JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API

diff --git a/resources/fts/uniprot_data_columns-2022.txt b/resources/fts/uniprot_data_columns-2022.txt
new file mode 100644 (file)
index 0000000..7e51cd8
--- /dev/null
+++ b/resources/fts/uniprot_data_columns-2022.txt
@@ -0,0 +1,356 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+uniprot_data_columns
+#
+_group.id
+_group.name
+_group.sort_order
+g3;Names & Taxonomy;1
+g6;Miscellaneous;6
+g7;Sequences;7
+g8;Function;8
+g9;Interaction;9
+g10;Expression;10
+g11;Gene Ontology (GO);11
+g12;Pathology & Biotech;12
+g13;Subcellular location;13
+g14;PTM / Processing;14
+g15;Structure;15
+g16;Publications;16
+g17;Date of;17
+g18;Family & Domains;18
+g19;2D Gel Databases;1000
+g20;3D Structure Databases;1000
+g21;Chemistry Databases;1000
+g22;Enzyme And Pathway Databases;1000
+g23;Family And Domain Databases;1000
+g24;Gene Expression Databases;1000
+g25;Genetic Variation Databases;1000
+g26;Genome Annotation Databases;1000
+g27;Miscellaneous Databases;1000
+g28;Organism-Specific Databases;1000
+g29;Phylogenomic Databases;1000
+g30;Protein Family/Group Databases;1000
+g31;Protein-Protein Interaction Databases;1000
+g32;Proteomic Databases;1000
+g33;Protocols And Materials Databases;1000
+g34;Ptm Databases;1000
+g35;Sequence Databases;1000
+#
+_data_column.primary_key;id
+_data_column.default_response_page_size;500
+#
+_data_column.name
+_data_column.code|_data_column.alt_code (optional: used for specifying search code when different from original code)
+_data_column.group_id
+_data_column.data_type
+_data_column.min_col_width
+_data_column.max_col_width
+_data_column.preferred_col_width
+_data_column.is_shown_by_default
+_data_column.is_searchable
+ALL;Search All;String;g7;50;1000;95;false;true
+Entry;accession;String;g3;80;150;85;true;true
+Entry name;id|accession_id;String;g3;100;150;105;true;true
+Gene names;gene_names|gene;String;g3;100;1000;145;true;true
+Gene names (primary);gene_primary;String;g3;50;1000;95;false;false
+Gene names (synonym);gene_synonym;String;g3;50;1000;95;false;false
+Gene names (ordered locus);gene_oln;String;g3;50;1000;95;false;false
+Gene names (ORF);gene_orf;String;g3;50;1000;95;false;false
+Organism;organism_name;String;g3;100;1000;200;true;true
+Organism ID;organism_id;int;g3;60;100;80;false;true
+Protein names;protein_name;String;g3;300;1500;500;true;true
+Proteomes;xref_proteomes;String;g3;50;1000;95;false;false
+Taxonomic lineage;lineage|taxonomy_name;String;g3;50;400;95;false;false
+Taxonomic lineage (IDs);lineage_ids|taxonomy_id;String;g3;50;400;95;false;false
+Virus hosts;virus_hosts|virus_host;String;g3;50;1000;95;false;true
+Annotation;annotation_score;String;g6;50;1000;95;false;false
+Caution;cc_caution;String;g6;50;1000;95;false;false
+Comment Count;comment_count;String;g6;50;1000;95;false;false
+Features;feature_count;String;g6;50;1000;95;false;false
+Keyword ID;keywordid;String;g6;50;1000;95;false;false
+Keywords;keyword;String;g6;50;1000;95;false;true
+Miscellaneous [CC];cc_miscellaneous;String;g6;50;1000;95;false;false
+Protein existence;protein_existence|existence;String;g6;50;1000;95;false;true
+Reviewed;reviewed;String;g6;50;100;95;true;true
+Tools;tools;String;g6;50;1000;95;false;false
+UniParc;uniparc_id;String;g6;50;1000;95;false;false
+Alternative products;cc_alternative_products;String;g7;50;1000;95;false;false
+Alternative sequence;ft_var_seq;String;g7;50;1000;95;false;false
+Erroneous gene model prediction;error_gmodel_pred;String;g7;50;1000;95;false;false
+Fragment;fragment;String;g7;50;1000;95;false;false
+Gene encoded by;organelle;String;g7;50;1000;95;false;false
+Length;length;int|T|0;g7;50;100;65;true;true
+Mass;mass;int|T|0;g7;50;100;80;false;true
+Mass spectrometry;cc_mass_spectrometry;String;g7;50;1000;95;false;false
+Natural variant;ft_variant;String;g7;50;1000;95;false;false
+Non-adjacent residues;ft_non_cons;String;g7;50;1000;95;false;false
+Non-standard residue;ft_non_std;String;g7;50;1000;95;false;false
+Non-terminal residue;ft_non_ter;String;g7;50;1000;95;false;false
+Polymorphism;cc_polymorphism;String;g7;50;1000;95;false;false
+RNA editing;cc_rna_editing;String;g7;50;1000;95;false;false
+Sequence;sequence;String;g7;50;1000;95;false;false
+Sequence caution;cc_sequence_caution;String;g7;50;1000;95;false;false
+Sequence conflict;ft_conflict;String;g7;50;1000;95;false;false
+Sequence uncertainty;ft_unsure;String;g7;50;1000;95;false;false
+Sequence version;sequence_version;String;g7;50;1000;95;false;false
+Absorption;absorption;String;g8;50;1000;95;false;false
+Active site;ft_act_site;String;g8;50;1000;95;false;false
+Activity regulation;cc_activity_regulation;String;g8;50;1000;95;false;false
+Binding site;ft_binding;String;g8;50;1000;95;false;false
+Calcium binding;ft_ca_bind;String;g8;50;1000;95;false;false
+Catalytic activity;cc_catalytic_activity;String;g8;50;1000;95;false;false
+Cofactor;cc_cofactor;String;g8;50;1000;95;false;false
+DNA binding;ft_dna_bind;String;g8;50;1000;95;false;false
+EC number;ec;String;g8;50;1000;95;false;true
+Function [CC];cc_function;String;g8;50;1000;95;false;false
+Kinetics;kinetics;String;g8;50;1000;95;false;false
+Metal binding;ft_metal;String;g8;50;1000;95;false;false
+Nucleotide binding;ft_np_bind;String;g8;50;1000;95;false;false
+Pathway;cc_pathway;String;g8;50;1000;95;false;false
+pH dependence;ph_dependence;String;g8;50;1000;95;false;false
+Redox potential;redox_potential;String;g8;50;1000;95;false;false
+Rhea ID;rhea;String;g8;50;1000;95;false;false
+Site;ft_site;String;g8;50;1000;95;false;false
+Temperature dependence;temp_dependence;String;g8;50;1000;95;false;false
+Interacts with;cc_interaction;String;g9;50;1000;95;false;false
+Subunit structure[CC];cc_subunit;String;g9;50;1000;95;false;false
+Developmental stage;cc_developmental_stage;String;g10;50;1000;95;false;false
+Induction;cc_induction;String;g10;50;1000;95;false;false
+Tissue specificity;cc_tissue_specificity;String;g10;50;1000;95;false;false
+Gene ontology (biological process);go_p;String;g11;50;1000;95;false;false
+Gene ontology (cellular component);go_c;String;g11;50;1000;95;false;false
+Gene ontology (GO);go;String;g11;50;1000;95;false;true
+Gene ontology (molecular function);go_f;String;g11;50;1000;95;false;false
+Gene ontology IDs;go_id;String;g11;50;1000;95;false;false
+Allergenic properties;cc_allergen;String;g12;50;1000;95;false;false
+Biotechnological use;cc_biotechnology;String;g12;50;1000;95;false;false
+Disruption phenotype;cc_disruption_phenotype;String;g12;50;1000;95;false;false
+Involvement in disease;cc_disease;String;g12;50;1000;95;false;false
+Mutagenesis;ft_mutagen;String;g12;50;1000;95;false;false
+Pharmaceutical use;cc_pharmaceutical;String;g12;50;1000;95;false;false
+Toxic dose;cc_toxic_dose;String;g12;50;1000;95;false;false
+Intramembrane;ft_intramem;String;g13;50;1000;95;false;false
+Subcellular location[CC];cc_subcellular_location;String;g13;50;1000;95;false;false
+Topological domain;ft_topo_dom;String;g13;50;1000;95;false;false
+Transmembrane;ft_transmem;String;g13;50;1000;95;false;false
+Chain;ft_chain;String;g14;50;1000;95;false;false
+Cross-link;ft_crosslnk;String;g14;50;1000;95;false;false
+Disulfide bond;ft_disulfid;String;g14;50;1000;95;false;false
+Glycosylation;ft_carbohyd;String;g14;50;1000;95;false;false
+Initiator methionine;ft_init_met;String;g14;50;1000;95;false;false
+Lipidation;ft_lipid;String;g14;50;1000;95;false;false
+Modified residue;ft_mod_res;String;g14;50;1000;95;false;false
+Peptide;ft_peptide;String;g14;50;1000;95;false;false
+Post-translational modification;cc_ptm;String;g14;50;1000;95;false;false
+Propeptide;ft_propep;String;g14;50;1000;95;false;false
+Signal peptide;ft_signal;String;g14;50;1000;95;false;false
+Transit peptide;ft_transit;String;g14;50;1000;95;false;false
+3D;structure_3d;String;g15;50;1000;95;false;false
+Beta strand;ft_strand;String;g15;50;1000;95;false;false
+Helix;ft_helix;String;g15;50;1000;95;false;false
+Turn;ft_turn;String;g15;50;1000;95;false;false
+PubMed ID;lit_pubmed_id;String;g16;50;1000;95;false;false
+Date of creation;date_created;String;g17;80;150;100;false;true
+Date of last modification;date_modified;String;g17;80;150;100;false;true
+Date of last sequence modification;date_sequence_modified;String;g17;80;150;100;false;true
+Entry version;version;int;g17;80;100;80;false;false
+Coiled coil;ft_coiled;String;g18;50;1000;95;false;false
+Compositional bias;ft_compbias;String;g18;50;1000;95;false;false
+Domain[CC];cc_domain;String;g18;80;1000;95;false;false
+Domain[FT];ft_domain;String;g18;50;1000;95;false;false
+Motif;ft_motif;String;g18;50;1000;95;false;false
+Protein families;protein_families|family;String;g18;50;1000;95;false;true
+Region;ft_region;String;g18;50;1000;95;false;false
+Repeat;ft_repeat;String;g18;50;1000;95;false;false
+Zinc finger;ft_zn_fing;String;g18;50;1000;95;false;false
+COMPLUYEAST-2DPAGE;xref_compluyeast-2dpage;String;g19;50;1000;95;false;false
+DOSAC-COBS-2DPAGE;xref_dosac-cobs-2dpage;String;g19;50;1000;95;false;false
+OGP;xref_ogp;String;g19;50;1000;95;false;false
+REPRODUCTION-2DPAGE;xref_reproduction-2dpage;String;g19;50;1000;95;false;false
+SWISS-2DPAGE;xref_swiss-2dpage;String;g19;50;1000;95;false;false
+UCD-2DPAGE;xref_ucd-2dpage;String;g19;50;1000;95;false;false
+World-2DPAGE;xref_world-2dpage;String;g19;50;1000;95;false;false
+AlphaFoldDB;xref_alphafolddb;String;g20;50;1000;95;false;false
+BMRB;xref_bmrb;String;g20;50;1000;95;false;false
+PCDDB;xref_pcddb;String;g20;50;1000;95;false;false
+PDB;xref_pdb;String;g20;50;1000;95;false;false
+PDBsum;xref_pdbsum;String;g20;50;1000;95;false;false
+SASBDB;xref_sasbdb;String;g20;50;1000;95;false;false
+SMR;xref_smr;String;g20;50;1000;95;false;false
+BindingDB;xref_bindingdb;String;g21;50;1000;95;false;false
+ChEMBL;xref_chembl;String;g21;50;1000;95;false;false
+DrugBank;xref_drugbank;String;g21;50;1000;95;false;false
+DrugCentral;xref_drugcentral;String;g21;50;1000;95;false;false
+GuidetoPHARMACOLOGY;xref_guidetopharmacology;String;g21;50;1000;95;false;false
+SwissLipids;xref_swisslipids;String;g21;50;1000;95;false;false
+BRENDA;xref_brenda;String;g22;50;1000;95;false;false
+BioCyc;xref_biocyc;String;g22;50;1000;95;false;false
+PathwayCommons;xref_pathwaycommons;String;g22;50;1000;95;false;false
+PlantReactome;xref_plantreactome;String;g22;50;1000;95;false;false
+Reactome;xref_reactome;String;g22;50;1000;95;false;false
+SABIO-RK;xref_sabio-rk;String;g22;50;1000;95;false;false
+SIGNOR;xref_signor;String;g22;50;1000;95;false;false
+SignaLink;xref_signalink;String;g22;50;1000;95;false;false
+UniPathway;xref_unipathway;String;g22;50;1000;95;false;false
+CDD;xref_cdd;String;g23;50;1000;95;false;false
+DisProt;xref_disprot;String;g23;50;1000;95;false;false
+Gene3D;xref_gene3d;String;g23;50;1000;95;false;false
+HAMAP;xref_hamap;String;g23;50;1000;95;false;false
+IDEAL;xref_ideal;String;g23;50;1000;95;false;false
+InterPro;xref_interpro;String;g23;50;1000;95;false;false
+PANTHER;xref_panther;String;g23;50;1000;95;false;false
+PIRSF;xref_pirsf;String;g23;50;1000;95;false;false
+PRINTS;xref_prints;String;g23;50;1000;95;false;false
+PROSITE;xref_prosite;String;g23;50;1000;95;false;false
+Pfam;xref_pfam;String;g23;50;1000;95;false;false
+ProDom;xref_prodom;String;g23;50;1000;95;false;false
+SFLD;xref_sfld;String;g23;50;1000;95;false;false
+SMART;xref_smart;String;g23;50;1000;95;false;false
+SUPFAM;xref_supfam;String;g23;50;1000;95;false;false
+TIGRFAMs;xref_tigrfams;String;g23;50;1000;95;false;false
+Bgee;xref_bgee;String;g24;50;1000;95;false;false
+CleanEx;xref_cleanex;String;g24;50;1000;95;false;false
+CollecTF;xref_collectf;String;g24;50;1000;95;false;false
+ExpressionAtlas;xref_expressionatlas;String;g24;50;1000;95;false;false
+Genevisible;xref_genevisible;String;g24;50;1000;95;false;false
+BioMuta;xref_biomuta;String;g25;50;1000;95;false;false
+DMDM;xref_dmdm;String;g25;50;1000;95;false;false
+dbSNP;xref_dbsnp;String;g25;50;1000;95;false;false
+Ensembl;xref_ensembl;String;g26;50;1000;95;false;false
+EnsemblBacteria;xref_ensemblbacteria;String;g26;50;1000;95;false;false
+EnsemblFungi;xref_ensemblfungi;String;g26;50;1000;95;false;false
+EnsemblMetazoa;xref_ensemblmetazoa;String;g26;50;1000;95;false;false
+EnsemblPlants;xref_ensemblplants;String;g26;50;1000;95;false;false
+EnsemblProtists;xref_ensemblprotists;String;g26;50;1000;95;false;false
+GeneID;xref_geneid;String;g26;50;1000;95;false;false
+Gramene;xref_gramene;String;g26;50;1000;95;false;false
+KEGG;xref_kegg;String;g26;50;1000;95;false;false
+MANE-Select;xref_mane-select;String;g26;50;1000;95;false;false
+PATRIC;xref_patric;String;g26;50;1000;95;false;false
+UCSC;xref_ucsc;String;g26;50;1000;95;false;false
+VectorBase;xref_vectorbase;String;g26;50;1000;95;false;false
+WBParaSite;xref_wbparasite;String;g26;50;1000;95;false;false
+WBParaSiteTranscriptProtein;xref_wbparasitetranscriptprotein;String;g26;50;1000;95;false;false
+BioGRID-ORCS;xref_biogrid-orcs;String;g27;50;1000;95;false;false
+ChiTaRS;xref_chitars;String;g27;50;1000;95;false;false
+EvolutionaryTrace;xref_evolutionarytrace;String;g27;50;1000;95;false;false
+GeneWiki;xref_genewiki;String;g27;50;1000;95;false;false
+GenomeRNAi;xref_genomernai;String;g27;50;1000;95;false;false
+PHI-base;xref_phi-base;String;g27;50;1000;95;false;false
+PRO;xref_pro;String;g27;50;1000;95;false;false
+Pharos;xref_pharos;String;g27;50;1000;95;false;false
+RNAct;xref_rnact;String;g27;50;1000;95;false;false
+ArachnoServer;xref_arachnoserver;String;g28;50;1000;95;false;false
+Araport;xref_araport;String;g28;50;1000;95;false;false
+CGD;xref_cgd;String;g28;50;1000;95;false;false
+CTD;xref_ctd;String;g28;50;1000;95;false;false
+ConoServer;xref_conoserver;String;g28;50;1000;95;false;false
+DisGeNET;xref_disgenet;String;g28;50;1000;95;false;false
+EchoBASE;xref_echobase;String;g28;50;1000;95;false;false
+FlyBase;xref_flybase;String;g28;50;1000;95;false;false
+GeneCards;xref_genecards;String;g28;50;1000;95;false;false
+GeneReviews;xref_genereviews;String;g28;50;1000;95;false;false
+HGNC;xref_hgnc;String;g28;50;1000;95;false;false
+HPA;xref_hpa;String;g28;50;1000;95;false;false
+LegioList;xref_legiolist;String;g28;50;1000;95;false;false
+Leproma;xref_leproma;String;g28;50;1000;95;false;false
+MGI;xref_mgi;String;g28;50;1000;95;false;false
+MIM;xref_mim;String;g28;50;1000;95;false;false
+MaizeGDB;xref_maizegdb;String;g28;50;1000;95;false;false
+MalaCards;xref_malacards;String;g28;50;1000;95;false;false
+NIAGADS;xref_niagads;String;g28;50;1000;95;false;false
+OpenTargets;xref_opentargets;String;g28;50;1000;95;false;false
+Orphanet;xref_orphanet;String;g28;50;1000;95;false;false
+PharmGKB;xref_pharmgkb;String;g28;50;1000;95;false;false
+PomBase;xref_pombase;String;g28;50;1000;95;false;false
+PseudoCAP;xref_pseudocap;String;g28;50;1000;95;false;false
+RGD;xref_rgd;String;g28;50;1000;95;false;false
+SGD;xref_sgd;String;g28;50;1000;95;false;false
+TAIR;xref_tair;String;g28;50;1000;95;false;false
+TubercuList;xref_tuberculist;String;g28;50;1000;95;false;false
+VEuPathDB;xref_veupathdb;String;g28;50;1000;95;false;false
+VGNC;xref_vgnc;String;g28;50;1000;95;false;false
+WormBase;xref_wormbase;String;g28;50;1000;95;false;false
+Xenbase;xref_xenbase;String;g28;50;1000;95;false;false
+ZFIN;xref_zfin;String;g28;50;1000;95;false;false
+dictyBase;xref_dictybase;String;g28;50;1000;95;false;false
+euHCVdb;xref_euhcvdb;String;g28;50;1000;95;false;false
+neXtProt;xref_nextprot;String;g28;50;1000;95;false;false
+GeneTree;xref_genetree;String;g29;50;1000;95;false;false
+HOGENOM;xref_hogenom;String;g29;50;1000;95;false;false
+InParanoid;xref_inparanoid;String;g29;50;1000;95;false;false
+KO;xref_ko;String;g29;50;1000;95;false;false
+OMA;xref_oma;String;g29;50;1000;95;false;false
+OrthoDB;xref_orthodb;String;g29;50;1000;95;false;false
+PhylomeDB;xref_phylomedb;String;g29;50;1000;95;false;false
+TreeFam;xref_treefam;String;g29;50;1000;95;false;false
+eggNOG;xref_eggnog;String;g29;50;1000;95;false;false
+Allergome;xref_allergome;String;g30;50;1000;95;false;false
+CAZy;xref_cazy;String;g30;50;1000;95;false;false
+CLAE;xref_clae;String;g30;50;1000;95;false;false
+ESTHER;xref_esther;String;g30;50;1000;95;false;false
+IMGT_GENE-DB;xref_imgt_gene-db;String;g30;50;1000;95;false;false
+MEROPS;xref_merops;String;g30;50;1000;95;false;false
+MoonDB;xref_moondb;String;g30;50;1000;95;false;false
+MoonProt;xref_moonprot;String;g30;50;1000;95;false;false
+PeroxiBase;xref_peroxibase;String;g30;50;1000;95;false;false
+REBASE;xref_rebase;String;g30;50;1000;95;false;false
+TCDB;xref_tcdb;String;g30;50;1000;95;false;false
+UniLectin;xref_unilectin;String;g30;50;1000;95;false;false
+BioGRID;xref_biogrid;String;g31;50;1000;95;false;false
+CORUM;xref_corum;String;g31;50;1000;95;false;false
+ComplexPortal;xref_complexportal;String;g31;50;1000;95;false;false
+DIP;xref_dip;String;g31;50;1000;95;false;false
+ELM;xref_elm;String;g31;50;1000;95;false;false
+IntAct;xref_intact;String;g31;50;1000;95;false;false
+MINT;xref_mint;String;g31;50;1000;95;false;false
+STRING;xref_string;String;g31;50;1000;95;false;false
+CPTAC;xref_cptac;String;g32;50;1000;95;false;false
+EPD;xref_epd;String;g32;50;1000;95;false;false
+MassIVE;xref_massive;String;g32;50;1000;95;false;false
+MaxQB;xref_maxqb;String;g32;50;1000;95;false;false
+PRIDE;xref_pride;String;g32;50;1000;95;false;false
+PaxDb;xref_paxdb;String;g32;50;1000;95;false;false
+PeptideAtlas;xref_peptideatlas;String;g32;50;1000;95;false;false
+ProMEX;xref_promex;String;g32;50;1000;95;false;false
+ProteomicsDB;xref_proteomicsdb;String;g32;50;1000;95;false;false
+TopDownProteomics;xref_topdownproteomics;String;g32;50;1000;95;false;false
+jPOST;xref_jpost;String;g32;50;1000;95;false;false
+ABCD;xref_abcd;String;g33;50;1000;95;false;false
+Antibodypedia;xref_antibodypedia;String;g33;50;1000;95;false;false
+CPTC;xref_cptc;String;g33;50;1000;95;false;false
+DNASU;xref_dnasu;String;g33;50;1000;95;false;false
+CarbonylDB;xref_carbonyldb;String;g34;50;1000;95;false;false
+DEPOD;xref_depod;String;g34;50;1000;95;false;false
+GlyConnect;xref_glyconnect;String;g34;50;1000;95;false;false
+GlyGen;xref_glygen;String;g34;50;1000;95;false;false
+MetOSite;xref_metosite;String;g34;50;1000;95;false;false
+PhosphoSitePlus;xref_phosphositeplus;String;g34;50;1000;95;false;false
+SwissPalm;xref_swisspalm;String;g34;50;1000;95;false;false
+UniCarbKB;xref_unicarbkb;String;g34;50;1000;95;false;false
+iPTMnet;xref_iptmnet;String;g34;50;1000;95;false;false
+CCDS;xref_ccds;String;g35;50;1000;95;false;false
+EMBL;xref_embl;String;g35;50;1000;95;false;false
+PIR;xref_pir;String;g35;50;1000;95;false;false
+RefSeq;xref_refseq;String;g35;50;1000;95;false;false
+#

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 2606b62..05ccba7 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -19,8 +19,37 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 
+/*
+ * 2022-07-20 bsoares
+ * See https://issues.jalview.org/browse/JAL-4036
+ * The new Uniprot API is not dissimilar to the old one, but has some important changes.
+ * Some group names have changed slightly, some old groups have gone and there are quite a few new groups.
+ * 
+ * Most changes are mappings of old column ids to new field ids. There are a handful of old
+ * columns not mapped to new fields, and new fields without an old column.
+ * [aside: not all possible columns were listed in the resources/fts/uniprot_data_columns.txt file.
+ * These were presumably additions after the file was created]
+ * For existing/mapped fields, the same preferences found in the resource file have been migrated to
+ * the new file with the new field name, id and group.
+ * 
+ * The new mapped groups and files are stored and read from resources/fts/uniprot_data_columns-2022.txt.
+ * 
+ * There is now no "sort" query string parameter.
+ * 
+ * See https://www.uniprot.org/help/api_queries
+ * 
+ * SIGNIFICANT CHANGE: Pagination is no longer performed using a record offset, but with a "cursor"
+ * query string parameter that is not really a cursor.  The value is an opaque string that is passed (or
+ * rather a whole URL is passed) in the "Link" header of the HTTP response of the previous page.
+ * Where such a link is passed it is put into the cursors ArrayList.
+ * There are @Overridden methods in UniprotFTSPanel.
+ */
+
 package jalview.fts.service.uniprot;
 
+import java.lang.invoke.MethodHandles;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
@@ -37,31 +66,37 @@ import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSRestClientI;
 import jalview.fts.core.FTSRestClient;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
+import jalview.util.ChannelProperties;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
 public class UniProtFTSRestClient extends FTSRestClient
 {
-  private static final String DEFAULT_UNIPROT_DOMAIN = "https://legacy.uniprot.org";
+  private static final String DEFAULT_UNIPROT_DOMAIN = "https://rest.uniprot.org";
+
+  private static final String USER_AGENT = ChannelProperties
+          .getProperty("app_name", "Jalview") + " "
+          + Cache.getDefault("VERSION", "Unknown") + " "
+          + MethodHandles.lookup().lookupClass() + " help@jalview.org";
 
   static
   {
     Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
   }
 
-  private static FTSRestClientI instance = null;
+  private static UniProtFTSRestClient instance = null;
 
   public final String uniprotSearchEndpoint;
 
   public UniProtFTSRestClient()
   {
     super();
+    this.clearCursors();
     uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
-            DEFAULT_UNIPROT_DOMAIN) + "/uniprot/";
+            DEFAULT_UNIPROT_DOMAIN) + "/uniprotkb/search";
   }
 
   @SuppressWarnings("unchecked")
@@ -69,6 +104,12 @@ public class UniProtFTSRestClient extends FTSRestClient
   public FTSRestResponse executeRequest(FTSRestRequest uniprotRestRequest)
           throws Exception
   {
+    return executeRequest(uniprotRestRequest, null);
+  }
+
+  public FTSRestResponse executeRequest(FTSRestRequest uniprotRestRequest,
+          String cursor) throws Exception
+  {
     try
     {
       String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
@@ -85,11 +126,10 @@ public class UniProtFTSRestClient extends FTSRestClient
       }
       else
       {
-        query = uniprotRestRequest.getFieldToSearchBy()
-                .equalsIgnoreCase("Search All")
-                        ? uniprotRestRequest.getSearchTerm()
-                                + " or mnemonic:"
-                                + uniprotRestRequest.getSearchTerm()
+        query = uniprotRestRequest.getFieldToSearchBy().equalsIgnoreCase(
+                "Search All") ? uniprotRestRequest.getSearchTerm()
+                        // + " or mnemonic:"
+                        // + uniprotRestRequest.getSearchTerm()
                         : uniprotRestRequest.getFieldToSearchBy() + ":"
                                 + uniprotRestRequest.getSearchTerm();
       }
@@ -119,18 +159,62 @@ public class UniProtFTSRestClient extends FTSRestClient
 
       WebResource webResource = null;
       webResource = client.resource(uniprotSearchEndpoint)
-              .queryParam("format", "tab")
-              .queryParam("columns", wantedFields)
-              .queryParam("limit", String.valueOf(responseSize))
-              .queryParam("offset", String.valueOf(offSet))
-              .queryParam("sort", "score").queryParam("query", query);
-      if (Console.isDebugEnabled())
+              .queryParam("format", "tsv")
+              .queryParam("fields", wantedFields)
+              .queryParam("size", String.valueOf(responseSize))
+              /* 2022 new api has no "sort"
+               * .queryParam("sort", "score")
+               */
+              .queryParam("query", query);
+      if (offSet != 0 && cursor != null && cursor.length() > 0)
+      // 2022 new api does not do pagination with an offset, it requires a
+      // "cursor" parameter with a key (given for the next page).
+      // (see https://www.uniprot.org/help/pagination)
       {
-        Console.debug("Uniprot FTS Request: " + webResource.toString());
+        webResource = webResource.queryParam("cursor", cursor);
       }
+      Console.debug(
+              "Uniprot FTS Request: " + webResource.getURI().toString());
       // Execute the REST request
-      ClientResponse clientResponse = webResource
-              .accept(MediaType.TEXT_PLAIN).get(clientResponseClass);
+      WebResource.Builder wrBuilder = webResource
+              .accept(MediaType.TEXT_PLAIN);
+      if (!Platform.isJS())
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
+      {
+        wrBuilder.header("User-Agent", USER_AGENT);
+      }
+      ClientResponse clientResponse = wrBuilder.get(clientResponseClass);
+
+      if (!Platform.isJS())
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
+      {
+        if (clientResponse.getHeaders().containsKey("Link"))
+        {
+          // extract the URL from the 'Link: <URL>; ref="stuff"' header
+          String linkHeader = clientResponse.getHeaders().get("Link")
+                  .get(0);
+          if (linkHeader.indexOf("<") > -1)
+          {
+            String temp = linkHeader.substring(linkHeader.indexOf("<") + 1);
+            if (temp.indexOf(">") > -1)
+            {
+              String nextUrl = temp.substring(0, temp.indexOf(">"));
+              // then get the cursor value from the query string parameters
+              String nextCursor = getQueryParam("cursor", nextUrl);
+              setCursor(cursorPage + 1, nextCursor);
+            }
+          }
+        }
+      }
+
       String uniProtTabDelimittedResponseString = clientResponse
               .getEntity(String.class);
       // Make redundant objects eligible for garbage collection to conserve
@@ -144,15 +228,26 @@ public class UniProtFTSRestClient extends FTSRestClient
         throw new Exception(errorMessage);
 
       }
-      int xTotalResults = Platform.isJS() ? 1
-              : Integer.valueOf(clientResponse.getHeaders()
-                      .get("X-Total-Results").get(0));
+      // new Uniprot API is not including a "X-Total-Results" header when there
+      // are 0 results
+      List<String> resultsHeaders = clientResponse.getHeaders()
+              .get("X-Total-Results");
+      int xTotalResults = 0;
+      if (Platform.isJS())
+      {
+        xTotalResults = 1;
+      }
+      else if (resultsHeaders != null && resultsHeaders.size() >= 1)
+      {
+        xTotalResults = Integer.valueOf(resultsHeaders.get(0));
+      }
       clientResponse = null;
       client = null;
       return parseUniprotResponse(uniProtTabDelimittedResponseString,
               uniprotRestRequest, xTotalResults);
     } catch (Exception e)
     {
+      Console.debug("Exception caught from response", e);
       String exceptionMsg = e.getMessage();
       if (exceptionMsg.contains("SocketException"))
       {
@@ -352,7 +447,7 @@ public class UniProtFTSRestClient extends FTSRestClient
     };
   }
 
-  public static FTSRestClientI getInstance()
+  public static UniProtFTSRestClient getInstance()
   {
     if (instance == null)
     {
@@ -364,7 +459,95 @@ public class UniProtFTSRestClient extends FTSRestClient
   @Override
   public String getColumnDataConfigFileName()
   {
-    return "/fts/uniprot_data_columns.txt";
+    return "/fts/uniprot_data_columns-2022.txt";
+  }
+
+  /* 2022-07-20 bsoares
+   * used for the new API "cursor" pagination. See https://www.uniprot.org/help/pagination
+   */
+  private ArrayList<String> cursors;
+
+  private int cursorPage = 0;
+
+  protected int getCursorPage()
+  {
+    return cursorPage;
+  }
+
+  protected void setCursorPage(int i)
+  {
+    cursorPage = i;
+  }
+
+  protected void setPrevCursorPage()
+  {
+    if (cursorPage > 0)
+      cursorPage--;
+  }
+
+  protected void setNextCursorPage()
+  {
+    cursorPage++;
+  }
+
+  protected void clearCursors()
+  {
+    cursors = new ArrayList(10);
   }
 
-}
+  protected String getCursor(int i)
+  {
+    return cursors.get(i);
+  }
+
+  protected String getNextCursor()
+  {
+    if (cursors.size() < cursorPage + 2)
+      return null;
+    return cursors.get(cursorPage + 1);
+  }
+
+  protected String getPrevCursor()
+  {
+    if (cursorPage == 0)
+      return null;
+    return cursors.get(cursorPage - 1);
+  }
+
+  protected void setCursor(int i, String c)
+  {
+    cursors.ensureCapacity(i + 1);
+    while (cursors.size() <= i)
+    {
+      cursors.add(null);
+    }
+    cursors.set(i, c);
+    Console.debug(
+            "Set UniprotFRSRestClient cursors[" + i + "] to '" + c + "'");
+    // cursors.add(c);
+  }
+
+  public static String getQueryParam(String param, String u)
+  {
+    if (param == null || u == null)
+      return null;
+    try
+    {
+      URL url = new URL(u);
+      String[] kevs = url.getQuery().split("&");
+      for (int j = 0; j < kevs.length; j++)
+      {
+        String[] kev = kevs[j].split("=", 2);
+        if (param.equals(kev[0]))
+        {
+          return kev[1];
+        }
+      }
+    } catch (MalformedURLException e)
+    {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+    }
+    return null;
+  }
+}
\ No newline at end of file

diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
index 33ad8c4..0d9767c 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
+++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
@@ -21,6 +21,13 @@
 
 package jalview.fts.service.uniprot;
 
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import javax.help.HelpSetException;
+
+import jalview.bin.Console;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
 import jalview.fts.core.FTSRestRequest;
@@ -31,12 +38,6 @@ import jalview.gui.Help.HelpId;
 import jalview.gui.SequenceFetcher;
 import jalview.util.MessageManager;
 
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-
-import javax.help.HelpSetException;
-
 @SuppressWarnings("serial")
 public class UniprotFTSPanel extends GFTSPanel
 {
@@ -69,10 +70,19 @@ public class UniprotFTSPanel extends GFTSPanel
   @Override
   public void searchAction(boolean isFreshSearch)
   {
+    searchAction(null, isFreshSearch);
+  }
+
+  public void searchAction(String cursor, boolean isFreshSearch)
+  {
     mainFrame.requestFocusInWindow();
     if (isFreshSearch)
     {
       offSet = 0;
+      UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+      c.clearCursors();
+      c.setCursorPage(0);
+      c.setCursor(0, "");
     }
     new Thread()
     {
@@ -97,12 +107,12 @@ public class UniprotFTSPanel extends GFTSPanel
           request.setSearchTerm(searchTerm);
           request.setOffSet(offSet);
           request.setWantedFields(wantedFields);
-          FTSRestClientI uniProtRestClient = UniProtFTSRestClient
+          UniProtFTSRestClient uniProtRestClient = UniProtFTSRestClient
                   .getInstance();
           FTSRestResponse resultList;
           try
           {
-            resultList = uniProtRestClient.executeRequest(request);
+            resultList = uniProtRestClient.executeRequest(request, cursor);
           } catch (Exception e)
           {
             setErrorMessage(e.getMessage());
@@ -268,4 +278,68 @@ public class UniprotFTSPanel extends GFTSPanel
       e1.printStackTrace();
     }
   }
+
+  /*
+   * 2022-07-20 bsoares
+   * The new Uniprot API has a strange pagination process described at
+   * https://www.uniprot.org/help/pagination
+   * When a successful request returns results, with more results past the size
+   * limit, the response sends a "Link" header with a URL containing the a "cursor"
+   * parameter with an opaque string that refers to the next page of results.
+   * These are store as nextCursor in the UniProtFTSRestClient along with the currCursor.
+   * When navigation across pages occurs these should be swapped around.
+   */
+  @Override
+  public void refreshPaginatorState()
+  {
+    UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+    setNextPageButtonEnabled(c.getNextCursor() != null);
+    setPrevPageButtonEnabled(c.getPrevCursor() != null);
+  }
+
+  @Override
+  public void prevPageAction()
+  {
+    updatePaginatorCart();
+    UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+    String prevCursor = c.getPrevCursor();
+    if (prevCursor != null)
+    {
+      if (offSet >= pageLimit)
+      {
+        offSet -= pageLimit;
+      }
+      else
+      {
+        // not sure what's happening if we get here though it wouldn't surprise
+        // me
+        Console.warn(
+                "UniprotFTSPanel: prevCursor exists but offset < pageLimit. This probably shouldn't be happening.");
+      }
+      c.setPrevCursorPage();
+      searchAction(prevCursor, false);
+    }
+    else
+    {
+      refreshPaginatorState();
+    }
+  }
+
+  @Override
+  public void nextPageAction()
+  {
+    UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+    String nextCursor = c.getNextCursor();
+    if (nextCursor != null)
+    {
+      offSet += pageLimit;
+      c.setNextCursorPage();
+      searchAction(nextCursor, false);
+    }
+    else
+    {
+      refreshPaginatorState();
+    }
+  }
+
 }