    ( number(JifGot) -> JifGot = Jif; Jif is 0 ),
  883    !.
  884pub_graph_table_jif( DownJ, _J, _Mif, Jif ) :-
  885    pub_graph_jif_alternative( DownJ, AlteJ ),
  886    user:jif( _, AlteJ, _, JifGot, _, _ ),
  887    ( number(JifGot) -> JifGot = Jif; Jif is 0 ),
  888    !.
  889pub_graph_table_jif( DownJ, _J, _Mif, Jif ) :-
  890    missing_jif( DownJ, Jif ),
  891    !.
  892pub_graph_table_jif( _DownJ, J, Mif, Jif ) :-
  893    pub_graph_table_jif_missing( Mif, J, Jif ),
  894    !. % i dont think the above leaves b.points
  895
  896pub_graph_table_jif_missing( has(Val), J, Val ) :-
  897    debug( pub_graph, 'No IF for: ~w', J ).
  898pub_graph_table_jif_missing( quiet(Val), _J, Val ).
  899pub_graph_table_jif_missing( throw, J, _Jif ) :-
  900    throw( no_jif_for_journal(J) ).
  901
  902pub_graph_jif_alternative( Jname, Alternative ) :-
  903    member( Mfx, [', ',' : ',' and ','. '] ),
  904    atom_length( Mfx, Len ),
  905    sub_atom( Jname, Bef, Len, Aft, Mfx ),
  906    sub_atom( Jname, 0, Bef, _, Pfx ), 
  907    ToAft is Bef + Len,
  908    sub_atom( Jname, ToAft, Aft, 0, Psf ),
  909    member( Nfx, ['-',' ',' & '] ),
  910    atomic_list_concat( [Pfx,Nfx,Psf], Alternative ).
  911pub_graph_jif_alternative( Jname, Alternative ) :-
  912    member( Bp, [' : ','; '] ),
  913    atom_length( Bp, Len ),
  914    sub_atom( Jname, Bef, Len, _Aft, ' : ' ),
  915    sub_atom( Jname, 0, Bef, _, Alternative ).
  916pub_graph_jif_alternative( Jname, Alternative ) :-
  917    atom_concat( 'the ', Alternative, Jname ).
  918
  919missing_jif( metabolites, 0 ).
  920missing_jif( 'genomics, proteomics & bioinformatics', 0 ).
  921missing_jif( 'frontiers in pharmacology', 0 ). % http://www.frontiersin.org/news/Frontiers_Impact_Factors_2013/875
  922missing_jif( 'advances in experimental medicine and biology', 2.012 ).  % http://www.springer.com/series/5584
  923missing_jif( 'expert review of clinical pharmacology', -2 ). % don't think this has IF in general
  924missing_jif( 'dental research journal', -2 ). % don't think this has IF in general
  925missing_jif( 'brain and nerve = shinkei kenkyu no shinpo', -2 ). % only in Japanese
  926missing_jif( 'critical reviews in biomedical engineering', -2 ). % discontinued i think
  927missing_jif( 'yao xue xue bao = acta pharmaceutica sinica', -2 ). % in Chinese
  928missing_jif( 'gan to kagaku ryoho. cancer & chemotherapy', -2 ). % in Japanese
  929missing_jif( 'chinese journal of cancer', 0 ). % http://www.researchgate.net/journal/1944-446X_Chinese_journal_of_cancer
  930missing_jif( 'seminars in oncology nursing', -2 ). % http://www.researchgate.net/journal/1878-3449_Seminars_in_Oncology_Nursing
  931missing_jif( 'critical reviews in oncogenesis', -2 ). % http://www.researchgate.net/journal/0893-9675_Critical_reviews_in_oncogenesis
  932missing_jif( 'praxis', -2 ). % in German
  933
  934
  935pub_graph_journal_synonym( 'Cellular and molecular life sciences : CMLS', 'CELLULAR AND MOLECULAR LIFE SCIENCES' ).
  936pub_graph_journal_synonym( 'Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine', 'TUMOR BIOLOGY' ). % http://www.ncbi.nlm.nih.gov/nlmcatalog/8409922
  937pub_graph_journal_synonym( 'American journal of physiology. Heart and circulatory physiology', 'AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY' ). % http://www.ncbi.nlm.nih.gov/nlmcatalog/8409922
  938pub_graph_journal_synonym( 'The journals of gerontology. Series A, Biological sciences and medical sciences', 'JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES' ).
  939pub_graph_journal_synonym( 'Proteomics. Clinical applications', 'Proteomics Clinical applications' ).
  940pub_graph_journal_synonym( 'Future oncology (London, England)', 'Future Oncology' ).
  941pub_graph_journal_synonym( 'The oncologist', 'Oncologist' ).
  942pub_graph_journal_synonym( 'Cancer control : journal of the Moffitt Cancer Center', 'Cancer Control' ).
  943pub_graph_journal_synonym( 'Breast (Edinburgh, Scotland)', 'Breast' ).
  944pub_graph_journal_synonym( 'Cancer journal (Sudbury, Mass.)', 'Cancer Journal' ).
  945pub_graph_journal_synonym( 'Hematology / the Education Program of the American Society of Hematology. American Society of Hematology. Education Program', 'Hematology-American Society of Hematology Education Program' ).
  946
  947pub_graph_table_output( [], _Form,  _Iif, _Search, _Rows ) :- !.
  948pub_graph_table_output( Stem, Form, Iif, Search, Rows ) :-
  949    file_name_extension( Stem, Form, OutF ),
  950    pub_graph_table_file_output( Form, OutF, Iif, Search, Rows ),
  951    !.
  952pub_graph_table_output( _Stem, Form, _Iif, _Search, _Rows ) :-
  953    write( user_error, 'Dont know how to write onto: ~w', [Form] ), nl( user_error ). % fixme
  954
  955pub_graph_table_file_output( html, OutF, _Iif, Search, Rows ) :-
  956    tell( OutF ),
  957    maplist( pub_graph_table_html_row, Rows, HtmlRows ),
  958    term_string( Search, SearchString ),
  959    atom_string( SearchAtom, SearchString ),
  960    atom_concat( 'search term: ', SearchAtom, HtmlH1 ),
  961    reply_html_page( title(HtmlH1), [h1(HtmlH1),table(HtmlRows)] ).
  962pub_graph_table_file_output( csv, OutF, Iif, _Search, Rows ) :-
  963    pub_graph_iif_header( Iif, Hdr ),
  964    csv_write_file( OutF, [Hdr|Rows] ).
  965
  966pub_graph_table_html_row( row(C,I,P,J,T,A,B), Html ) :-
  967    atomic_list_concat( ['https://www.ncbi.nlm.nih.gov/pubmed/?term=',B], Href ),
  968    Anc = a(href(Href),T),
  969    atomic_list_concat( PParts, ' ', P ),
  970    atomic_list_concat( PParts, '_', U ),
  971    Html = tr( [
  972                   td(C),
  973                td(I),
  974                td(U),
  975                td(J),
  976                td(Anc),
  977                td(A),
  978                td(B)
  979            ] ).
  980
  981pub_graph_iif_header( true, Hdr ) :- 
  982    Hdr = row('Cited','IF','Published','Journal','Title','Author','Pubmed').
  983pub_graph_iif_header( false, Hdr ) :- 
  984    Hdr = row('Cited','Published','Journal','Title','Author','Pubmed').

 pub_graph_summary_info(+IdS, -Summaries, +Opts)

Summaries is the summary information for pub_graph id(s) IdS.
The form of results depends on whether IdS is a single PubMed Id,
in which case Summaries is a list of Name-Value pairs.
Whereas, when IdS is a list, Summaries is a list Id-Info pairs, where Info
is a Name-Value list. The predicate fetches the information with curn
via the http interface Summaries are deposited in local temporary files which are subsequently parsed.

Options is a single term, or list of the following terms:

names(Names)

list of info slot names to be found in the xml file

retmax(100)

the maximum number of records that will be returned

tmp_file(Tmp)

temporary file to be used for saving xml files. If Tmp is a variable, or option is missing, a temporary file is created with tmp_file_stream/3.

tmp_keep(false)

if true, keep the temporary xml file, otherwise, and by default, delete it.

verbose(Verb)

When true be verbose.

cache(Type, Handle, Update)

Use a cache with Type and Handle. Update should be boolean, set to false if you dont want the cache to be updated with newly downloaded information.

?-
  date(Date),
  Opts = names(['Author','PmcRefCount','Title']),
  pub_graph_summary_info( 12075665, Results, Opts ),
  write( date:Date ), nl,
  member( R, Results ), write( R ), nl,
  fail.

date:date(2018,9,22)
Author-[Kemp GJ,Angelopoulos N,Gray PM]
PmcRefCount-3
Title-Architecture of a mediator for a bioinformatics database federation.
false.


?-
    pub_graph_summary_info(12075665,Res,[]),
    member(R,Res), write( R ), nl,
    fail.

Author-[Kemp GJ,Angelopoulos N,Gray PM]
Title-Architecture of a mediator for a bioinformatics database federation.
Source-IEEE Trans Inf Technol Biomed
Pages-116-22
PubDate-2002 Jun
Volume-6
Issue-2
ISSN-1089-7771
PmcRefCount-3
PubType-Journal Article
FullJournalName-IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society

?-
    pub_graph_summary_info( cbd251a03b1a29a94f7348f4f5c2f830ab80a909, Res, true ),
    member( R, Res ), write( R ), nl,
    fail.

arxivId-[]
authors-[Graham J. L. Kemp,Nicos Angelopoulos,Peter M. D. Gray]
doi-10.1109/TITB.2002.1006298
title-Architecture of a mediator for a bioinformatics database federation
topics-[]
venue-IEEE Transactions on Information Technology in Biomedicine
year-2002
false.

*/

 1064pub_graph_summary_info( IdS, Results, OptS ) :-
 1065    non_var_list( OptS, Opts ),
 1066    non_var_list( IdS, Ids ),
 1067     !,
 1068     maplist( pub_graph_summary_info_single(Opts), Ids, UnsResults ),
 1069     ( memberchk(sort_by(SortField,Order,Nums),Opts) ->
 1070               pub_graph_summary_sort( UnsResults, SortField, Order, Nums, OrdResults )
 1071               ;
 1072               UnsResults=OrdResults
 1073     ),
 1074    de_kv_list_on( OrdResults, IdS, Results ).
 1075pub_graph_summary_info( Id, Results, OptS ) :-
 1076    non_var_list( OptS, Opts ),
 1077     pub_graph_summary_info_single( Opts, Id, Id-Results ).
 1078
 1079pub_graph_summary_info_single( Opts, Id, Id-Results ) :-
 1080     memberchk( cache(Type,Handle,_Update), Opts ),
 1081     pub_graph_summary_info_cached( Type, Handle, Id, Results, Opts ),
 1082     debug( pub_graph, 'Summary from cache for: ~w', Id ),
 1083     !.
 1084pub_graph_summary_info_single( Opts, Id, Id-Info ) :-
 1085     % fixme use _defaults
 1086     debug( pub_graph, 'Summary not in cache for: ~w', Id ),
 1087     pub_graph_id( Id, IdType ),
 1088     ( memberchk(names(Names),Opts) -> true; default_names(IdType,Names) ),
 1089     ( memberchk(tmp_file(Tmp),Opts) -> true; true ),
 1090     ( memberchk(cache(Type,Handle,true),Opts) -> 
 1091               summary_info( Tmp, Id, all, ResAll, Opts ) ,
 1092               findall( Name-Val, (member(Name,Names),memberchk(Name-Val,ResAll)), Info ),
 1093               pub_graph_summary_info_cached_update( Type, Handle, Id, ResAll )
 1094               ;
 1095               summary_info( Tmp, Id, Names, Info, Opts)
 1096     ).
 1097
 1098pub_graph_summary_info_cached( csv, Handle, Id, Results, Opts ) :-
 1099     pub_graph_summary_info_cached( in_mem, Handle, Id, Results, Opts ).
 1100pub_graph_summary_info_cached( prolog, Handle, Id, Results, Opts ) :-
 1101     pub_graph_summary_info_cached( in_mem, Handle, Id, Results, Opts ).
 1102pub_graph_summary_info_cached( sqlite, Handle, Id, Results, Opts ) :-
 1103     pub_graph_summary_info_cached( db_facts, Handle, Id, Results, Opts ).
 1104pub_graph_summary_info_cached( odbc, Handle, Id, Results, Opts ) :-
 1105     pub_graph_summary_info_cached( db_facts, Handle, Id, Results, Opts ).
 1106pub_graph_summary_info_cached( db_facts, Handle, Id, Results, Opts ) :-
 1107     ( memberchk(names(Names),Opts) -> true; default_names(Names) ),
 1108     findall(K-(O-V),(member(K,Names),db_holds(Handle,info(Id,K,O,V))), OPRes),
 1109     OPRes \== [],
 1110     keysort( OPRes, OPRord ),
 1111     % kv_decompose_vs( OPRord, PRord ),
 1112     nest_pair_flatten_removes( OPRord, PRord ),
 1113     PRord = [K1-V1|PRTail],
 1114     kvs_to_unique_k_v_as_list( PRTail, K1, [V1], Results ).
 1115pub_graph_summary_info_cached( in_mem, _Handle, Id, Results, Opts ) :-
 1116     ( memberchk(names(Names),Opts) -> true; default_names(Names) ),
 1117     findall( K-V, (member(K,Names),pub_graph_cache_info:info(Id,K,V)), PRes ),
 1118     PRes \== [],
 1119     keysort( PRes, PRord ),
 1120     PRord = [K1-V1|PRTail],
 1121     kvs_to_unique_k_v_as_list( PRTail, K1, [V1], Results ).
 1122
 1123pub_graph_summary_info_cached_update( csv, Alias, Id, KVs ) :-
 1124     pub_graph_summary_info_cached_update( in_mem, Alias, Id, KVs ).
 1125pub_graph_summary_info_cached_update( prolog, Alias, Id, KVs ) :-
 1126     pub_graph_summary_info_cached_update( in_mem, Alias, Id, KVs ).
 1127pub_graph_summary_info_cached_update( in_mem, Alias, Id, KVs ) :-
 1128     retractall( info(Id,_K,_O,_V) ),
 1129     retractall( info_date(Id,_) ),
 1130     date( Date ), 
 1131     assert( info_date(Id,Date) ),
 1132     findall( _, ( member(K-V,KVs), (is_list(V)->nth1(N,V,Ve);Ve=V,N=1),assert(Alias, info(Id,K,N,Ve),_) ), _ ).
 1133pub_graph_summary_info_cached_update( sqlite, Alias, Id, KVs ) :-
 1134     pub_graph_summary_info_cached_update( db_facts, Alias, Id, KVs ).
 1135pub_graph_summary_info_cached_update( odbc, Alias, Id, KVs ) :-
 1136     pub_graph_summary_info_cached_update( db_facts, Alias, Id, KVs ).
 1137pub_graph_summary_info_cached_update( db_facts, Alias, Id, KVs ) :-
 1138     db_retractall( Alias, info(Id,_K,_O,_V), _Aff1 ),
 1139     db_retractall( Alias, info_date(Id,_), _Aff2 ),
 1140     date( Date ), 
 1141     db_date_sql_atom( Date, SqlDate ),
 1142     db_assert( Alias, info_date(Id,SqlDate), _ ),
 1143     findall( _, ( member(K-V,KVs), (is_list(V)->nth1(N,V,Ve);Ve=V,N=1),db_assert(Alias, info(Id,K,N,Ve),_) ), _ ).

 pub_graph_abstracts(+IdS, -IdsAbs)

For a list of IdS get all their respective IdAbs (ID-Abstracts) pairs. If IdS is a single PubMed Id then IDsAbs is simply the abstract (not a pair). Abstracts are returned as lists of atom, representing lines in the original reply.

  ?- pub_graph_abstracts( 24939894, Abs ).
  Abs = ['Lemur tyrosine kinase 3 (LMTK3) is associated with cell proliferation and',...].

To be done

- add option for returning the full response of the querny (includes sections for, Citation, Title, Aurhors, Affiliation and PMCID if one exists (last is in PMID section).

 1159pub_graph_abstracts( IdS, Abstracts ) :-
 1160    non_var_list( IdS, Ids ),
 1161    pub_graph_get_abstracts( Ids, Ibs ),
 1162    de_kv_list_on( Ibs, IdS, Abstracts ).
 1163
 1164pub_graph_get_abstracts( Ids, Ibs ) :-
 1165    atomic_list_concat( Ids, ',', IdsAtom ),
 1166    atomic_list_concat( [id,IdsAtom], '=', IdsReq ),
 1167    url_eutils( Eutils ),
 1168    url_efetch_pubmed( Efetch ),
 1169    atom_concat( Eutils, Efetch, EEReq ),
 1170    RmdReq = 'retmode=text',
 1171    RtpReq = 'rettype=abstract',
 1172    atomic_list_concat( [EEReq,IdsReq,RmdReq,RtpReq], '&', Url ),
 1173    get_url_in_file( Url, true, Tmp ),
 1174    % write( file_is(Tmp) ), nl,
 1175    file_abstracts( Tmp, Ibs ).
 1176
 1177file_abstracts( File, Ibs ) :-
 1178    read_file_to_codes( File, Codes, [] ),
 1179    Codes = [0'\n|Tcodes],
 1180    codes_abstracts( Tcodes, Ibs ).
 1181
 1182% Each abstract-entry has sections seperated by \n.
 1183codes_abstracts( Codes, Ibs ) :-
 1184    % write( codes(Codes) ), nl,
 1185    codes_abstracts_sections( Sections, [], Codes, [] ),
 1186    % length( Sections, Len ),
 1187    % maplist( write_codes_ln, Sections ),
 1188    % write( sections_length(Len) ), nl,
 1189    code_sections_abstracts( Sections, Ibs ).
 1190
 1191write_codes_ln( Codes ) :-
 1192    atom_codes( Atom, Codes ),
 1193    write( Atom ), nl.
 1194
 1195codes_abstracts_sections( Sects, Acc ) -->
 1196    "\n\n", consume_new_line,
 1197    !,
 1198    { ( Acc==[] -> Sects=TSects; 
 1199        reverse(Acc,Sect),Sects=[Sect|TSects]
 1200         %, atom_codes( Att, Sect), write( att_acc(Att,Acc) ), nl 
 1201      ) },
 1202    codes_abstracts_sections( TSects, [] ).
 1203codes_abstracts_sections( Sects, Acc ) -->
 1204    [C],
 1205    !,
 1206    codes_abstracts_sections( Sects, [C|Acc] ).
 1207codes_abstracts_sections( Sects, Acc ) -->
 1208    { ( Acc == [] -> Sects = []
 1209                 ; reverse( Acc, Sect ), 
 1210                % atom_codes( SectAtom, Sect ),
 1211                % write( section(SectAtom,Acc) ), nl,
 1212                 Sects = [Sect] ) }.
 1213
 1214consume_new_line --> "\n", {!}.
 1215consume_new_line --> [].
 1216
 1217code_sections_abstracts( [], [] ).
 1218code_sections_abstracts( [_A,_B,_C,_D,_Comm,E,_Copy,F|T], [Id-Elns|Ibs] ) :-
 1219    atom_codes( Fat, F ),
 1220    debug( pub_graph, 'Parsing abstract from line:~w', Fat ),
 1221    code_section_pub_med_id( Id, F, _ ),
 1222    debug( pub_graph, 'Parsing abstract for id:~w', Id ),
 1223    code_section_lines( E, Elns ),
 1224    !,
 1225    code_sections_abstracts( T, Ibs ).
 1226code_sections_abstracts( [_Ref,_Ttl,_Ath,_Ainf,Abs,Copy,Pmi|T], [Id-AbsLns|Ibs] ) :-
 1227    copyright_line( Copy, _ ),
 1228    atom_codes( Pat, Pmi ),
 1229    debug( pub_graph, 'Parsing abstract from line:~w', Pat ),
 1230    code_section_pub_med_id( Id, Pmi, _ ),
 1231    debug( pub_graph, 'Parsing abstract for id:~w', Id ),
 1232    code_section_lines( Abs, AbsLns ),
 1233    !,
 1234    code_sections_abstracts( T, Ibs ).
 1235code_sections_abstracts( [_Ref,_Ttl,_Ath,_Ainf,_Cmnt,Abs,Pmi|T], [Id-AbsLns|Ibs] ) :-
 1236    atom_codes( Pat, Pmi ),
 1237    debug( pub_graph, 'Parsing abstract from line:~w', Pat ),
 1238    code_section_pub_med_id( Id, Pmi, _ ),
 1239    !,
 1240    debug( pub_graph, 'Parsing abstract for id:~w', Id ),
 1241    code_section_lines( Abs, AbsLns ),
 1242    code_sections_abstracts( T, Ibs ).
 1243code_sections_abstracts( [_Ref,_Ttl,_Ath,_Anf,Abs,Pmi|T], [Id-AbsLns|Ibs] ) :-
 1244    atom_codes( Pat, Pmi ),
 1245    debug( pub_graph, 'Parsing abstract from line:~w', Pat ),
 1246    code_section_pub_med_id( Id, Pmi, _ ),
 1247    !,
 1248    debug( pub_graph, 'Parsing abstract for id:~w', Id ),
 1249    code_section_lines( Abs, AbsLns ),
 1250    code_sections_abstracts( T, Ibs ).
 1251code_sections_abstracts( [_Ref,_Ttl,_Ath,Pmi|T], [Id-[]|Ibs] ) :-
 1252    atom_codes( Pat, Pmi ),
 1253    debug( pub_graph, 'Parsing abstract from line:~w', Pat ),
 1254    code_section_pub_med_id( Id, Pmi, _ ),
 1255    debug( pub_graph, 'Parsing abstract for id:~w', Id ),
 1256    !,
 1257    code_sections_abstracts( T, Ibs ).
 1258code_sections_abstracts( [_A,_B,_C,_D,F|T], [Id-Elns|Ibs] ) :-
 1259    atom_codes( Fat, F ),
 1260    debug( pub_graph, 'Parsing non-abstract from line:~w', Fat ),
 1261    code_section_pub_med_id( Id, F, _ ),
 1262    Elns = [],
 1263    code_sections_abstracts( T, Ibs ).
 1264
 1265/*
 1266code_sections_abstracts( [_Ref,_Ttl,_Ath,Abs,Copy,Pmi|T], [Id-AbsLns|Ibs] ) :-
 1267    copyright_line( Copy, _ ),
 1268    atom_codes( Pat, Pmi ),
 1269    debug( pub_graph, 'Parsing abstract from line:~w', Pat ),
 1270    code_section_pub_med_id( Id, Pmi, _ ),
 1271    !,
 1272    debug( pub_graph, 'Parsing abstract for id:~w', Id ),
 1273    code_section_lines( Abs, AbsLns ),
 1274    code_sections_abstracts( T, Ibs ).
 1275code_sections_abstracts( [_Ref,_Ttl,_Ath,_Anf,Abs,Pmi|T], [Id-AbsLns|Ibs] ) :-
 1276    atom_codes( Pat, Pmi ),
 1277    debug( pub_graph, 'Parsing abstract from line:~w', Pat ),
 1278    code_section_pub_med_id( Id, Pmi, _ ),
 1279    !,
 1280    debug( pub_graph, 'Parsing abstract for id:~w', Id ),
 1281    code_section_lines( Abs, AbsLns ),
 1282    code_sections_abstracts( T, Ibs ).
 1283code_sections_abstracts( [_Ref,_Ttl,_Ath,Pmi|T], [Id-[]|Ibs] ) :-
 1284    atom_codes( Pat, Pmi ),
 1285    debug( pub_graph, 'Parsing abstract from line:~w', Pat ),
 1286    code_section_pub_med_id( Id, Pmi, _ ),
 1287    !,
 1288    debug( pub_graph, 'Parsing abstract for id:~w', Id ),
 1289    code_sections_abstracts( T, Ibs ).
 1290code_sections_abstracts( [_A,_B,_C,_D,F|T], [Id-Elns|Ibs] ) :-
 1291    atom_codes( Fat, F ),
 1292    debug( pub_graph, 'Parsing non-abstract from line:~w', Fat ),
 1293    code_section_pub_med_id( Id, F, _ ),
 1294    Elns = [],
 1295    code_sections_abstracts( T, Ibs ).
 1296    */
 1297
 1298code_section_lines( E, Elns ) :-
 1299    code_section_code_lines( EcLns, [], E, [] ),
 1300    maplist( atom_codes, Elns, EcLns ).
 1301
 1302code_section_code_lines( Lns, Acc ) -->
 1303    "\n",
 1304    !,
 1305    { Acc == [] -> Lns = TLns; reverse( Acc, Ln ), Lns = [Ln|TLns] },
 1306    code_section_code_lines( TLns, [] ).
 1307code_section_code_lines( Lns, Acc ) -->
 1308    [C],
 1309    !,
 1310    code_section_code_lines( Lns, [C|Acc] ).
 1311code_section_code_lines( Lns, Acc ) -->
 1312    { Acc == [] -> Lns = []; reverse(Acc,Ln), Lns = [Ln] }.
 1313
 1314copyright_line -->
 1315    "Copyright", !.
 1316copyright_line -->
 1317    "©", !.
 1318
 1319code_section_pub_med_id( Id ) -->
 1320    "PMID: ",
 1321    !,
 1322    code_section_in_pub_med_id( IdCs ),
 1323    {number_codes(Id,IdCs)}.
 1324code_section_pub_med_id( Id ) -->
 1325    [_C],
 1326    code_section_pub_med_id( Id ).
 1327
 1328code_section_in_pub_med_id( [C|Cs] ) -->
 1329    [C],
 1330    { 0'0 =< C, C =< 0'9},
 1331    !,
 1332    code_section_in_pub_med_id( Cs ).
 1333code_section_in_pub_med_id( [] ) --> [].
 1334
 1335pub_graph_summary_sort( Summ, By, Ord, Nums, Sorted ) :-
 1336     summary_items_have( Summ, By, Nums, Have, Havenots ),
 1337     sort( Have, Sorto ),
 1338     ( Ord == asc -> Sorto = Ordo; reverse(Sorto,Ordo) ),
 1339     kv_decompose_vs( Ordo, Disc ),
 1340     % disconnect_double_minus( Ordo, Disc ),
 1341     append( Disc, Havenots, Sorted ).
 1342
 1343disconnect_double_minus( [], [] ).
 1344disconnect_double_minus( [_K1-K-V|T], [K-V|M] ) :-
 1345     disconnect_double_minus( T, M ).
 1346
 1347summary_items_have( [], _By, _Nums, [], [] ).
 1348summary_items_have( [K-List|T], By, Nums, Haves, Havenots ) :-
 1349     ( memberchk(By-ByItem,List) ->
 1350          ( Nums == true ->
 1351               to_number( ByItem, ByItemNum ),
 1352               Haves = [ByItemNum-(K-List)|THaves],
 1353               Havenots = THavenots
 1354               ;
 1355               Haves = [ByItem-(K-List)|THaves],
 1356               Havenots = THavenots
 1357          )
 1358          ;
 1359          Haves = THaves,
 1360          Havenots = [K-List|THavenots]
 1361     ),
 1362     summary_items_have( T, By, Nums, THaves, THavenots ).

 pub_graph_cited_by_graph(+Ids, -Graph, +Opts)

Graph of all ancestors reaching Ids within Depth moves. The graph grows upwards from the roots (Ids) to find the papers that cite the growing bag of papers recursively.

Options is a single term, or list of the following terms:

cache(Type)

use cache of Type. Type == false or absent to turn caching off

location(Object)

if using cache, which location should be used

date(CoffDate)

if caching is used, at what date do cache expires. Default: 1 month ago.

depth(Depth)

maximum depth to chase

ext(Ext)

superseed the extension on Object.

flat(Flat)

Boolean value. If csv cited_by should be one per line or of the form Id1;Id2;

flat_input(InpFlat)

should the input cache be imported as flat (def. = Flat).

verbose(Verbose)

prints progress messages if true

Type is one of csv,prolog,sqlite and odbc. In the first 3 cases, Object should be a filename and for odbc it should be a DSN token. In the case of filenames, the default value for Object is formed as, <type>_<id1>{_<id2>}.<type_ext>. <type_ext> is either set to Ext or if this is missing it is deduced from Type. It can be set to '' if you want no extension added.

Graph is compatible with the graph representation of Prolog unweighted graphs. That is, all vertices should appear in a keysorted list as V-Ns pairs, where V is the vertex and Ns is the sorted list of all its neighbours. Ns is the empty list if V has no neighbours, although this should only be the case here, if one of the input Ids has no citing papers or for the nodes at the edge of Depth.

?-
     pub_graph_cited_by_graph( 12075665, G, cache(sqlite) ).

*/

 1407pub_graph_cited_by_graph( IdS, Graph, Args ) :-
 1408    % non_var_list( OptS, Opts ),
 1409     % pub_graph_graph_defaults( Defs ),
 1410     options_append( pub_graph_graph, Args, Opts ),
 1411     options( depth(Depth), Opts ),
 1412     ( Depth =:= 0 -> Ds = inf, De = 0; integer(Depth), Ds = bound, De = Depth ),
 1413     non_var_list( IdS, Ids ),
 1414     maplist( kv_elem_set(0), Ids, IDs ),
 1415    options( verbose(Pgs), Opts ),
 1416     opts_list_opens_cby_cache( Opts, Ids, COpts ), % maybe listed(Opts) instead of All ?
 1417     pub_graph_cited_by_graph_depth( IDs, [], Ds, De, Pgs, [], COpts, Orph, Graph1 ),
 1418     opts_list_closes_cby_cache( COpts ),
 1419     sort( Orph, Overts ),
 1420     keysort( Graph1, GraphOrd ),
 1421     add_vertices( GraphOrd, Overts, Graph ).
 1422
 1423opts_list_opens_cby_cache( Opts, Ids, Copts ) :-
 1424     ( (memberchk(cache(Type),Opts),\+Type==false) ->
 1425          ( memberchk(ext(Ext),Opts) -> true ; file_type_extension(Type,Ext) ),
 1426          ( memberchk(location(Loc),Opts) ->
 1427               ext_file( Loc, Ext, Obj )
 1428               ;
 1429               ( Ids = [A,B|_] -> IList = [A,B]; Ids = [A|_], IList = [A] ),
 1430               atomic_list_concat( [Type|IList], '_', FStem ),
 1431               file_name_extension( FStem, Ext, Obj )
 1432          ),
 1433          memberchk( date(Date), Opts ),
 1434          memberchk( update(Upd), Opts ),
 1435          pub_graph_cache_open( Type, Obj, cited_by, Handle, Opts ),
 1436          Copts = [cache(Type,Handle,Date,Upd)|Opts]
 1437          ;
 1438          Copts = Opts
 1439     ).
 1440
 1441opts_list_closes_cby_cache( COpts ) :-
 1442     memberchk( cache(Type,Handle,_,_) ,COpts ),
 1443     !,
 1444     pub_graph_cache_save( Type, Handle, cited_by/3, [] ).
 1445opts_list_closes_cby_cache( _ ).
 1446
 1447pub_graph_cited_by_treadmill_defaults( Defs ) :-
 1448          Defs      =  [ depth(5),
 1449                         ext(pl),
 1450                         file(graph_treadmilling),
 1451                         single_file(false)
 1452                       ].

 pub_graph_cited_by_treadmill(+Ids, -Graph, +Opts)

Use iterative increase of depth limit on pumed_cited_by_graph/3 with until to the overall Depth is reached. Results are saved to a cache file before proceeding to rerun the whole thing with an unit increase on the depth limit. Previous results will be fished out from the cache files.

Options is a single term or list of the following:

• file(File) file to use for storage
• single_file(Single) boolean value, def. is true. if false seperate (aggregating) files are created at each iteration
• depth(D) the overall depth limit

To be done

- use ODBC

*/

 1471pub_graph_cited_by_treadmill( Ids, Graph, Args ) :-
 1472     % pub_graph_treadmill_defaults( Defs ),
 1473     options_append( pub_graph_cited_by_treadmill, Args, Opts ),
 1474     options( file(File), Opts ),
 1475     options( single_file(Single), Opts ),
 1476     options( depth(D), Opts ),
 1477     options( ext(Ext), Opts ),
 1478     ext_file( File, Ext, PlFile ),
 1479     ( exists_file(PlFile) -> 
 1480          consult( pub_graph_cache:PlFile )
 1481          ;
 1482          true
 1483     ),
 1484     Oterm = topts(D,File,Single),
 1485     pub_graph_cited_by_treadmill_deepening( 1, Oterm, Ids, _, Graph ).
 1486
 1487
 1488pub_graph_cited_by_treadmill_deepening( Di, topts(Dlim,_,_), _Ids, Graph, Graph ) :-
 1489     Di > Dlim,
 1490     !, 
 1491     % write( overall_depth_limit_reached(Dlim) ), nl.
 1492     true.
 1493pub_graph_cited_by_treadmill_deepening( Di, Topts, Ids, _Current, Graph ) :-
 1494     Topts = topts(Dlim,File,Single),
 1495     Opts = [verbose(true),cache(prolog,_,date(2012,09,01),true),depth(Di),verbose(true)],
 1496     pub_graph_cited_by_graph( Ids, GraphI, Opts ),
 1497     % length( GraphI, LenGI ),
 1498     % write( population_at_depth(Di,LenGI) ), nl,
 1499     pub_graph_treadmill_file_name( Single, File, Di, Dlim, Fname ),
 1500     % write( onto_file(Fname) ), nl,
 1501     pub_graph_cache_save( prolog, Fname, cited_by/3, [] ),
 1502     Dstar is Di + 1,
 1503     pub_graph_cited_by_treadmill_deepening( Dstar, Topts, Ids, GraphI, Graph ).

 pub_graph_cache_open(+Type, +File, +Which, -Handle, Opts)

Open a pub_graph File of a given Type. A Handle is returned if appropriate. Currently csv,prolog,odbc and sqlite files are recognised. The former two are consulted into module pub_graph_cache, and Handle is therofore not used. For odbc/sqlite files the lookups and database access is via the odbc and prosqlite libraries respectively. Handle can be named to an alias of choise, otherwise a opaque atom is returned with which the db is accessed. Which, should either be cited_by or info .

Options is a term or list of terms from:

• ext(Ext) extension to try on the file. Use the empty atom if you do not want the library to use the default extension for the type of cache used.

Options are also passed to the underlying open operations for the type chosen. So for instance you can provide the username and passward for the odbc connection with user(U) and password(P).

*/

 1524pub_graph_cache_open( csv, FileIn, Which, Handle, Opts ) :-
 1525     memberchk( Which, [cited_by,info] ),
 1526     % atom_concat( pub_graph_cache_, Which, Module ),
 1527     pub_graph_cache_open_csv_file( FileIn, pub_graph_cache, Which, Handle, Opts ).
 1528pub_graph_cache_open( prolog, FileIn, Which, Handle, Opts ) :-
 1529     memberchk( Which, [cited_by,info] ),
 1530     % atom_concat( pub_graph_cache_, Which, Module ),
 1531     pub_graph_cache_open_pl_file( FileIn, pub_graph_cache, Handle, Opts ).
 1532pub_graph_cache_open( sqlite, FileIn, Which, Alias, Opts ) :-
 1533     memberchk( Which, [cited_by,info] ),
 1534     pub_graph_cache_open_sqlite( FileIn, Alias, Which,  Opts ).
 1535pub_graph_cache_open( odbc, Dsn, _Which, Alias, Opts ) :-
 1536     ( db_current_connection(Alias,Type) -> 
 1537          Fail = failed_to_open_odbc_on_existing_alias(Alias,Type,Dsn),
 1538          write( user_error, Fail ), nl( user_error ), fail
 1539          ;
 1540          Defs = [alias(Alias),user(pub_graph),password(pmed123)],
 1541          append( Opts, Defs, All ),
 1542          odbc_connect( Dsn, Alias, All )
 1543     ).
 1544     
 1545pub_graph_cache_open_csv_file( FileIn, Module, Pname, CbyF, Opts ) :-
 1546     append( Opts, [ext(csv)], All ),
 1547     options( ext(Ext), All ),
 1548     ext_file( FileIn, Ext, CbyF ),
 1549     (exists_file(CbyF) -> 
 1550               csv_read_file( CbyF, Rows, [functor(Pname)] ),
 1551               ( memberchk(flat_input(IFlat),Opts) -> true; memberchk(flat(IFlat),Opts) ),
 1552               ( IFlat==true -> 
 1553                         sort(Rows,Ord),
 1554                         ord_facts_aggregate_arg(Ord,3,Agr)
 1555                         ;
 1556                         maplist( csv_row_to_nest_row, Rows, Agr ) 
 1557               ),
 1558               maplist( assert_at(Module), Agr )
 1559               ;
 1560               true
 1561     ).
 1562pub_graph_cache_open_pl_file( FileIn, Module, CbyF, Opts ) :-
 1563     append( Opts, [ext(pl)], All ),
 1564     memberchk( ext(Ext), All ),
 1565     ext_file( FileIn, Ext, CbyF ),
 1566     (exists_file(CbyF) -> call( Module:consult(CbyF) ) ; true ).
 1567
 1568pub_graph_cache_open_sqlite( FileIn, Alias, Type,  Opts ) :-
 1569     append( Opts, [ext(sqlite)], All ),
 1570     memberchk( ext(Ext), All ),
 1571     ext_file( FileIn, Ext, SqliteF ),
 1572     ( exists_file(SqliteF) ->
 1573          true
 1574          ;
 1575          atomic_list_concat( ['Creating pub_graph',Type,'SQLite database at'], ' ', Create ),
 1576          write( Create:SqliteF ), nl,
 1577          sqlite_connect( SqliteF, HandleC, exists(false) ),
 1578          findall( _, 
 1579                         ( pub_graph_create_sqlite_type_statement( Type, Statement ),
 1580                           prosqlite:sqlite_query( HandleC, Statement, _Row )
 1581                         ),
 1582                                   _ ),
 1583
 1584          sqlite_disconnect( HandleC )  % fixme: make sure prosqlite closes with handles as well as with aliases.
 1585     ),
 1586     % atom_concat( pub_graph_cache_, Type, Mod ),
 1587     Mod = pub_graph_cache,
 1588     ( var(Alias) -> Alias = HandleD ; Ao = [alias(Alias)] ),
 1589     OptsD = [as_predicates(true),at_module(Mod)|Ao],
 1590     sqlite_connect( SqliteF, HandleD, OptsD ).
 1591
 1592pub_graph_create_sqlite_type_statement( cited_by, 'CREATE TABLE cited_by (pubmed_id bigint(20), ret_date date, citer bigint(20), Primary Key (pubmed_id,citer) );' ).
 1593pub_graph_create_sqlite_type_statement( info, 'CREATE TABLE info_date (pubmed_id bigint(20), rec_date date, Primary Key (pubmed_id) );' ).
 1594pub_graph_create_sqlite_type_statement( info, 'CREATE TABLE info (pubmed_id bigint(20), key_name tinytext, nth integer, key_value smalltext, Primary Key (pubmed_id,key_name,nth) );' ).

 pub_graph_cache_save(+Type, +FileinORHandle, What, Opts)

Close or save a cache to a file. Currently Types csv, `prolog', `odbc' and `sqlite' are recognised. In the case of prolog, the list of predicates What is dumped to the prolog file Filein. Likewise for `csv' but as data rows. The predicates are looked for in module `pub_graph_cache'. Once the preds are saved, their retracted from memory.

Opts a term or list of terms from:

flat(Flat)

should csv and prolog rows be compressed by third argument ? */

 1607pub_graph_cache_save( prolog, FileIn, WhatIf, Opts ) :-
 1608     pub_graph_cache_save( in_mem,  prolog, FileIn, WhatIf, Opts ).
 1609pub_graph_cache_save( csv, FileIn, WhatIf, Opts ) :-
 1610     pub_graph_cache_save_in_mem( csv, FileIn, WhatIf, Opts ).
 1611pub_graph_cache_save( sqlite, Handle, _, _Opts ) :-
 1612     sqlite_disconnect( Handle ).
 1613pub_graph_cache_save( odbc, Handle, _, _Opts ) :-
 1614     odbc_disconnect( Handle ).
 1615pub_graph_cache_save( db_facts, Handle, _, Opts ) :-
 1616     db_current_connection( Handle, Type ),
 1617     Type \== db_facts,
 1618     pub_graph_cache_save( Type, Handle, _, Opts ).
 1619
 1620pub_graph_cache_save_in_mem( Which, File, WhatIf, Opts ) :-
 1621     pg_en_list( WhatIf, What ),
 1622     /* ( file_name_extension(_,'',FileIn) ->
 1623          file_name_extension( FileIn, pl, File ) ; File = FileIn),
 1624     */
 1625     ( (memberchk(flat(true),Opts),Which=_Something/3) -> Flat = true; Flat = false ),
 1626     open( File, write, Out ),
 1627     pub_graph_cache_dump( Which, What, Out, Flat ),
 1628     close( Out ),
 1629     forall( member(W,What), (W=Pname/Arity,functor(G,Pname,Arity),retractall(pub_graph_cache:G)) ).
 1630
 1631pub_graph_cache_dump( Which, What, Out, Flat ) :-
 1632     member( Name/Arity, What ),
 1633     functor( Goal, Name, Arity ),
 1634     once(pl_cache_predicate_module(Name,Arity,Module) ),
 1635     forall( call(Module:Goal), record_in_mem_clause(Which,Flat,Out,Goal) ).
 1636
 1637record_in_mem_clause( Which, Flat, Out, Fact ) :-
 1638     ( Flat == true ->
 1639          arg( 3, Fact, Third ),
 1640          ( Third == [] -> 
 1641               arg( 1, Fact, First ), arg( 2, Fact, Second ),
 1642               functor( Fact, Name, 3 ),
 1643               functor( New, Name, 3 ),
 1644               arg( 1, New, First ), arg( 2, New, Second ), arg( 3, New, 0 )
 1645               ;
 1646               ( is_list(Third) ->
 1647                    arg( 1, Fact, First ), arg( 2, Fact, Second ),
 1648                    functor( Fact, Name, 3 ),
 1649                    functor( New, Name, 3 ),
 1650                    arg( 1, New, First ), arg( 2, New, Second ),
 1651                    forall( member(Elem,Third), (arg(3,New,Elem),record_fact(Which,Out,New)) )
 1652                    ;
 1653                    record_fact( Which, Out, Fact )
 1654               )
 1655          )
 1656          ;
 1657          record_fact( Which, Out, Fact )
 1658     ).
 1659     /* wouldn't be cool to have portray clause/2 write on csvs automatically ?
 1660        then we need open_csv to register the csv files 
 1661     */
 1662record_fact( prolog, Out, Fact ) :-
 1663     portray_clause( Out, Fact ).
 1664record_fact( csv, Out, Fact ) :-
 1665     % not-checked !
 1666     % see if we can get away with the []
 1667     mapargs( pl_term_csv_atom, Fact, Csv ),
 1668     csv_write_stream( Out, [Csv], [] ).
 1669
 1670pl_cache_predicate_module( cited_by, 3, pub_graph_cache ).
 1671pl_cache_predicate_module( info, 3, pub_graph_cache ).
 1672pl_cache_predicate_module( info_date, 2, pub_graph_cache ).
 1673
 1674% Section: non-interface predicates...
 1675
 1676pub_graph_cited_by_graph_depth( [], _Seen, _Ds, _De, _Pgs, Graph, _Opts, [], Graph ).
 1677pub_graph_cited_by_graph_depth( [Id-D|T], Seen, Ds, De, Pgs,  Acc, Opts, Orph, Graph ) :-
 1678     ( Pgs==true -> length(T,Len), 
 1679                    writeq(id(Id,Len)), write('.'), nl
 1680                    ; true ),
 1681     ( ord_memberchk(Id,Seen) -> 
 1682          Pairs = T,
 1683          NxSeen = Seen,
 1684          Nxt = Acc,
 1685          Orph = TOrph
 1686          ;
 1687          pub_graph_cited_by( Id, IdAnc, Opts ),
 1688          ( Pgs==true -> 
 1689               write( has(Id,IdAnc) ), write( '.' ), nl
 1690               ;
 1691               true
 1692          ),
 1693          D1 is D + 1,
 1694          ( depth_limit_reached(Ds,De,D1) -> 
 1695               Pairs = T,
 1696               NxSeen = Seen,
 1697               Nxt = Acc,
 1698               Orph = [Id|TOrph]
 1699               ;
 1700               ord_add_element( Seen, Id, NxSeen ),
 1701               maplist( kv_elem_set(D1), IdAnc, New ),
 1702               append( T, New, Pairs ),
 1703               sort( IdAnc, AncSort ),
 1704               Nxt = [Id-AncSort|Acc],
 1705               Orph = TOrph
 1706          )
 1707     ),
 1708     pub_graph_cited_by_graph_depth( Pairs, NxSeen, Ds, De, Pgs, Nxt, Opts, TOrph, Graph ).
 1709
 1710depth_limit_reached( bound, Lim, Val ) :-
 1711     Lim < Val.
 1712
 1713kv_elem_set( Val, Key, Key-Val ).
 1714          
 1715summary_info( Tmp, Id, WhichIn, Results, OptS ) :-
 1716    pub_graph_id( Id, IdType ),
 1717    non_var_list( OptS, Opts ),
 1718    ( WhichIn == all -> default_names(IdType,Which) ;  pg_en_list(WhichIn,Which) ),
 1719    summary_info( IdType, Tmp, Id, Which, Results, Opts ).
 1720
 1721summary_info( ncbi, Tmp, Id, Which, Results, Opts ) :-
 1722     url_eutils( Eutils ),
 1723     ( memberchk(retmax(RMax),Opts) -> true; RMax = 100 ),
 1724     atomic_list_concat( ['esummary.fcgi?report=xml&mode=text&tool=wget&retmax=',RMax,'&db=pubmed&id='], Query ),
 1725     atomic_list_concat( [Eutils,Query,Id], Url ),
 1726     get_url_in_file( Url, false, Tmp ), % fixme
 1727     load_xml_file( Tmp, Xml ),
 1728     Elem = element(_,_,[Entry]),
 1729     findall( Name-Info, ( 
 1730                           member( Name, Which ),
 1731                           findall( Entry,
 1732                             search_element_in_list(Xml, 'Item', ['Name'=Name], Elem ),
 1733                                   PInfo ),
 1734                           ( PInfo = [Info] -> true; PInfo = Info )
 1735                         ), Results ),
 1736     ( memberchk(tmp_keep(true),Opts) -> true; delete_file(Tmp) ).
 1737summary_info( semscholar, _Tmp, Id, Which, Results, _Opts ) :-
 1738    semscholar_id_json( Id, Json ),
 1739    findall( Name-Info, ( member(Name,Which),
 1740                          member(Name=InfoPrv,Json),
 1741                          json_value(InfoPrv,Info)
 1742                        ),
 1743                            Results
 1744           ).
 1745
 1746pub_graph_date_cached( prolog, Explicit, Default, Cutoff, Id, Return ) :-
 1747     pub_graph_date_cached( in_mem, Explicit, Default, Cutoff, Id, Return ).
 1748pub_graph_date_cached( csv, Explicit, Default, Cutoff, Id, Return ) :-
 1749     pub_graph_date_cached( in_mem, Explicit, Default, Cutoff, Id, Return ).
 1750pub_graph_date_cached( in_mem, _Handle, Pname, Cutoff, Id, Return ) :-
 1751     % ( var(Explicit) -> Explicit=Default; true ),
 1752     G =.. [Pname,Id,Date,Return],
 1753     once(pl_cache_predicate_module(Pname,3,Module) ),
 1754     call( Module:G ),
 1755     Cutoff @=< Date.
 1756pub_graph_date_cached( sqlite, Handle, Pname, Cutoff, Id, Return ) :-
 1757     pub_graph_date_cached( db_facts, Handle, Pname, Cutoff, Id, Return ).
 1758pub_graph_date_cached( odbc, Handle, Pname, Cutoff, Id, Return ) :-
 1759     pub_graph_date_cached( db_facts, Handle, Pname, Cutoff, Id, Return ).
 1760pub_graph_date_cached( db_facts, Handle, Pname, Cutoff, Id, Return ) :-
 1761     G =.. [Pname,Id,SQLDate,R],
 1762     findall( R, db_holds(Handle,G), PrvReturn ),
 1763     PrvReturn \== [],
 1764     once( db_holds(Handle,G) ),
 1765     ( atom(SQLDate) -> 
 1766          db_date_sql_atom( Date, SQLDate )
 1767          ;
 1768          % odbc translates this, so should sqlite
 1769          Date = SQLDate
 1770     ),
 1771
 1772     ( PrvReturn = [0] -> Return = [] ; Return = PrvReturn ),
 1773     Cutoff @=< Date.
 1774
 1775/* commenting this out probably makes as_predicates(true) obsolete
 1776     G =.. [PredName,Id,SQLDate,R],
 1777     once(pl_cache_predicate_module(PredName,3,Module) ),
 1778     findall( R, call(Module:G), PrvReturn ),
 1779     PrvReturn \== [],
 1780     once( Module:G ), 
 1781     date_sql_atom( Date, SQLDate ),
 1782     ( PrvReturn = [0] -> Return = [] ; Return = PrvReturn ),
 1783     Cutoff @=< Date.
 1784     */
 1785
 1786pub_graph_update_cache( csv, Explicit, Default, Id, Return ) :-
 1787     pub_graph_update_cache( in_mem, Explicit, Default, Id, Return ).
 1788pub_graph_update_cache( prolog, Explicit, Default, Id, Return ) :-
 1789     pubned_update_cache( in_mem, Explicit, Default, Id, Return ).
 1790pub_graph_update_cache( in_mem, _Handle, Pname, Id, Return ) :-
 1791     % ( var(Explicit) -> Explicit=Default; true ),
 1792     date(Date),
 1793     R =.. [Pname,Id,_,_],
 1794     retractall( pub_graph_cache:R ),
 1795     G =.. [Pname,Id,Date,Return],
 1796     assert( pub_graph_cache:G ).
 1797
 1798pub_graph_update_cache( sqlite, Handle, PredName, Id, PrvReturn ) :-
 1799     pub_graph_update_cache( db_facts, Handle, PredName, Id, PrvReturn ).
 1800pub_graph_update_cache( odbc, Handle, PredName, Id, PrvReturn ) :-
 1801     pub_graph_update_cache( db_facts, Handle, PredName, Id, PrvReturn ).
 1802pub_graph_update_cache( db_facts, Handle, PredName, Id, PrvReturn ) :-
 1803     % ( var(Explicit) -> Explicit=Default; true ),
 1804     date(Date),
 1805     R =.. [PredName,Id,_,_],
 1806     db_retractall( Handle, R, _ ),
 1807     db_date_sql_atom( Date, SqlDate ),
 1808     G =.. [PredName,Id,SqlDate,Ret],
 1809     ( PrvReturn = [] -> Return = [0]; Return = PrvReturn ),
 1810     findall( Ret, (member(Ret,Return),db_assert(Handle,G,_)), _ ).
 1811
 1812pub_graph_cited_by_parse_file(Tmp, Ids) :-
 1813     load_xml_file( Tmp, Xml ),
 1814     once( search_element_in_list( Xml, 'LinkSetDb', [], element(_,_,LXml) ) ),
 1815     findall( CId, 
 1816               ( search_element_in_list(LXml,'Id',[],element(_,_,[CIdA])),
 1817                 atom_codes(CIdA,CIdCs), number_codes(CId,CIdCs)
 1818               ),
 1819               Ids ).
 1820
 1821% Section: auxiliaries

 pub_graph_search_period_opts(+Pfx, -Period, +Opts)

Create a Period atom DateKey=DateValue separated by '&' for each of the DateKey(DateValue) terms in Opts for which pub_graph_elink_date_option(DateKey) holds.

 ?- pub_graph_search_period_opts( '', Period, [reldate(60)] ).
 Period = 'reldate=60'.

 ?- pub_graph_search_period_opts( '', Period, [mindate(2014),mindate(2015)] ).
 Period = 'mindate=2014&mindate=2015'.

 ?- pub_graph_search_period_opts( '', Period, [mindate(2014),maxdate(2015)] ).
 Period = 'mindate=2014&maxdate=2015'.

 

 1842pub_graph_search_period_opts( Pfx, Period, Opts ) :-
 1843    select( Opt, Opts, Rpts ),
 1844    functor( Opt, Oname, 1 ),
 1845    pub_graph_elink_date_option( Oname ),
 1846    arg( 1, Opt, Arg ),
 1847    !,
 1848    atomic_list_concat( [Oname,Arg], '=', Atom ),
 1849    atomic_list_concat( [Pfx,Atom], '&', Rfx ),
 1850    pub_graph_search_period_opts( Rfx, Period, Rpts ).
 1851pub_graph_search_period_opts( Period, Period, _Opts ).
 1852
 1853pub_graph_elink_date_option( reldate ).
 1854pub_graph_elink_date_option( mindate ).
 1855pub_graph_elink_date_option( maxdate ).

 search_term_to_query(+Sterm, +Gap, +Qv, -Query)

Convert a pubmed term to an atomic query that can be passed through http.

Gap is an integer, used for fields that take approximate search (0 is strictest for allowing 0 interving words) Qv is the quote_value(Qv) option value.

 1865search_term_to_query( (A,B), Gap, Qv, Query ) :-
 1866     !,
 1867     search_term_to_query( A, Gap, Qv, Aq ),
 1868     search_term_to_query( B, Gap, Qv, Bq ),
 1869     atomic_list_concat( [Aq,'+AND+',Bq], Query ).
 1870search_term_to_query( (A;B), Gap, Qv, Query ) :-
 1871     !,
 1872     search_term_to_query( A, Gap, Qv, Aq ),
 1873     search_term_to_query( B, Gap, Qv, Bq ),
 1874     atomic_list_concat( [Aq,'OR',Bq], '+', Query ).
 1875search_term_to_query( (A=B), Gap, Qv, Query ) :-
 1876     !,
 1877     maplist( quote_curl_atom, [A,B], [Aq,Bq] ),
 1878     search_term_proximity_field( A, Gap, Pxf ),
 1879     ( Qv == false ->   % true is defaulty
 1880          atomic_list_concat( [Bq,'[',Aq,Pxf,']'], Query )
 1881          ;
 1882          atomic_list_concat( ['%22',Bq,'%22','[',Aq,Pxf,']'], Query )
 1883     ).
 1884search_term_to_query( C, _Gap, _Qv, Query ) :-
 1885     pg_en_list( C, Clist ),
 1886     maplist( quote_curl_atom, Clist, Qlist ),
 1887     atomic_list_concat( Qlist, '+', Query ).
 1888
 1889search_term_proximity_field( A, Gap, Pxf ) :-
 1890     search_term_proximity_field( A ),
 1891     !,
 1892     atomic_list_concat( [':~',Gap], Pxf ).
 1893search_term_proximity_field( _A, _Gap, '' ).
 1894
 1895search_term_proximity_field('Affiliation').
 1896search_term_proximity_field(affiliation).
 1897search_term_proximity_field('Title').
 1898search_term_proximity_field(title).
 1899search_term_proximity_field('Title/Abstract').
 1900search_term_proximity_field('title/abstract').
 1901% abbreviations
 1902search_term_proximity_field(ti).   % Title
 1903search_term_proximity_field(tiab). % Title/Abstract
 1904search_term_proximity_field(ad).   % affiliation ? 
 1905
 1906% very basic. for now we are just translating space to %20
 1907% we should use some SWI http internals here
 1908%
 1909quote_curl_atom( In, Out ) :-
 1910     atom_codes( In, InCs ),
 1911     maplist( quote_curl_code, InCs, NestOutCs ),
 1912     flatten( NestOutCs, OutCs ),
 1913     atom_codes( Out, OutCs ).
 1914
 1915quote_curl_code( 0' , [0'%,0'2,0'0] ) :- !.
 1916quote_curl_code( 0'", [0'%,0'2,0'2] ) :- !.
 1917% quote_curl_code( 0' , [0'+] ) :- !.
 1918quote_curl_code( Code, Code ).