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Updating database NOT READY FOR REVIEW #1175

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Updating database NOT READY FOR REVIEW #1175

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29 changes: 20 additions & 9 deletions server/dals/network-dal.js
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Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,20 @@
);

const buildNetworkSourceQuery = function () {
return "SELECT * FROM gene_regulatory_network.source ORDER BY time_stamp DESC;";
return `SELECT * FROM gene_regulatory_network.source
UNION ALL
SELECT * FROM gene_regulatory_network_new.source
ORDER BY time_stamp DESC;`;
};

const buildNetworkGeneFromSourceQuery = function (gene) {
const buildNetworkGeneFromSourceQuery = function (gene, timestamp) {
const namespace =
timestamp < new Date("2025-01-01")
? "gene_regulatory_network.gene"
: "gene_regulatory_network_new.gene";
return `SELECT DISTINCT gene_id, display_gene_id FROM
gene_regulatory_network.gene WHERE (gene.gene_id ='${gene}'
OR gene.display_gene_id ='${gene}')`;
${namespace} WHERE (gene.gene_id ='${gene}'
OR gene.display_gene_id ='${gene}') AND gene.time_stamp ='${timestamp}'`;
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Old namespace doesn't have timestamp so this would cause error

};

const buildNetworkGenesQuery = function (geneString) {
Expand All @@ -34,14 +41,18 @@
genes = `${genes.substring(0, genes.length - 4)}) AND (`;
geneList.forEach(x => genes += ( `(network.target_gene_id =\'${x}\') OR `));
return `${genes.substring(0, genes.length - 4)})`;

};

const buildGenerateNetworkQuery = function (genes, source, timestamp) {
return `SELECT DISTINCT regulator_gene_id, target_gene_id FROM
gene_regulatory_network.network WHERE
time_stamp='${timestamp}' AND source='${source}' AND
${buildNetworkGenesQuery(genes)} ORDER BY regulator_gene_id DESC;`;
const namespace =
timestamp < new Date("2025-01-01")
? "gene_regulatory_network.network"
: "gene_regulatory_network_new.network";
const annotation = timestamp < new Date("2025-01-01") ? "" : ", annotation_type";
return `SELECT DISTINCT regulator_gene_id, target_gene_id${annotation} FROM ${namespace}
WHERE time_stamp='${timestamp}' AND source='${source}' AND
${buildNetworkGenesQuery(genes)} ORDER BY regulator_gene_id DESC;`;

Check failure on line 55 in server/dals/network-dal.js

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};

const buildQueryByType = function (queryType, query) {
Expand Down
32 changes: 22 additions & 10 deletions server/dals/protein-dal.js
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Original file line number Diff line number Diff line change
Expand Up @@ -18,15 +18,22 @@ var sequelize = new Sequelize(
);

const buildNetworkSourceQuery = function () {
return "SELECT * FROM protein_protein_interactions.source ORDER BY time_stamp DESC;";
return `SELECT * FROM protein_protein_interactions.source
UNION ALL
SELECT * FROM protein_protein_interactions_new.source
ORDER BY time_stamp DESC;`;
};

const buildNetworkFromGeneProteinQuery = function (geneProtein) {
const buildNetworkFromGeneProteinQuery = function (geneProtein, timestamp) {
const namespace =
timestamp < new Date("2025-01-01")
? "protein_protein_interactions"
: "protein_protein_interactions_new";
return `SELECT DISTINCT gene_id, display_gene_id, standard_name, length, molecular_weight, PI FROM
protein_protein_interactions.gene, protein_protein_interactions.protein WHERE
(LOWER(gene.gene_id)=LOWER('${geneProtein}') OR LOWER(gene.display_gene_id)=LOWER('${geneProtein}')
OR LOWER(protein.standard_name) =LOWER('${geneProtein}')) AND
LOWER(gene.gene_id) = LOWER(protein.gene_systematic_name);`;
${namespace}.gene, ${namespace}.protein WHERE
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Similar here, old namepsace doesn't have timestamp. Additionally, if we query from protein table, then we should check the timestamp from the protein table. If we query from gene table, then we should check the timestamp from the gene table.

(LOWER(gene.gene_id)=LOWER('${geneProtein}') OR LOWER(gene.display_gene_id)=LOWER('${geneProtein}')
OR LOWER(protein.standard_name) =LOWER('${geneProtein}')) AND
LOWER(gene.gene_id) = LOWER(protein.gene_systematic_name) AND gene.time_stamp = ${timestamp};`;
};

const buildNetworkProteinsQuery = function (proteinString) {
Expand All @@ -40,10 +47,15 @@ const buildNetworkProteinsQuery = function (proteinString) {
};

const buildGenerateProteinNetworkQuery = function (proteins, timestamp, source) {
return `SELECT DISTINCT protein1, protein2 FROM
protein_protein_interactions.physical_interactions WHERE
physical_interactions.time_stamp='${timestamp}' AND physical_interactions.source='${source}' AND
${buildNetworkProteinsQuery(proteins)} ORDER BY protein1 DESC;`;
const namespace =
timestamp < new Date("2025-01-01")
? "protein_protein_interactions"
: "protein_protein_interactions_new";
const annotation =
timestamp < new Date("2025-01-01") ? "" : ", annotation_type";
return `SELECT DISTINCT protein1, protein2${annotation} FROM ${namespace}.physical_interactions
${namespace}.time_stamp='${timestamp}' AND ${namespace}.source='${source}' AND
${buildNetworkProteinsQuery(proteins)} ORDER BY protein1 DESC;`;
};

const buildQueryByType = function (query) {
Expand Down
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