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Add access control filtering for protein_structure queries #151

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Add access control filtering for protein_structure queries #151

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23 changes: 18 additions & 5 deletions middleware/DecorateQuery.js
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Original file line number Diff line number Diff line change
@@ -1,13 +1,26 @@
// Collections that need join-based access control (they reference genomes but don't have their own permission fields)
const joinAccessControlCollections = {
protein_structure: { fromIndex: 'genome', from: 'genome_id', to: 'genome_id' }
}

module.exports = function (req, res, next) {
if (req.call_method !== 'query') { return next() }

req.call_params[0] = req.call_params[0] || '&q=*:*'
if (!req.user) {
if (!req.publicFree || (req.publicFree && (req.publicFree.indexOf(req.call_collection) < 0))) {
req.call_params[0] = req.call_params[0] + '&fq=public:true'

// Check if this collection needs join-based access control
const joinConfig = joinAccessControlCollections[req.call_collection]
if (joinConfig) {
// Use a Solr cross-collection join to filter by the referenced collection's access control
if (!req.user) {
req.call_params[0] = req.call_params[0] + `&fq={!join method=crossCollection from=${joinConfig.from} to=${joinConfig.to} fromIndex=${joinConfig.fromIndex}}public:true`
} else {
req.call_params[0] = req.call_params[0] + `&fq={!join method=crossCollection from=${joinConfig.from} to=${joinConfig.to} fromIndex=${joinConfig.fromIndex}}(public:true OR owner:${req.user} OR user_read:${req.user})`
}
} else {
if (!req.publicFree || (req.publicFree && (req.publicFree.indexOf(req.call_collection) < 0))) {
} else if (!req.publicFree || (req.publicFree && (req.publicFree.indexOf(req.call_collection) < 0))) {
if (!req.user) {
req.call_params[0] = req.call_params[0] + '&fq=public:true'
} else {
req.call_params[0] = req.call_params[0] + ('&fq=(public:true OR owner:' + req.user + ' OR user_read:' + req.user + ')')
}
}
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2 changes: 1 addition & 1 deletion middleware/PublicDataTypes.js
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

const publicFree = ['antibiotics', 'enzyme_class_ref', 'epitope', 'epitope_assay', 'experiment', 'bioset', 'bioset_result', 'gene_ontology_ref', 'id_ref', 'misc_niaid_sgc', 'pathway_ref', 'ppi', 'pig', 'protein_family_ref', 'sp_gene_evidence', 'sp_gene_ref', 'spike_lineage', 'spike_variant', 'subsystem_ref', 'taxonomy', 'transcriptomics_experiment', 'transcriptomics_gene', 'transcriptomics_sample', 'model_reaction', 'model_complex_role', 'model_compound', 'model_template_biomass', 'model_template_reaction', 'feature_sequence', 'protein_structure', 'protein_feature', 'surveillance', 'serology', 'sequence_feature', 'sequence_feature_vt']
const publicFree = ['antibiotics', 'enzyme_class_ref', 'epitope', 'epitope_assay', 'experiment', 'bioset', 'bioset_result', 'gene_ontology_ref', 'id_ref', 'misc_niaid_sgc', 'pathway_ref', 'ppi', 'pig', 'protein_family_ref', 'sp_gene_evidence', 'sp_gene_ref', 'spike_lineage', 'spike_variant', 'subsystem_ref', 'taxonomy', 'transcriptomics_experiment', 'transcriptomics_gene', 'transcriptomics_sample', 'model_reaction', 'model_complex_role', 'model_compound', 'model_template_biomass', 'model_template_reaction', 'feature_sequence', 'protein_feature', 'surveillance', 'serology', 'sequence_feature', 'sequence_feature_vt']

module.exports = function (req, res, next) {
req.publicFree = publicFree
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