text: -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
  -- Copyright [2016-2019] EMBL-European Bioinformatics Institute
  -- 
  -- Licensed under the Apache License, Version 2.0 (the "License");
  -- you may not use this file except in compliance with the License.
  -- You may obtain a copy of the License at
  -- 
  --      http://www.apache.org/licenses/LICENSE-2.0
  -- 
  -- Unless required by applicable law or agreed to in writing, software
  -- distributed under the License is distributed on an "AS IS" BASIS,
  -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  -- See the License for the specific language governing permissions and
  -- limitations under the License.
  
  
  # add top level menus
  insert into meta(species_id, meta_key, meta_value)
  values
  (NULL, 'web_config', "menu#dbSNP#dbsnp#"),
  (NULL, 'web_config', "menu#1000 Genomes & HapMap#1kg_hapmap#"),
  (NULL, 'web_config', "menu#Phenotype and curated variants#phenotype#"),
  (NULL, 'web_config', "menu#Individual genomes#ind_genomes#"),
  (NULL, 'web_config', "menu#Arrays and other#var_other#"),
  (NULL, 'web_config', "menu#Failed variants#failed#");
  
  # add all variants
  insert into meta(species_id, meta_key, meta_value)
  values
  (NULL, 'web_config', "source#Sequence variants (dbSNP and all other sources)#variation_feature_variation#dbsnp");
  
  # add dbSNP
  insert into meta(species_id, meta_key, meta_value)
  values
  (NULL, 'web_config', "source#dbSNP variants#variation_feature_variation_dbSNP#dbsnp");
  
  
  # add HapMap sets
  insert into meta(species_id, meta_key, meta_value)
  values
  (NULL, 'web_config', "menu#HapMap#hapmap#1kg_hapmap");
  
  insert into meta(species_id, meta_key, meta_value)
  select NULL, "web_config",  concat("set#", vs.name, "#variation_set_", a.value, "#hapmap")
  from variation_set vs, attrib a
  where vs.short_name_attrib_id = a.attrib_id
  and a.value like 'hapmap%';
  
  # add 1000 genomes sets
  insert into meta(species_id, meta_key, meta_value)
  values
  (NULL, 'web_config', "menu#1000 Genomes#1kg#1kg_hapmap");
  
  insert into meta(species_id, meta_key, meta_value)
  select NULL, "web_config",  concat("set#", vs.name, "#variation_set_", a.value, "#1kg")
  from variation_set vs, attrib a
  where vs.short_name_attrib_id = a.attrib_id
  and a.value like '1kg%'
  and a.value != '1kg_hq'
  order by vs.name asc;
  
  # add phenotype sets
  insert into meta(species_id, meta_key, meta_value)
  select NULL, "web_config",  concat("set#", vs.name, "#variation_set_", a.value, "#phenotype")
  from variation_set vs, attrib a
  where vs.short_name_attrib_id = a.attrib_id
  and a.value like 'ph%'
  and vs.name not like '%cosmic%';
  
  # add phenotype sources
  insert into meta(species_id, meta_key, meta_value)
  values
  (NULL, 'web_config', "menu#LSDB-associated variants#lsdb#phenotype");
  
  insert into meta(species_id, meta_key, meta_value)
  select NULL, "web_config",  concat("source#", name, " variants", "#variation_feature_variation_", replace(name, " ", "_"), "#lsdb")
  from source
  where name like 'LSDB%';
  
  # add clinical set (phenotype)
  insert into meta(species_id, meta_key, meta_value)
  select NULL, "web_config",  concat("set#", vs.name, "#variation_set_", a.value, "#phenotype")
  from variation_set vs, attrib a
  where vs.short_name_attrib_id = a.attrib_id
  and a.value like 'precious%';
  
  # add individual genotype sets
  insert into meta(species_id, meta_key, meta_value)
  select NULL, "web_config",  concat("set#", vs.name, "#variation_set_", a.value, "#ind_genomes")
  from variation_set vs, attrib a
  where vs.short_name_attrib_id = a.attrib_id
  and a.value like 'ind%'
  order by vs.name asc;
  
  # add failed sets
  insert into meta(species_id, meta_key, meta_value)
  select NULL, "web_config",  concat("set#", vs.name, "#variation_set_", a.value, "#failed")
  from variation_set vs, attrib a
  where vs.short_name_attrib_id = a.attrib_id
  and a.value like 'fail%'
  order by vs.variation_set_id asc;
  
  # add chips and uniprot
  insert into meta(species_id, meta_key, meta_value)
  select NULL, "web_config",  concat("source#", name, " variants", "#variation_feature_variation_",
  replace(name, " ", "_"), "#var_other")
  from source
  where name like 'Affy%'
  or name like 'Illumina%'
  or name like 'Uniprot%'
  order by name asc;
  
  # add structural variation sets
  insert into meta(species_id, meta_key, meta_value)
  values (NULL, 'web_config', "sv_set#1000 Genomes - Low coverage#sv_set_1kg_lc");
  
  insert into meta(species_id, meta_key, meta_value)
  values (NULL, 'web_config', "sv_set#1000 Genomes - High coverage - Trios#sv_set_1kg_hct");
  
  insert into meta(species_id, meta_key, meta_value)
  values (NULL, 'web_config', "sv_set#1000 Genomes - All#sv_set_1kg");
  
  insert into meta(species_id, meta_key, meta_value)
  values (NULL, 'web_config', "sv_set#1000 Genomes - EUR#sv_set_1kg_eur");
  
  insert into meta(species_id, meta_key, meta_value)
  values (NULL, 'web_config', "sv_set#1000 Genomes - ASN#sv_set_1kg_asn");
  
  insert into meta(species_id, meta_key, meta_value)
  values (NULL, 'web_config', "sv_set#1000 Genomes - AMR#sv_set_1kg_amr");
  
  insert into meta(species_id, meta_key, meta_value)
  values (NULL, 'web_config', "sv_set#1000 Genomes - AFR#sv_set_1kg_afr");
  
  insert into meta(species_id, meta_key, meta_value) 
  values (NULL, 'web_config', "sv_set#1000 Genomes - High quality#sv_set_1kg_hq");
  
  # add structural variation studies (selection of)
  insert into meta(species_id, meta_key, meta_value) values (NULL, 'web_config', "sv_study#Study estd199#estd199");
  insert into meta(species_id, meta_key, meta_value) values (NULL, 'web_config', "sv_study#Study nstd37#nstd37");
  insert into meta(species_id, meta_key, meta_value) values (NULL, 'web_config', "sv_study#Study estd203#estd203");
  insert into meta(species_id, meta_key, meta_value) values (NULL, 'web_config', "sv_study#Study nstd71#nstd71");
  