m

.gitignore

@@ -1 +1,2 @@
-node_modules
+node_modules
+test.json

index.js

@@ -19,6 +19,7 @@ const NCBIGeneTemplate = (id) => {
     return {
         db: 'gene',
         id,
+        api_key: '47796c7650360571735f00f510315f871607',
         retmode: 'xml',
         endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
         query: [
@@ -52,10 +53,10 @@ const NCBIGeneTemplate = (id) => {
                     }
                 },
                 "Transcript": {
-                    "Accession" : **.'Entrezgene_comments'.'Gene_commentary'[Gene_commentary_heading='NCBI Reference Sequences (RefSeq)'].**.Gene_commentary[Gene_commentary_heading='mRNA Sequence'][0].Gene_commentary_accession,
-                    "Exon_Count": **.'Entrezgene_properties'.'Gene_commentary'[Gene_commentary_label='Exon count'].Gene_commentary_text
+                    "Accession" : **.Entrezgene_comments.Gene_commentary[Gene_commentary_heading='NCBI Reference Sequences (RefSeq)'].**.Gene_commentary[Gene_commentary_heading='mRNA Sequence'][0].Gene_commentary_accession,
+                    "Exon_Count": **.Entrezgene_properties.Gene_commentary[Gene_commentary_label='Exon count'].Gene_commentary_text
                 },
-                "Products": **.'Entrezgene_comments'.'Gene_commentary'[Gene_commentary_heading='NCBI Reference Sequences (RefSeq)'].**.Gene_commentary[Gene_commentary_heading='mRNA Sequence'][0].Gene_commentary_products.Gene_commentary[Gene_commentary_heading='Product'][0].{
+                "Products": **.Entrezgene_comments.Gene_commentary[Gene_commentary_heading='NCBI Reference Sequences (RefSeq)'].**.Gene_commentary[Gene_commentary_heading='mRNA Sequence'][0].Gene_commentary_products.Gene_commentary[Gene_commentary_heading='Product'][0].{
                     "Accession": Gene_commentary_accession,
                     "Domains"  : Gene_commentary_comment.Gene_commentary[Gene_commentary_heading='Conserved Domains'].Gene_commentary_comment.Gene_commentary.{
                         "DB"      : Gene_commentary_source.**.Dbtag_db,
@@ -71,23 +72,154 @@ const NCBIGeneTemplate = (id) => {
 };
 const searchGeneTemplate = (name) => {
     return {
-        term: name + '[Gene Name]+AND+Human[Organism] ',
+        term: name + '[Gene Name]+AND+Human[Organism]',
         db: 'gene',
+        api_key: '47796c7650360571735f00f510315f871607',
         endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',
         query: `{"First_ID": **.Id[0]}`
     };
 };
+const searchTranscriptTemplate = (accession) => {
+    return {
+        term: accession + '+AND+Human[Organism]',
+        db: 'nuccore',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',
+        query: `{"First_ID": **.Id[0]}`
+    };
+};
+const searchProtTemplate = (accession) => {
+    return {
+        term: accession + '+AND+Human[Organism]',
+        db: 'protein',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',
+        query: `{"First_ID": **.Id[0]}`
+    };
+};
+const searchSNPTemplate = (accession) => {
+    return {
+        term: accession + '+AND+Human[Organism]',
+        db: 'snp',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',
+        query: `**.Id`
+    };
+};
+const NCBITranscriptTemplate = (id) => {
+    return {
+        db: 'nuccore',
+        id,
+        retmode: 'xml',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
+        query: `{
+            "Accession_version": GBSet[0].GBSeq[0].GBSeq_accession_version,
+            "Update_Date": GBSet[0].GBSeq[0].GBSeq_update_date,
+            "Molecular_Type": GBSet[0].GBSeq[0].GBSeq_moltype,
+            "Length": GBSet[0].GBSeq[0].GBSeq_length,
+            "Topology": GBSet[0].GBSeq[0].GBSeq_topology,
+            "Definition": GBSet[0].GBSeq[0].GBSeq_definition,
+            "Comment": GBSet[0].GBSeq[0].GBSeq_comment,
+            "Features": GBSet[0].GBSeq[0].GBSeq_feature_table.GBFeature.{
+                "key": GBFeature_key,
+                "location": GBFeature_location,
+                "value": 
+                    GBFeature_key in "gene" ? GBFeature_quals.GBQualifier[GBQualifier_name='gene'][0].GBQualifier_value : 
+                    GBFeature_key in "exon" ? GBFeature_quals.GBQualifier[GBQualifier_name='inference'][0].GBQualifier_value :
+                    GBFeature_key in "CDS" ? {
+                        "Codon_Start": GBFeature_quals.GBQualifier[GBQualifier_name='codon_start'][0].GBQualifier_value,
+                        "Protein_Id": GBFeature_quals.GBQualifier[GBQualifier_name='protein_id'][0].GBQualifier_value,
+                        "Translation": GBFeature_quals.GBQualifier[GBQualifier_name='translation'][0].GBQualifier_value
+                    } :
+                    GBFeature_quals.GBQualifier[GBQualifier_name='note'][0].GBQualifier_value 
+            },
+            "Sequence": GBSet[0].GBSeq[0].GBSeq_sequence
+        }`
+    };
+};
+const NCBIProteinTemplate = (id) => {
+    return {
+        db: 'protein',
+        id,
+        retmode: 'xml',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
+        query: `{
+            "Accession_version": GBSet[0].GBSeq[0].GBSeq_accession_version,
+            "Update_Date": GBSet[0].GBSeq[0].GBSeq_update_date,
+            "Molecular_Type": GBSet[0].GBSeq[0].GBSeq_moltype,
+            "Length": GBSet[0].GBSeq[0].GBSeq_length,
+            "Topology": GBSet[0].GBSeq[0].GBSeq_topology,
+            "Definition": GBSet[0].GBSeq[0].GBSeq_definition,
+            "Comment": GBSet[0].GBSeq[0].GBSeq_comment,
+            "Calculated_Mol_Wt": GBSet[0].GBSeq[0].GBSeq_feature_table.GBFeature[GBFeature_key='Protein'][0].GBFeature_quals.GBQualifier[GBQualifier_name='calculated_mol_wt'][0].GBQualifier_value,
+            "Features": GBSet[0].GBSeq[0].GBSeq_feature_table.GBFeature.{
+                "key": GBFeature_key,
+                "location": GBFeature_location,
+                "value": 
+                    GBFeature_key in "Region" ? GBFeature_quals.GBQualifier[GBQualifier_name='region_name'][0].GBQualifier_value & ' ' & GBFeature_quals.GBQualifier[GBQualifier_name='note'][0].GBQualifier_value :
+                    GBFeature_key in "Site" ? GBFeature_quals.GBQualifier[GBQualifier_name='site_type'][0].GBQualifier_value & ' ' & GBFeature_quals.GBQualifier[GBQualifier_name='note'][0].GBQualifier_value : GBFeature_quals.GBQualifier[GBQualifier_name='note'][0].GBQualifier_value 
+            },
+            "Sequence": GBSet[0].GBSeq[0].GBSeq_sequence
+        }`
+    };
+};
+const NCBISNPTemplate = (id) => {
+    return {
+        db: 'snp',
+        id,
+        retmode: 'xml',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
+        query: `**.DocumentSummary.{
+            "ID": SNP_ID,
+            "Accession": ACC ,
+            "Position": $number($split(CHRPOS, ":")[1]),
+            "Classe": FXN_CLASS,
+            "MAF": GLOBAL_MAFS.MAF.{
+                "Study": STUDY,
+                "Frequency": FREQ
+            },
+            "Update_Date": UPDATEDATE
+        }`
+    };
+};
 const getEsearch = new piscina_1.default({
-    filename: path_1.default.resolve(__dirname, './workers/esearch.js')
+    filename: path_1.default.resolve(__dirname, './workers/esearch.js'),
+    maxThreads: 4
 });
 const getGene = (name) => __awaiter(void 0, void 0, void 0, function* () {
     const id = (yield Promise.all([searchGeneTemplate(name)].map(e => getEsearch.run(e))))[0].value.First_ID;
     const result = (yield Promise.all([NCBIGeneTemplate(String(id))].map(e => getEsearch.run(e))))[0].value;
+    const accTranscript = result.Transcript.Accession;
+    const idTr = (yield Promise.all([searchTranscriptTemplate(accTranscript)].map(e => getEsearch.run(e))))[0].value.First_ID;
+    const resultTr = (yield Promise.all([NCBITranscriptTemplate(String(idTr))].map(e => getEsearch.run(e))))[0].value;
+    result.Transcript.nuccore = resultTr;
+    const prot = yield getProtein(result.Products.Accession);
+    result.Products.protein = prot;
     return result;
 });
+const getTranscript = (accession) => __awaiter(void 0, void 0, void 0, function* () {
+    const id = (yield Promise.all([searchTranscriptTemplate(accession)].map(e => getEsearch.run(e))))[0].value.First_ID;
+    const result = (yield Promise.all([NCBITranscriptTemplate(String(id))].map(e => getEsearch.run(e))))[0].value;
+    return result;
+});
+const getProtein = (accession) => __awaiter(void 0, void 0, void 0, function* () {
+    const id = (yield Promise.all([searchProtTemplate(accession)].map(e => getEsearch.run(e))))[0].value.First_ID;
+    const result = (yield Promise.all([NCBIProteinTemplate(String(id))].map(e => getEsearch.run(e))))[0].value;
+    return result;
+});
+const getSNPs = (name) => __awaiter(void 0, void 0, void 0, function* () {
+    const ids = (yield Promise.all([searchSNPTemplate(name)].map(e => getEsearch.run(e))))[0].value;
+    const result = (yield Promise.all(ids.map((id) => NCBISNPTemplate(String(id))).map((e) => getEsearch.run(e))));
+    return result.flatMap(e => e.value);
+});
 (() => __awaiter(void 0, void 0, void 0, function* () {
     // https://www.ncbi.nlm.nih.gov/books/NBK25499/
-    const r = yield getGene('ZFP36L2');
+    // const r = await getSNP('1667092841')
+    // const r = await getProtein('NP_008818')
+    const r = yield getSNPs('ZFP36L2');
     console.log(r);
     yield fs_1.default.promises.writeFile('test.json', JSON.stringify(r));
 }))();

index.ts

@@ -8,6 +8,7 @@ const NCBIGeneTemplate = (id:string) => {
     return {
         db: 'gene',
         id,
+        api_key: '47796c7650360571735f00f510315f871607',
         retmode: 'xml',
         endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
         query: [
@@ -41,10 +42,10 @@ const NCBIGeneTemplate = (id:string) => {
                     }
                 },
                 "Transcript": {
-                    "Accession" : **.'Entrezgene_comments'.'Gene_commentary'[Gene_commentary_heading='NCBI Reference Sequences (RefSeq)'].**.Gene_commentary[Gene_commentary_heading='mRNA Sequence'][0].Gene_commentary_accession,
-                    "Exon_Count": **.'Entrezgene_properties'.'Gene_commentary'[Gene_commentary_label='Exon count'].Gene_commentary_text
+                    "Accession" : **.Entrezgene_comments.Gene_commentary[Gene_commentary_heading='NCBI Reference Sequences (RefSeq)'].**.Gene_commentary[Gene_commentary_heading='mRNA Sequence'][0].Gene_commentary_accession,
+                    "Exon_Count": **.Entrezgene_properties.Gene_commentary[Gene_commentary_label='Exon count'].Gene_commentary_text
                 },
-                "Products": **.'Entrezgene_comments'.'Gene_commentary'[Gene_commentary_heading='NCBI Reference Sequences (RefSeq)'].**.Gene_commentary[Gene_commentary_heading='mRNA Sequence'][0].Gene_commentary_products.Gene_commentary[Gene_commentary_heading='Product'][0].{
+                "Products": **.Entrezgene_comments.Gene_commentary[Gene_commentary_heading='NCBI Reference Sequences (RefSeq)'].**.Gene_commentary[Gene_commentary_heading='mRNA Sequence'][0].Gene_commentary_products.Gene_commentary[Gene_commentary_heading='Product'][0].{
                     "Accession": Gene_commentary_accession,
                     "Domains"  : Gene_commentary_comment.Gene_commentary[Gene_commentary_heading='Conserved Domains'].Gene_commentary_comment.Gene_commentary.{
                         "DB"      : Gene_commentary_source.**.Dbtag_db,
@@ -63,24 +64,164 @@ const searchGeneTemplate = (name:string) => {
     return {
         term: name + '[Gene Name]+AND+Human[Organism]',
         db: 'gene',
+        api_key: '47796c7650360571735f00f510315f871607',
         endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',
-        query: `{"First_ID": **.Id[0]}` 
+        query: `{"First_ID": **.Id[0]}`
+    }
+}
+
+const searchTranscriptTemplate = (accession:string) => {
+    return {
+        term: accession + '+AND+Human[Organism]',
+        db: 'nuccore',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',
+        query: `{"First_ID": **.Id[0]}`
+    }
+}
+
+const searchProtTemplate = (accession:string) => {
+    return {
+        term    : accession + '+AND+Human[Organism]',
+        db      : 'protein',
+        api_key : '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',
+        query   : `{"First_ID": **.Id[0]}`
+    }
+}
+
+const searchSNPTemplate = (accession:string) => {
+    return {
+        term    : accession + '+AND+Human[Organism]',
+        db      : 'snp',
+        api_key : '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',
+        query   : `**.Id`
+    }
+}
+
+const NCBITranscriptTemplate = (id:string) => {
+    return {
+        db: 'nuccore',
+        id,
+        retmode: 'xml',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
+        query : `{
+            "Accession_version": GBSet[0].GBSeq[0].GBSeq_accession_version,
+            "Update_Date": GBSet[0].GBSeq[0].GBSeq_update_date,
+            "Molecular_Type": GBSet[0].GBSeq[0].GBSeq_moltype,
+            "Length": GBSet[0].GBSeq[0].GBSeq_length,
+            "Topology": GBSet[0].GBSeq[0].GBSeq_topology,
+            "Definition": GBSet[0].GBSeq[0].GBSeq_definition,
+            "Comment": GBSet[0].GBSeq[0].GBSeq_comment,
+            "Features": GBSet[0].GBSeq[0].GBSeq_feature_table.GBFeature.{
+                "key": GBFeature_key,
+                "location": GBFeature_location,
+                "value": 
+                    GBFeature_key in "gene" ? GBFeature_quals.GBQualifier[GBQualifier_name='gene'][0].GBQualifier_value : 
+                    GBFeature_key in "exon" ? GBFeature_quals.GBQualifier[GBQualifier_name='inference'][0].GBQualifier_value :
+                    GBFeature_key in "CDS" ? {
+                        "Codon_Start": GBFeature_quals.GBQualifier[GBQualifier_name='codon_start'][0].GBQualifier_value,
+                        "Protein_Id": GBFeature_quals.GBQualifier[GBQualifier_name='protein_id'][0].GBQualifier_value,
+                        "Translation": GBFeature_quals.GBQualifier[GBQualifier_name='translation'][0].GBQualifier_value
+                    } :
+                    GBFeature_quals.GBQualifier[GBQualifier_name='note'][0].GBQualifier_value 
+            },
+            "Sequence": GBSet[0].GBSeq[0].GBSeq_sequence
+        }`
+    }
+}
+
+const NCBIProteinTemplate = (id:string) => {
+    return {
+        db: 'protein',
+        id,
+        retmode: 'xml',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
+        query : `{
+            "Accession_version": GBSet[0].GBSeq[0].GBSeq_accession_version,
+            "Update_Date": GBSet[0].GBSeq[0].GBSeq_update_date,
+            "Molecular_Type": GBSet[0].GBSeq[0].GBSeq_moltype,
+            "Length": GBSet[0].GBSeq[0].GBSeq_length,
+            "Topology": GBSet[0].GBSeq[0].GBSeq_topology,
+            "Definition": GBSet[0].GBSeq[0].GBSeq_definition,
+            "Comment": GBSet[0].GBSeq[0].GBSeq_comment,
+            "Calculated_Mol_Wt": GBSet[0].GBSeq[0].GBSeq_feature_table.GBFeature[GBFeature_key='Protein'][0].GBFeature_quals.GBQualifier[GBQualifier_name='calculated_mol_wt'][0].GBQualifier_value,
+            "Features": GBSet[0].GBSeq[0].GBSeq_feature_table.GBFeature.{
+                "key": GBFeature_key,
+                "location": GBFeature_location,
+                "value": 
+                    GBFeature_key in "Region" ? GBFeature_quals.GBQualifier[GBQualifier_name='region_name'][0].GBQualifier_value & ' ' & GBFeature_quals.GBQualifier[GBQualifier_name='note'][0].GBQualifier_value :
+                    GBFeature_key in "Site" ? GBFeature_quals.GBQualifier[GBQualifier_name='site_type'][0].GBQualifier_value & ' ' & GBFeature_quals.GBQualifier[GBQualifier_name='note'][0].GBQualifier_value : GBFeature_quals.GBQualifier[GBQualifier_name='note'][0].GBQualifier_value 
+            },
+            "Sequence": GBSet[0].GBSeq[0].GBSeq_sequence
+        }`
+    }
+}
+
+const NCBISNPTemplate = (id:string) => {
+    return {
+        db: 'snp',
+        id,
+        retmode: 'xml',
+        api_key: '47796c7650360571735f00f510315f871607',
+        endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
+        query : `**.DocumentSummary.{
+            "ID": SNP_ID,
+            "Accession": ACC ,
+            "Position": $number($split(CHRPOS, ":")[1]),
+            "Classe": FXN_CLASS,
+            "MAF": GLOBAL_MAFS.MAF.{
+                "Study": STUDY,
+                "Frequency": FREQ
+            },
+            "Update_Date": UPDATEDATE
+        }`
     }
 }
 
 const getEsearch = new Piscina({
-    filename: path.resolve(__dirname, './workers/esearch.js')
+    filename: path.resolve(__dirname, './workers/esearch.js'),
+    maxThreads: 4
 })
 
 const getGene = async (name:string) => {
     const id = (await Promise.all([searchGeneTemplate(name)].map(e => getEsearch.run(e))))[0].value.First_ID
     const result = (await Promise.all([NCBIGeneTemplate(String(id))].map(e => getEsearch.run(e))))[0].value
+    const accTranscript = result.Transcript.Accession
+    const idTr = (await Promise.all([searchTranscriptTemplate(accTranscript)].map(e => getEsearch.run(e))))[0].value.First_ID
+    const resultTr = (await Promise.all([NCBITranscriptTemplate(String(idTr))].map(e => getEsearch.run(e))))[0].value
+    result.Transcript.nuccore = resultTr
+    const prot = await getProtein(result.Products.Accession)
+    result.Products.protein = prot
+    return result
+}
+
+const getTranscript = async (accession:string) => {
+    const id = (await Promise.all([searchTranscriptTemplate(accession)].map(e => getEsearch.run(e))))[0].value.First_ID
+    const result = (await Promise.all([NCBITranscriptTemplate(String(id))].map(e => getEsearch.run(e))))[0].value
     return result
 }
 
+const getProtein = async (accession:string) => {
+    const id = (await Promise.all([searchProtTemplate(accession)].map(e => getEsearch.run(e))))[0].value.First_ID
+    const result = (await Promise.all([NCBIProteinTemplate(String(id))].map(e => getEsearch.run(e))))[0].value
+    return result
+}
+
+const getSNPs = async (name:string) => {
+    const ids = (await Promise.all([searchSNPTemplate(name)].map(e => getEsearch.run(e))))[0].value
+    const result = (await Promise.all(ids.map((id:string) => NCBISNPTemplate(String(id))).map((e:any) => getEsearch.run(e))))
+    return result.flatMap(e => e.value)
+}
+
 (async()=>{
     // https://www.ncbi.nlm.nih.gov/books/NBK25499/
-    const r = await getGene('ZFP36L2')
+    // const r = await getSNP('1667092841')
+    // const r = await getProtein('NP_008818')
+    const r = await getSNPs('ZFP36L2')
     console.log(r)
     await fs.promises.writeFile('test.json', JSON.stringify(r))
 })()

workers/esearch.js

@@ -66,17 +66,17 @@ const getEsearch = (params) => __awaiter(void 0, void 0, void 0, function* () {
     let allowedParams;
     let connType = 'get';
     if (endpoint.match('esearch')) {
-        allowedParams = ['db', 'term', 'retmax', 'retstart'];
+        allowedParams = ['db', 'term', 'retmax', 'retstart', 'api_key'];
         params = Object.assign(Object.assign({}, params), { retmax: 100000, retmode: 'xml' });
     }
     else if (endpoint.match('efetch')) {
         connType = 'get';
-        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retmax'];
+        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retmax', 'api_key'];
         const retmode = (params === null || params === void 0 ? void 0 : params.rettype) === 'fasta' || (params === null || params === void 0 ? void 0 : params.rettype) === 'gb' ? 'txt' : 'xml';
         params = Object.assign(Object.assign({}, params), { retmax: 10000, retmode });
     }
     else if (endpoint.match('esummary')) {
-        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retstart', 'version'];
+        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retstart', 'version', 'api_key'];
         params = Object.assign(Object.assign({}, params), { retmax: 10000, retmode: 'xml', version: '2.0' });
     }
     let response = '';
@@ -89,7 +89,18 @@ const getEsearch = (params) => __awaiter(void 0, void 0, void 0, function* () {
         case 'get':
             const q = `${endpoint}?${Object.keys(params).flatMap(k => allowedParams.includes(k) ? k + '=' + params[k] : []).join('&')}`;
             console.log(q);
-            response = yield axios_1.default.get(q);
+            let block = 0;
+            let ctrl = true;
+            while (ctrl && block <= 5) {
+                try {
+                    response = yield axios_1.default.get(q);
+                    ctrl = false;
+                }
+                catch (error) {
+                    console.log(error);
+                }
+                block++;
+            }
         default:
             break;
     }

workers/esearch.ts

@@ -45,15 +45,15 @@ const getEsearch = async (params: any) => {
     let allowedParams: string[]
     let connType: string = 'get'
     if (endpoint.match('esearch')) {
-        allowedParams = ['db', 'term', 'retmax', 'retstart']
+        allowedParams = ['db', 'term', 'retmax', 'retstart', 'api_key']
         params = {...params, retmax: 100000, retmode: 'xml'}
     } else if (endpoint.match('efetch')) {
         connType = 'get'
-        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retmax']
+        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retmax', 'api_key']
         const retmode = params?.rettype === 'fasta' || params?.rettype === 'gb'? 'txt' : 'xml'
         params = {...params, retmax: 10000, retmode}
     } else if (endpoint.match('esummary')) {
-        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retstart', 'version']
+        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retstart', 'version', 'api_key']
         params = {...params, retmax: 10000, retmode: 'xml', version: '2.0'}
     }
 
@@ -67,7 +67,18 @@ const getEsearch = async (params: any) => {
         case 'get':
             const q = `${endpoint}?${Object.keys(params).flatMap(k => allowedParams.includes(k) ? k + '=' + params[k] : []).join('&')}`
             console.log(q);
-            response = await axios.get(q)
+            let block = 0
+            let ctrl = true
+            while(ctrl && block <= 5) {
+                try {
+                    response = await axios.get(q)
+                    ctrl = false
+                } catch (error) {}
+                block++
+                if(block === 6) {
+                    console.log("Dropping !!! ", q);
+                }
+            }
         default:
             break;
     }