@apollo-annotation/cli 1.1.0 → 1.1.2

package/dist/commands/feature/delete.d.ts

@@ -3,10 +3,11 @@ export default class Delete extends BaseCommand<typeof Delete> {
     static summary: string;
     static description: string;
     static flags: {
-        'feature-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[], import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        force: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
-        'dry-run': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        'feature-id': import("@oclif/core/interfaces").OptionFlag<string[], import("@oclif/core/interfaces").CustomOptions>;
+        force: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        'dry-run': import("@oclif/core/interfaces").BooleanFlag<boolean>;
     };
     run(): Promise<void>;
+    private deleteFeature;
 }
 //# sourceMappingURL=delete.d.ts.map

package/dist/commands/feature/delete.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"delete.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/delete.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW,CAAC,OAAO,MAAM,CAAC;IAC5D,MAAM,CAAC,OAAO,SAAsC;IACpD,MAAM,CAAC,WAAW,SACiG;IAEnH,MAAM,CAAC,KAAK;;;;MAeX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YA0BnB,aAAa;CAkB5B"}

package/dist/commands/feature/delete.js

@@ -1,37 +1,6 @@
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
-async function deleteFeature(address, accessToken, feature) {
-    const changeJson = {
-        typeName: 'DeleteFeatureChange',
-        changedIds: [feature._id],
-        assembly: '111222333444555666777888', // Use a placeholder objectId (i.e. some 24 chars)
-        deletedFeature: {
-            _id: feature._id,
-            refSeq: feature.refSeq,
-            type: feature.type,
-            min: feature.min,
-            max: feature.max,
-            attributes: feature.attributes,
-        },
-    };
-    const url = new URL(localhostToAddress(`${address}/changes`));
-    const auth = {
-        method: 'POST',
-        body: JSON.stringify(changeJson),
-        headers: {
-            authorization: `Bearer ${accessToken}`,
-            'Content-Type': 'application/json',
-        },
-    };
-    const response = await fetch(url, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'deleteFeature failed');
-        throw new Error(errorMessage);
-    }
-    return response;
-}
+import { idReader } from '../../utils.js';
 export default class Delete extends BaseCommand {
     static summary = 'Delete one or more features by ID';
     static description = 'Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.';
@@ -58,28 +27,38 @@ export default class Delete extends BaseCommand {
         for (const x of tmpIds) {
             featureIds.add(x);
         }
-        const access = await this.getAccess();
         for (const featureId of featureIds) {
-            const res = await getFeatureById(access.address, access.accessToken, featureId);
-            if (res.status === 404 && flags.force) {
-                continue;
-            }
-            if (!res.ok) {
-                const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
-                throw new Error(errorMessage);
+            const response = await this.fetchWithoutCheck(`features/${featureId}`);
+            if (!response.ok) {
+                if (response.status === 404 && flags.force) {
+                    continue;
+                }
+                await this.check(response);
             }
-            const feature = JSON.parse(await res.text());
+            const feature = (await response.json());
             if (flags['dry-run']) {
                 this.log(JSON.stringify(feature, null, 2));
             }
             else {
-                const delFet = await deleteFeature(access.address, access.accessToken, feature);
-                if (!delFet.ok) {
-                    const errorMessage = await createFetchErrorMessage(delFet, 'Delete feature failed');
-                    throw new Error(errorMessage);
-                }
+                await this.deleteFeature(feature);
             }
         }
     }
+    async deleteFeature(feature) {
+        const changeJson = {
+            typeName: 'DeleteFeatureChange',
+            changedIds: [feature._id],
+            assembly: '111222333444555666777888', // Use a placeholder objectId (i.e. some 24 chars)
+            deletedFeature: {
+                _id: feature._id,
+                refSeq: feature.refSeq,
+                type: feature.type,
+                min: feature.min,
+                max: feature.max,
+                attributes: feature.attributes,
+            },
+        };
+        await this.post('changes', JSON.stringify(changeJson));
+    }
 }
 //# sourceMappingURL=delete.js.map

package/dist/commands/feature/delete.js.map

@@ -1 +1 @@
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+{"version":3,"file":"delete.js","sourceRoot":"","sources":["../../../src/commands/feature/delete.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAA0B;IAC5D,MAAM,CAAC,OAAO,GAAG,mCAAmC,CAAA;IACpD,MAAM,CAAC,WAAW,GAChB,iHAAiH,CAAA;IAEnH,MAAM,CAAC,KAAK,GAAG;QACb,YAAY,EAAE,KAAK,CAAC,MAAM,CAAC;YACzB,IAAI,EAAE,GAAG;YACT,OAAO,EAAE,CAAC,GAAG,CAAC;YACd,WAAW,EAAE,uBAAuB;YACpC,QAAQ,EAAE,IAAI;SACf,CAAC;QACF,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC;YACnB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,8BAA8B;SAC5C,CAAC;QACF,SAAS,EAAE,KAAK,CAAC,OAAO,CAAC;YACvB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,gCAAgC;SAC9C,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE1C,MAAM,MAAM,GAAG,MAAM,QAAQ,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,CAAA;QAClD,MAAM,UAAU,GAAG,IAAI,GAAG,EAAU,CAAA;QACpC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;YACvB,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;QACnB,CAAC;QAED,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;YACnC,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,iBAAiB,CAAC,YAAY,SAAS,EAAE,CAAC,CAAA;YACtE,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,IAAI,KAAK,CAAC,KAAK,EAAE,CAAC;oBAC3C,SAAQ;gBACV,CAAC;gBACD,MAAM,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAA;YAC5B,CAAC;YACD,MAAM,OAAO,GAAG,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAA8B,CAAA;YACpE,IAAI,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBACrB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;YAC5C,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;IACH,CAAC;IAEO,KAAK,CAAC,aAAa,CACzB,OAAkC;QAElC,MAAM,UAAU,GAAkC;YAChD,QAAQ,EAAE,qBAAqB;YAC/B,UAAU,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC;YACzB,QAAQ,EAAE,0BAA0B,EAAE,kDAAkD;YACxF,cAAc,EAAE;gBACd,GAAG,EAAE,OAAO,CAAC,GAAG;gBAChB,MAAM,EAAE,OAAO,CAAC,MAAM;gBACtB,IAAI,EAAE,OAAO,CAAC,IAAI;gBAClB,GAAG,EAAE,OAAO,CAAC,GAAG;gBAChB,GAAG,EAAE,OAAO,CAAC,GAAG;gBAChB,UAAU,EAAE,OAAO,CAAC,UAAU;aAC/B;SACF,CAAA;QACD,MAAM,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CAAA;IACxD,CAAC"}

package/dist/commands/feature/edit-attribute.d.ts

@@ -7,10 +7,10 @@ export default class EditAttibute extends BaseCommand<typeof EditAttibute> {
         command: string;
     }[];
     static flags: {
-        'feature-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        attribute: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        value: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[] | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        delete: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        'feature-id': import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+        attribute: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+        value: import("@oclif/core/interfaces").OptionFlag<string[] | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        delete: import("@oclif/core/interfaces").BooleanFlag<boolean>;
     };
     run(): Promise<void>;
 }

package/dist/commands/feature/edit-attribute.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"edit-attribute.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/edit-attribute.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,WAAW,CAAC,OAAO,YAAY,CAAC;IACxE,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SAGQ;IAE1B,MAAM,CAAC,QAAQ;;;QAcd;IAED,MAAM,CAAC,KAAK;;;;;MAqBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAwDlC"}

package/dist/commands/feature/edit-attribute.js

@@ -1,7 +1,6 @@
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class EditAttibute extends BaseCommand {
     static summary = 'Add, edit, or view a feature attribute';
     static description = 'Be aware that there is no checking whether attributes names and values are valid. \
@@ -52,13 +51,7 @@ terms to non-existing terms';
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess();
-        const response = await getFeatureById(access.address, access.accessToken, featureId);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');
-            throw new Error(errorMessage);
-        }
-        const featureJson = JSON.parse(await response.text());
+        const featureJson = await this.getFeatureById(featureId);
         featureJson.attributes ??= {};
         const oldAttributes = {};
         for (const [key, val] of Object.entries(featureJson.attributes)) {
@@ -85,7 +78,7 @@ terms to non-existing terms';
         else {
             throw new Error(`Unexpected condition: value is "${flags.value}"`);
         }
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
+        const assembly = await this.getAssemblyFromRefseq(featureJson.refSeq);
         const changeJson = {
             typeName: 'FeatureAttributeChange',
             changedIds: [featureId],
@@ -94,20 +87,7 @@ terms to non-existing terms';
             oldAttributes,
             newAttributes,
         };
-        const url = new URL(localhostToAddress(`${access.address}/changes`));
-        const auth = {
-            method: 'POST',
-            body: JSON.stringify(changeJson),
-            headers: {
-                authorization: `Bearer ${access.accessToken}`,
-                'Content-Type': 'application/json',
-            },
-        };
-        const res = await fetch(url, auth);
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'edit-attribute failed');
-            throw new Error(errorMessage);
-        }
+        await this.post('changes', JSON.stringify(changeJson));
     }
 }
 //# sourceMappingURL=edit-attribute.js.map

package/dist/commands/feature/edit-attribute.js.map

@@ -1 +1 @@
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package/dist/commands/feature/edit-coords.d.ts

@@ -7,9 +7,9 @@ export default class Get extends BaseCommand<typeof Get> {
         command: string;
     }[];
     static flags: {
-        'feature-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        start: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        end: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'feature-id': import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+        start: import("@oclif/core/interfaces").OptionFlag<number | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        end: import("@oclif/core/interfaces").OptionFlag<number | undefined, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
 }

package/dist/commands/feature/edit-coords.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"edit-coords.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/edit-coords.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAA8C;IAC5D,MAAM,CAAC,WAAW,SAEwF;IAE1G,MAAM,CAAC,QAAQ;;;QASd;IAED,MAAM,CAAC,KAAK;;;;MAcX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAoFlC"}

package/dist/commands/feature/edit-coords.js

@@ -1,7 +1,6 @@
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Edit feature start and/or end coordinates';
     static description = "If editing a child feature that new coordinates must be within the parent's coordinates.\
@@ -52,14 +51,8 @@ To get the identifier of the feature to edit consider using `apollo feature get`
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess();
-        const res = await getFeatureById(access.address, access.accessToken, featureId);
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
-            throw new Error(errorMessage);
-        }
-        const featureJson = JSON.parse(await res.text());
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
+        const featureJson = await this.getFeatureById(featureId);
+        const assembly = await this.getAssemblyFromRefseq(featureJson.refSeq);
         const currentEnd = featureJson.max;
         let edit = ['Start', 'End'];
         if (flags.start !== undefined && flags.start > currentEnd) {
@@ -102,20 +95,7 @@ To get the identifier of the feature to edit consider using `apollo feature get`
             else {
                 throw new Error(`Unexpected coordinate name: "${coord}"`);
             }
-            const url = new URL(localhostToAddress(`${access.address}/changes`));
-            const auth = {
-                method: 'POST',
-                body: JSON.stringify(body),
-                headers: {
-                    authorization: `Bearer ${access.accessToken}`,
-                    'Content-Type': 'application/json',
-                },
-            };
-            const response = await fetch(url, auth);
-            if (!response.ok) {
-                const errorMessage = await createFetchErrorMessage(response, 'edit-coords failed');
-                throw new Error(errorMessage);
-            }
+            await this.post('changes', JSON.stringify(body));
         }
     }
 }

package/dist/commands/feature/edit-coords.js.map

@@ -1 +1 @@
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package/dist/commands/feature/edit-type.d.ts

@@ -3,8 +3,8 @@ export default class Get extends BaseCommand<typeof Get> {
     static summary: string;
     static description: string;
     static flags: {
-        'feature-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        type: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'feature-id': import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+        type: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
 }

package/dist/commands/feature/edit-type.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"edit-type.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/edit-type.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAA8B;IAC5C,MAAM,CAAC,WAAW,SAEiF;IAEnG,MAAM,CAAC,KAAK;;;MAWX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAoClC"}

package/dist/commands/feature/edit-type.js

@@ -1,7 +1,6 @@
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Edit or view feature type';
     static description = 'Feature type is column 3 in gff format.\
@@ -24,13 +23,7 @@ It must be a valid sequence ontology term although but the valifdity of the new
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess();
-        const response = await getFeatureById(access.address, access.accessToken, featureId);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');
-            throw new Error(errorMessage);
-        }
-        const featureJson = JSON.parse(await response.text());
+        const featureJson = await this.getFeatureById(featureId);
         const currentType = featureJson.type;
         if (flags.type === undefined) {
             this.log(currentType);
@@ -40,7 +33,7 @@ It must be a valid sequence ontology term although but the valifdity of the new
             this.logToStderr(`NOTE: Feature ${featureId} is already of type "${flags.type}"`);
             return;
         }
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
+        const assembly = await this.getAssemblyFromRefseq(featureJson.refSeq);
         const changeJson = {
             typeName: 'TypeChange',
             changedIds: [featureId],
@@ -49,20 +42,7 @@ It must be a valid sequence ontology term although but the valifdity of the new
             oldType: currentType,
             newType: flags.type,
         };
-        const url = new URL(localhostToAddress(`${access.address}/changes`));
-        const auth = {
-            method: 'POST',
-            body: JSON.stringify(changeJson),
-            headers: {
-                authorization: `Bearer ${access.accessToken}`,
-                'Content-Type': 'application/json',
-            },
-        };
-        const res = await fetch(url, auth);
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'edit-type failed');
-            throw new Error(errorMessage);
-        }
+        await this.post('changes', JSON.stringify(changeJson));
     }
 }
 //# sourceMappingURL=edit-type.js.map

package/dist/commands/feature/edit-type.js.map

@@ -1 +1 @@
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+{"version":3,"file":"edit-type.js","sourceRoot":"","sources":["../../../src/commands/feature/edit-type.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAuB;IACtD,MAAM,CAAC,OAAO,GAAG,2BAA2B,CAAA;IAC5C,MAAM,CAAC,WAAW,GAChB;qGACiG,CAAA;IAEnG,MAAM,CAAC,KAAK,GAAG;QACb,YAAY,EAAE,KAAK,CAAC,MAAM,CAAC;YACzB,IAAI,EAAE,GAAG;YACT,OAAO,EAAE,GAAG;YACZ,WAAW,EAAE,iDAAiD;SAC/D,CAAC;QACF,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC;YACjB,IAAI,EAAE,GAAG;YACT,WAAW,EACT,+DAA+D;SAClE,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAEvC,MAAM,EAAE,GAAG,MAAM,QAAQ,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAChD,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACpB,IAAI,CAAC,KAAK,CAAC,6CAA6C,EAAE,CAAC,MAAM,EAAE,CAAC,CAAA;QACtE,CAAC;QACD,MAAM,CAAC,SAAS,CAAC,GAAG,EAAE,CAAA;QAEtB,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;QAExD,MAAM,WAAW,GAAG,WAAW,CAAC,IAAI,CAAA;QACpC,IAAI,KAAK,CAAC,IAAI,KAAK,SAAS,EAAE,CAAC;YAC7B,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;YACrB,OAAM;QACR,CAAC;QACD,IAAI,KAAK,CAAC,IAAI,KAAK,WAAW,EAAE,CAAC;YAC/B,IAAI,CAAC,WAAW,CACd,iBAAiB,SAAS,wBAAwB,KAAK,CAAC,IAAI,GAAG,CAChE,CAAA;YACD,OAAM;QACR,CAAC;QAED,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,qBAAqB,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAErE,MAAM,UAAU,GAAyB;YACvC,QAAQ,EAAE,YAAY;YACtB,UAAU,EAAE,CAAC,SAAS,CAAC;YACvB,QAAQ;YACR,SAAS;YACT,OAAO,EAAE,WAAW;YACpB,OAAO,EAAE,KAAK,CAAC,IAAI;SACpB,CAAA;QAED,MAAM,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CAAA;IACxD,CAAC"}

package/dist/commands/feature/edit.d.ts

@@ -7,7 +7,7 @@ export default class Get extends BaseCommand<typeof Get> {
         command: string;
     }[];
     static flags: {
-        'json-input': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'json-input': import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
 }

package/dist/commands/feature/edit.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"edit.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/edit.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAOlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAAiD;IAC/D,MAAM,CAAC,WAAW,SAad;IAEJ,MAAM,CAAC,QAAQ;;;QAMd;IAED,MAAM,CAAC,KAAK;;MAMX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAuClC"}
+{"version":3,"file":"edit.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/edit.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAAiD;IAC/D,MAAM,CAAC,WAAW,SAad;IAEJ,MAAM,CAAC,QAAQ;;;QAMd;IAED,MAAM,CAAC,KAAK;;MAMX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAmBlC"}

package/dist/commands/feature/edit.js

@@ -1,9 +1,8 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import * as fs from 'node:fs';
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, localhostToAddress, readStdin, } from '../../utils.js';
+import { readStdin } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Edit features using an appropiate json input';
     static description = `Edit a feature by submitting a json input with all the required attributes for Apollo to process it. This is a very low level command which most users probably do not need.
@@ -46,23 +45,8 @@ export default class Get extends BaseCommand {
         if (!Array.isArray(json)) {
             json = [json];
         }
-        const access = await this.getAccess();
         for (const change of json) {
-            const str = JSON.stringify(change);
-            const url = new URL(localhostToAddress(`${access.address}/changes`));
-            const auth = {
-                method: 'POST',
-                body: str,
-                headers: {
-                    authorization: `Bearer ${access.accessToken}`,
-                    'Content-Type': 'application/json',
-                },
-            };
-            const response = await fetch(url, auth);
-            if (!response.ok) {
-                const errorMessage = await createFetchErrorMessage(response, 'edit failed');
-                throw new Error(errorMessage);
-            }
+            await this.post('changes', JSON.stringify(change));
         }
     }
 }

package/dist/commands/feature/edit.js.map

@@ -1 +1 @@
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+{"version":3,"file":"edit.js","sourceRoot":"","sources":["../../../src/commands/feature/edit.ts"],"names":[],"mappings":"AAAA,4DAA4D;AAC5D,OAAO,KAAK,EAAE,MAAM,SAAS,CAAA;AAE7B,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAA;AAE1C,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAuB;IACtD,MAAM,CAAC,OAAO,GAAG,8CAA8C,CAAA;IAC/D,MAAM,CAAC,WAAW,GAAG;;;;;;;;;;;;;MAajB,CAAA;IAEJ,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,qCAAqC;YAClD,OAAO,EACL,8FAA8F;SACjG;KACF,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,YAAY,EAAE,KAAK,CAAC,MAAM,CAAC;YACzB,IAAI,EAAE,GAAG;YACT,OAAO,EAAE,GAAG;YACZ,WAAW,EAAE,yDAAyD;SACvE,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAEvC,IAAI,OAAO,GAAG,KAAK,CAAC,YAAY,CAAC,CAAA;QACjC,IAAI,KAAK,CAAC,YAAY,CAAC,KAAK,GAAG,EAAE,CAAC;YAChC,OAAO,GAAG,MAAM,SAAS,EAAE,CAAA;QAC7B,CAAC;aAAM,IAAI,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC;YAC9C,OAAO,GAAG,EAAE,CAAC,YAAY,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAA;QAC3D,CAAC;QAED,IAAI,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;QAC9B,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YACzB,IAAI,GAAG,CAAC,IAAI,CAAC,CAAA;QACf,CAAC;QAED,KAAK,MAAM,MAAM,IAAI,IAAI,EAAE,CAAC;YAC1B,MAAM,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAA;QACpD,CAAC;IACH,CAAC"}

package/dist/commands/feature/get-id.d.ts

@@ -7,7 +7,7 @@ export default class Get extends BaseCommand<typeof Get> {
         command: string;
     }[];
     static flags: {
-        'feature-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[], import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'feature-id': import("@oclif/core/interfaces").OptionFlag<string[], import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
     private getFeatureId;

package/dist/commands/feature/get-id.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-id.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/get-id.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAOlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAAyC;IACvD,MAAM,CAAC,WAAW,SACuE;IAEzF,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,KAAK;;MAQX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YAuBnB,YAAY;CAyB3B"}
+{"version":3,"file":"get-id.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/get-id.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAAyC;IACvD,MAAM,CAAC,WAAW,SACuE;IAEzF,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,KAAK;;MAQX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YAiBnB,YAAY;CAU3B"}

package/dist/commands/feature/get-id.js

@@ -1,7 +1,6 @@
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, idReader, localhostToAddress, } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Get features given their identifiers';
     static description = 'Invalid identifiers or identifiers not found in the database will be silently ignored';
@@ -21,12 +20,11 @@ export default class Get extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Get);
-        const access = await this.getAccess();
         let ids = await idReader(flags['feature-id']);
         ids = [...new Set(ids)];
         const results = [];
         for (const id of ids) {
-            const res = await this.getFeatureId(access.address, access.accessToken, id);
+            const res = await this.getFeatureId(id);
             if (Object.keys(res).length === 0) {
                 continue;
             }
@@ -34,21 +32,13 @@ export default class Get extends BaseCommand {
         }
         this.log(JSON.stringify(results, null, 2));
     }
-    async getFeatureId(address, token, featureId) {
-        const url = new URL(localhostToAddress(`${address}/features/${featureId}`));
-        const auth = {
-            headers: {
-                authorization: `Bearer ${token}`,
-                'Content-Type': 'application/json',
-            },
-        };
-        const response = await fetch(url, auth);
+    async getFeatureId(featureId) {
+        const response = await this.fetchWithoutCheck(`features/${featureId}`);
         if (!response.ok) {
             if (response.status === 404) {
                 return {};
             }
-            const errorMessage = await createFetchErrorMessage(response, 'Failed to access Apollo with the current address and/or access token\nThe server returned:\n');
-            throw new Error(errorMessage);
+            await this.check(response);
         }
         return (await response.json());
     }

package/dist/commands/feature/get-id.js.map

@@ -1 +1 @@
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package/dist/commands/feature/get-indexed-id.d.ts

@@ -7,11 +7,11 @@ export default class Get extends BaseCommand<typeof Get> {
         command: string;
     }[];
     static args: {
-        id: import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+        id: import("@oclif/core/interfaces").Arg<string, Record<string, unknown>>;
     };
     static flags: {
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[] | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        topLevel: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string[] | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        topLevel: import("@oclif/core/interfaces").BooleanFlag<boolean>;
     };
     run(): Promise<void>;
 }

package/dist/commands/feature/get-indexed-id.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"get-indexed-id.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/get-indexed-id.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAA6C;IAC3D,MAAM,CAAC,WAAW,SAC4F;IAE9G,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,IAAI;;MAKV;IAED,MAAM,CAAC,KAAK;;;MAWX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA4BlC"}

package/dist/commands/feature/get-indexed-id.js

@@ -1,7 +1,6 @@
 import { Args, Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Get features given an indexed identifier';
     static description = 'Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file';
@@ -29,17 +28,14 @@ export default class Get extends BaseCommand {
     };
     async run() {
         const { args, flags } = await this.parse(Get);
-        const access = await this.getAccess();
         const { topLevel } = flags;
         const { id } = args;
         const assembly = flags.assembly && (await idReader(flags.assembly));
-        const assemblyIds = assembly &&
-            (await convertAssemblyNameToId(access.address, access.accessToken, assembly));
+        const assemblyIds = assembly && (await this.convertAssemblyNameToId(assembly));
         if (assemblyIds?.length === 0) {
             this.log(JSON.stringify([], null, 2));
             this.exit(0);
         }
-        const url = new URL(localhostToAddress(`${access.address}/features/getByIndexedId`));
         const searchParams = new URLSearchParams({ id });
         if (assemblyIds) {
             searchParams.append('assemblies', assemblyIds.join(','));
@@ -47,20 +43,7 @@ export default class Get extends BaseCommand {
         if (topLevel) {
             searchParams.append('topLevel', 'true');
         }
-        url.search = searchParams.toString();
-        const uri = url.toString();
-        const auth = {
-            headers: {
-                authorization: `Bearer ${access.accessToken}`,
-                'Content-Type': 'application/json',
-            },
-        };
-        const response = await fetch(uri, auth);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'Failed to access Apollo with the current address and/or access token\nThe server returned:\n');
-            throw new Error(errorMessage);
-        }
-        const results = (await response.json());
+        const results = await this.get(`features/getByIndexedId?${searchParams.toString()}`);
         this.log(JSON.stringify(results, null, 2));
     }
 }