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going back to old code from commit a0ab429 to troubleshoot queries. n…
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…ot currently using dbConstants file
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@ceciliazaragoza
ceciliazaragoza committed Feb 26, 2025
1 parent 0eaa53c commit 1e57de5
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121 changes: 35 additions & 86 deletions server/dals/network-dal.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,98 +2,63 @@ const Sequelize = require("sequelize");
require("dotenv").config();
var env = process.env.NODE_ENV || "development";
var config = require("../config/config")[env];
var sequelize = new Sequelize(
config.databaseName,
process.env.DB_USERNAME,
process.env.DB_PASSWORD,
{
host: config.databaseHost,
dialect: config.databaseDialect,
pool: {
max: 5,
min: 0,
idle: 10000,
},
}
);

//import { GRN_DATABASE_NAMESPACE, GRN_DATABASE_NAMESPACE_OLD, timestampNamespace, timestampOld } from "./constants";
const GRN_DATABASE_NAMESPACE = "gene_regulatory_network_new";
const GRN_DATABASE_NAMESPACE_OLD = "gene_regulatory_network";
const DATABASE_TIMESTAMP_CUTOFF = new Date("2025-01-01");

const timestampNamespace = function(timestamp, namespace, oldNamespace) {
return timestamp < new Date("2025-01-01") ? namespace : oldNamespace;
};

const timestampOld = function(timestamp) {
return timestamp < DATABASE_TIMESTAMP_CUTOFF;
};
var sequelize = new Sequelize(config.databaseName, process.env.DB_USERNAME, process.env.DB_PASSWORD, {
host: config.databaseHost,
dialect: config.databaseDialect,
pool: {
max: 5,
min: 0,
idle: 10000,
},
});

const buildNetworkSourceQuery = function () {
return `SELECT * FROM ${GRN_DATABASE_NAMESPACE_OLD}.source
const buildNetworkSourceQuery = function() {

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return `SELECT * FROM gene_regulatory_network.source
UNION ALL
SELECT * FROM ${GRN_DATABASE_NAMESPACE}.source
SELECT * FROM gene_regulatory_network_new.source
ORDER BY time_stamp DESC;`;
};

const buildNetworkGeneFromSourceQuery = function (gene, source, timestamp) {
const namespace = `${timestampNamespace(timestamp,
GRN_DATABASE_NAMESPACE,
GRN_DATABASE_NAMESPACE_OLD
)}.gene`;
const timestamp_query = timestampOld(timestamp)
? ""
: `AND gene.time_stamp ='${timestamp}`;
const buildNetworkGeneFromSourceQuery = function(gene, source, timestamp) {

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const namespace =
timestamp < new Date("2025-01-01") ? "gene_regulatory_network.gene" : "gene_regulatory_network_new.gene";
const timestamp_query = timestamp < new Date("2025-01-01") ? `AND gene.time_stamp ='${timestamp}` : "";

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return `SELECT DISTINCT gene_id, display_gene_id FROM
${namespace} WHERE (gene.gene_id ='${gene}'
OR gene.display_gene_id ='${gene}') ${timestamp_query};`;

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};

const buildNetworkGenesQuery = function (geneString) {
const buildNetworkGenesQuery = function(geneString) {

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let genes = "(";
let geneList = geneString.split(",");
geneList.forEach(
(x) => (genes += `(network.regulator_gene_id =\'${x}\') OR `)
);
geneList.forEach((x) => (genes += `(network.regulator_gene_id =\'${x}\') OR `));
genes = `${genes.substring(0, genes.length - 4)}) AND (`;
geneList.forEach(
(x) => (genes += `(network.target_gene_id =\'${x}\') OR `)
);
geneList.forEach((x) => (genes += `(network.target_gene_id =\'${x}\') OR `));
return `${genes.substring(0, genes.length - 4)})`;
};

const buildGenerateNetworkQuery = function (genes, source, timestamp) {
const namespace = `${timestampNamespace(
timestamp,
GRN_DATABASE_NAMESPACE,
GRN_DATABASE_NAMESPACE_OLD
)}.network`;
const annotation = timestampOld(timestamp) ? "" : ", annotation_type";
const buildGenerateNetworkQuery = function(genes, source, timestamp) {

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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;`;
};

const buildQueryByType = function (queryType, query) {
const buildQueryByType = function(queryType, query) {
const networkQueries = {
NetworkSource: () => buildNetworkSourceQuery(),
NetworkGeneFromSource: () =>
buildNetworkGeneFromSourceQuery(query.gene),
GenerateNetwork: () =>
buildGenerateNetworkQuery(
query.genes,
query.source,
query.timestamp
),
NetworkGeneFromSource: () => buildNetworkGeneFromSourceQuery(query.gene),
GenerateNetwork: () => buildGenerateNetworkQuery(query.genes, query.source, query.timestamp),
};
if (Object.keys(networkQueries).includes(query.type)) {
return networkQueries[query.type]();
}
};

// const response = convertResponseToJSON(req.query.type, req.query, stdname);
const convertResponseToJSON = function (queryType, query, totalOutput) {
const convertResponseToJSON = function(queryType, query, totalOutput) {
let JSONOutput = {};
switch (queryType) {
case "NetworkSource":
Expand All @@ -102,30 +67,20 @@ const convertResponseToJSON = function (queryType, query, totalOutput) {
const timestamp = connection.time_stamp;
const source = connection.source;
const displayName = connection.display_name;
JSONOutput.sources[
`${displayName}: ${timestamp.toISOString().split("T")[0]}`
] = { timestamp, source };
JSONOutput.sources[`${displayName}: ${timestamp.toISOString().split("T")[0]}`] = { timestamp, source };
});
return JSONOutput;
case "NetworkGeneFromSource":
JSONOutput.displayGeneId =
totalOutput.length > 0 ? totalOutput[0].display_gene_id : null;
JSONOutput.geneId =
totalOutput.length > 0 ? totalOutput[0].gene_id : null;
JSONOutput.displayGeneId = totalOutput.length > 0 ? totalOutput[0].display_gene_id : null;
JSONOutput.geneId = totalOutput.length > 0 ? totalOutput[0].gene_id : null;
return JSONOutput;
case "GenerateNetwork":
JSONOutput.links = {};
for (let connection of totalOutput) {
if (
JSONOutput.links[connection.regulator_gene_id] === undefined
) {
JSONOutput.links[connection.regulator_gene_id] = [
connection.target_gene_id,
];
if (JSONOutput.links[connection.regulator_gene_id] === undefined) {
JSONOutput.links[connection.regulator_gene_id] = [connection.target_gene_id];
} else {
JSONOutput.links[connection.regulator_gene_id].push(
connection.target_gene_id
);
JSONOutput.links[connection.regulator_gene_id].push(connection.target_gene_id);
}
}
return JSONOutput;
Expand All @@ -138,15 +93,9 @@ module.exports = {
buildNetworkSourceQuery: buildNetworkSourceQuery,
queryNetworkDatabase: function(req, res) {
sequelize
.query(buildQueryByType(req.query.type, req.query), {
type: sequelize.QueryTypes.SELECT,
})
.query(buildQueryByType(req.query.type, req.query), { type: sequelize.QueryTypes.SELECT })
.then(function(stdname) {
const response = convertResponseToJSON(
req.query.type,
req.query,
stdname
);
const response = convertResponseToJSON(req.query.type, req.query, stdname);
return res.send(response);
});
},
Expand Down
148 changes: 65 additions & 83 deletions server/dals/protein-dal.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,122 +2,104 @@ const Sequelize = require("sequelize");
require("dotenv").config();
var env = process.env.NODE_ENV || "development";
var config = require("../config/config")[env];
var sequelize = new Sequelize(
config.databaseName,
process.env.DB_USERNAME,
process.env.DB_PASSWORD,
{
host: config.databaseHost,
dialect: config.databaseDialect,
pool: {
max: 5,
min: 0,
idle: 10000
}
}
);

//import { PPI_DATABASE_NAMESPACE, PPI_DATABASE_NAMESPACE_OLD, timestampNamespace, timestampOld } from "./constants";
const PPI_DATABASE_NAMESPACE = "protein_protein_interactions_new";
const PPI_DATABASE_NAMESPACE_OLD = "protein_protein_interactions";
const DATABASE_TIMESTAMP_CUTOFF = new Date("2025-01-01");

const timestampNamespace = function(timestamp, namespace, oldNamespace) {
return timestamp < new Date("2025-01-01") ? namespace : oldNamespace;
};
var sequelize = new Sequelize(config.databaseName, process.env.DB_USERNAME, process.env.DB_PASSWORD, {
host: config.databaseHost,
dialect: config.databaseDialect,
pool: {
max: 5,
min: 0,
idle: 10000,
},
});

const timestampOld = function(timestamp) {
return timestamp < DATABASE_TIMESTAMP_CUTOFF;
};

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

const buildNetworkFromGeneProteinQuery = function (geneProtein, timestamp) {
const namespace = `${timestampNamespace(timestamp, PPI_DATABASE_NAMESPACE, PPI_DATABASE_NAMESPACE_OLD)}`;
const timestamp_query = timestampOld(timestamp) ? "": `AND gene.time_stamp ='${timestamp}`;
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
${namespace}.gene, ${namespace}.protein WHERE
(LOWER(gene.gene_id)=LOWER('${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) ${timestamp_query};`;
LOWER(gene.gene_id) = LOWER(protein.gene_systematic_name) AND gene.time_stamp = ${timestamp};`;
};

const buildNetworkProteinsQuery = function (proteinString) {
const buildNetworkProteinsQuery = function(proteinString) {
let proteins = "(";
let proteinList = proteinString.split(",");
proteinList.forEach(x => proteins += ( `(physical_interactions.protein1 =\'${x}\') OR `));
proteinList.forEach((x) => (proteins += `(physical_interactions.protein1 =\'${x}\') OR `));
proteins = `${proteins.substring(0, proteins.length - 4)}) AND (`;
proteinList.forEach(x => proteins += ( `(physical_interactions.protein2 =\'${x}\') OR `));
proteinList.forEach((x) => (proteins += `(physical_interactions.protein2 =\'${x}\') OR `));
return `${proteins.substring(0, proteins.length - 4)})`;
};

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

const buildQueryByType = function (query) {
const buildQueryByType = function(query) {
const networkQueries = {
"NetworkSource": () => buildNetworkSourceQuery(),
"NetworkFromGeneProtein": () => buildNetworkFromGeneProteinQuery(query.geneProtein),
"GenerateProteinNetwork": () => buildGenerateProteinNetworkQuery(query.proteins, query.timestamp, query.source)
NetworkSource: () => buildNetworkSourceQuery(),
NetworkFromGeneProtein: () => buildNetworkFromGeneProteinQuery(query.geneProtein),
GenerateProteinNetwork: () => buildGenerateProteinNetworkQuery(query.proteins, query.timestamp, query.source),
};
if (Object.keys(networkQueries).includes(query.type)) {
return networkQueries[query.type]();
}
};

const convertResponseToJSON = function (queryType, totalOutput) {
const convertResponseToJSON = function(queryType, totalOutput) {
let JSONOutput = {};
switch (queryType) {
case "NetworkSource":
JSONOutput.sources = {};
totalOutput.forEach(function (x) {
const timestamp = x.time_stamp;
const source = x.source;
const displayName = x.display_name;
JSONOutput.sources[`${displayName}: ${timestamp.toISOString().split("T")[0]}`] = {timestamp, source};
});
return JSONOutput;
case "NetworkFromGeneProtein":
if (totalOutput.length > 0) {
JSONOutput.standardName = totalOutput[0].standard_name;
JSONOutput.displayGeneId = totalOutput[0].display_gene_id;
JSONOutput.geneId = totalOutput[0].gene_id;
JSONOutput.length = totalOutput[0].length;
JSONOutput.molecularWeight = totalOutput[0].molecular_weight;
JSONOutput.PI = totalOutput[0].PI;
}
return JSONOutput;
case "GenerateProteinNetwork":
JSONOutput.links = {};
for (let connection of totalOutput) {
if (JSONOutput.links[connection.protein1] === undefined) {
JSONOutput.links[connection.protein1] = [connection.protein2];
} else {
JSONOutput.links[connection.protein1].push(connection.protein2);
case "NetworkSource":
JSONOutput.sources = {};
totalOutput.forEach(function(x) {
const timestamp = x.time_stamp;
const source = x.source;
const displayName = x.display_name;
JSONOutput.sources[`${displayName}: ${timestamp.toISOString().split("T")[0]}`] = { timestamp, source };
});
return JSONOutput;
case "NetworkFromGeneProtein":
if (totalOutput.length > 0) {
JSONOutput.standardName = totalOutput[0].standard_name;
JSONOutput.displayGeneId = totalOutput[0].display_gene_id;
JSONOutput.geneId = totalOutput[0].gene_id;
JSONOutput.length = totalOutput[0].length;
JSONOutput.molecularWeight = totalOutput[0].molecular_weight;
JSONOutput.PI = totalOutput[0].PI;
}
return JSONOutput;
case "GenerateProteinNetwork":
JSONOutput.links = {};
for (let connection of totalOutput) {
if (JSONOutput.links[connection.protein1] === undefined) {
JSONOutput.links[connection.protein1] = [connection.protein2];
} else {
JSONOutput.links[connection.protein1].push(connection.protein2);
}
}
}
return JSONOutput;
default:
return JSONOutput;
return JSONOutput;
default:
return JSONOutput;
}
};

module.exports = {
queryProteinDatabase: function (req, res) {
sequelize.query(buildQueryByType(req.query), { type: sequelize.QueryTypes.SELECT })
.then(function (stdname) {
const response = convertResponseToJSON(req.query.type, stdname);
return res.send(response);
});
}
};
queryProteinDatabase: function(req, res) {
sequelize.query(buildQueryByType(req.query), { type: sequelize.QueryTypes.SELECT }).then(function(stdname) {
const response = convertResponseToJSON(req.query.type, stdname);
return res.send(response);
});
},
};

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