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"style-loader": "^0.13.1", @@ -83,9 +82,6 @@ "query-string": "^4.1.0", "react": "^16.8.6", "react-dom": "^16.8.6", - "react-redux": "^5.0.7", - "redux": "^3.7.2", - "redux-thunk": "^2.3.0", "scriptjs": "^2.5.7", "source-map-support": "^0.4.11", "subprocess-middleware": "^0.1.0", diff --git a/src/encoded/docs/making_audits.md b/src/encoded/docs/making_audits.md deleted file mode 100644 index 8193da563e..0000000000 --- a/src/encoded/docs/making_audits.md +++ /dev/null @@ -1,78 +0,0 @@ -Adding audits -========================= - -This document describes how to add and update audits that check metadata consistency and integrity. - -Guide to where to edit Source Code ----------------- - -* **src** directory - contains all the python and javascript code for front and backends - * **audit** - python instructions for checking metadata stored in the schema - * **schemas** - JSON schemas ([JSONSchema], [JSON-LD]) describing allowed types and values for all metadata objects - * **tests** - Unit and integration tests - * **types** - business logic for dispatching URLs and producing the correct JSON - * **upgrade** - python instructions for upgrading old objects stored to the latest - * **loadxl.py** - python script that defines the schema objects to load - ------ - -Adding a new aduit ----------------- - -1. To add a new audit, navigate to the *audit** directory. Determine what metadata is needed to implement the consistency and integrity check. This helps to determine which object has the appropriate metadata available and where to place the new audit. In the directory make a new python file or edit an exisiting python file named after the determined object. - -2. Make a new audit definition, using the metadata needed as a guide to fall into one these 2 categories: - - * *Contained in an object* - all metadata need for audit are properties of the object where embedded -objects referred to by an identifier: - - @audit_checker('{metadata_object}', frame='object') - def audit_new_audit_name(value, system): - ''' - Description of audit - ''' - pass - - * *Requires metadata in other objects* - metadata need for audit are properties of the object as well as properoties within embedded objects: - - @audit_checker('{metadata_object}', frame=['{linked_object_1}']) - def audit_new_audit_name(value, system): - ''' - Description of audit - ''' - pass - -3. Write the logic for the metadata check and determine what the ```AuditFailure``` human readable name when displayed on faceted search and the details of the audit to be displayed. Also determine which of the following 4 categories this audit should fall into: - - * *ERROR* - This is wrong no matter what. Example: term mismatch - * *NOT COMPLIANT* - This should not be released this way. Example: in progress ChIP experiment with no control - * *WARNING* - Informational warning. Example: This library is paired end but the replicate is single end. - * *DCC ACTION* - DCC needs to update metadata or code to fix. Example NTRs. - - Example of ```library``` where RNA library should have a size_range specified : - - RNAs = ['SO:0000356', 'SO:0000871'] - - if (value['nucleic_acid_term_id'] in RNAs) and ('size_range' not in value): - detail = 'RNA library {} requires a value for size_range'.format(value['accession']) - raise AuditFailure('missing size_range', detail, level='ERROR') - - -4. In the **tests** directory add audit test to an existing/new python file named ```test_audit_{metadata_object}.py```. This example shows the basic structure of setting up ```pytest.fixture``` and test that ```property_1``` is present if ```property_2``` is RNA: - - @pytest.fixture - def {metadata_object}_1: - item = { - 'property_2': 'RNA', - } - return testapp.post_json('/{metadata_object}', item, status=201).json['@graph'][0] - - - def test_{metadata_object}_property_1(testapp, {metadata_object}_1): - res = testapp.get({metadata_object}_1['@id'] + '@@index-data') - errors = res.json['audit'] - errors_list = [] - for error_type in errors: - errors_list.extend(errors[error_type]) - assert any(error['category'] == 'missing prperty 1' for error in errors_list) - diff --git a/src/encoded/docs/schema-changes.md b/src/encoded/docs/schema-changes.md deleted file mode 100644 index db175b35d2..0000000000 --- a/src/encoded/docs/schema-changes.md +++ /dev/null @@ -1,244 +0,0 @@ -Making changes to encoded schemas -========================= - -This document describes how to make changes to the JSON schemas ([JSONSchema], [JSON-LD]) and source code that describes the encoded metadata model. For overview of code organization see [overview.rst]. - -Guide to where to edit Source Code ----------------- - -* **src** directory - contains all the python and javascript code for front and backends - * **audit** - python instructions for checking metadata stored in the schema - * **schemas** - JSON schemas ([JSONSchema], [JSON-LD]) describing allowed types and values for all metadata objects - * **tests** - Unit and integration tests - * **types** - business logic for dispatching URLs and producing the correct JSON - * **upgrade** - python instructions for upgrading old objects stored to the latest - * **loadxl.py** - python script that defines the schema objects to load - - ------ - -Adding a new schema ----------------- - -1. To add a new schema navigate to the **schemas** directory and make a new JSON file named after the object. Populate the file with basic schema definition: - - - { - "title": {Metadata Object}, - "description": "Description of the metadata that this object aims to capture.", - "id": "/profiles/{metadata object}.json", - "$schema": "http://json-schema.org/draft-04/schema#", - "identifyingProperties": ["uuid"], - "additionalProperties": false, - "mixinProperties": [ - { "$ref": "mixins.json#/schema_version" }, - { "$ref": "mixins.json#/uuid" } - ], - "type": "object", - "properties": { - "schema_version": { - "default": "1" - } - } - } - - -2. Add appropriate properties in the properties block. Example of different property types: - - { - "example_string": { - "title": "Example string", - "description": "An example of a free text property.", - "type": "string" - }, - "example_number": { - "title": "Example number", - "description": "An example of a free text property.", - "type": "integer" - }, - "example_enum": { - "title": "Example enum", - "description": "An example of a property with enumerated values.", - "type": "string", - "enum": [ - "option 1", - "option 2", - "option 3" - ] - }, - "example_pattern": { - "title": "Example string with pattern", - "description": "An example of a property that must match a pattern", - "type": "string", - "pattern": "^[\\S\\s\\d\\-\\(\\)\\+]+$" - } - } - - -3. Identify all required properties to make an object and add to the "required" array, for treatment we have:: - - - "required": ["treatment_term_name", "treatment_type"] - - -4. In the **types** directory add a collection class for the object to define the rendering of the object. -Refer to [object-lifecycle.rst] to understand object rendering. Example of basic collection definition for treatments:: - - - @collection( - name='treatments', - properties={ - 'title': 'Treatments', - 'description': 'Listing Biosample Treatments', - } - ) - class Treatment(Item): - item_type = 'treatment' - schema = load_schema('encoded:schemas/treatment.json') - - -5. Within in a class add in *embedding*, *reverse links*, and *calculated properties* as necessary. - - * *Embedding* - specifying the properties embeded in the object when specifying ```frame=object```, for construct we have: - - embedded = ['target'] - - * *Reverse links* - specifying the links that are back calculated from an object that ```linkTo``` this object, for file we have: - - rev = { - 'paired_with': ('File', 'paired_with'), - 'quality_metrics': ('QualityMetric', 'quality_metric_of'), - 'superseded_by': ('File', 'supersedes'), - } - - * *Calculated properties* - dynamically calculated before rendering of an object, for platforms we calculate the title: - - @calculated_property(schema={ - "title": "Title", - "type": "string", - }) - def title(self, term_name): - return term_name - -6. In ``loadxl.py`` add the new metadata object into the ```Order``` array, for example to add new object ```train.json```:: - - ORDER = [ - 'user', - 'award', - 'lab', - 'organism', - 'source', - ... - 'train', - ] - -7. Add in sample data to test the new schema in **tests** directory. Create a new JSON file in the **data/inserts** directory named after the new metadata object. -This new object is an array of example objects that can successfully POST against the schema defined, for example :: - - [ - { - "property_1": "value 1", - "property_2": 10, - "uuid": "1a594ade-218a-4697-9ee1-a3ab50024dfa" - }, - { - "property_1": "value 2", - "property_2": 100, - "uuid": "0137a084-57af-4f69-b756-d6a920393fde" - } - -8. If applicable you may want to add audits on the metadata. Please refer to [making_audits] - ------ - -Updating an existing schema ----------------- - -There are 2 categories when we talk about updating an existing schema: - -* No affect on schema version -* Update schema version - - -**The schema version is updated, requiring an upgrade of the schema, when the objects stored in the database will not validate and POST to the updated schema.** - - -### No affect on schema version - -1. In the **schemas** directory, make edits to properties in the JSON file named after the object. - -2. In the **types** directory, make appropriate updates to object class by adding *embedding*, *reverse links*, and *calculated properties* as necessary. - -3. Update sample data, **data/inserts** directory, to test the changes made to the schema in **tests** directory. - - -### Update schema version - -1. In the **schemas** directory, increment the schema version (1->2), if it meets the above rule: - - "schema_version": { - "default": "2" - } - -2. In the **upgrade** directory add an ```upgrade_step``` to an existing/new python file named after the object. An example upgrades the object from schema version (2->3): - - @upgrade_step('{metadata_object}', '2, '3') - def {metadata_object}_2_3(value, system): - # {Redmine Issue} - - # lowercase all values in property 1 - if 'property_1' in value: - value['property_1'] = value['property_1'].lower() - -3. In the **tests** directory add upgrade test to an existing/new python file named ```test_upgrade_{metadata_object}.py```. This example shows the basic structure of setting up ```pytest.fixture``` and upgrade to ```property_1```: - - - @pytest.fixture - def {metadata_object}(): - return{ - "property_1": "Value 1", - "property_2": 10, - } - - - @pytest.fixture - def {metadata_object}_2({metadata_object}): - item = {metadata_object}.copy() - item.update({ - 'schema_version': '2', - }) - return item - - - def test_{metadata_object}_lowercase_property_1(app, {metadata_object}_2): - migrator = app.registry['migrator'] - value = migrator.upgrade('{metadata_object}', {metadata_object}_2, target_version='3') - assert value['schema_version'] == '3' - assert value['property_1'] == 'value 1' - -5. You must check the results of your upgrade on the current database: - - **note** it is possible to write a "bad" upgrade that does not prevent your objects from loading or being shown. - - You can check using the following methods: - * Checking for errors in the /var/log/cloud-init-output.log (search for "batchupgrade" a few times) in any demo with your upgrade, this can be done about 30min after launch (after machine reboots post-install), no need to wait for the indexing to complete. - * Looking at the JSON for an object that should be upgraded by checking it's schema_version property. - * Updating and object and looking in the /var/log/apache2/error.log for stack traces. - - It is also possible that an upgrade can be clean under a current database but new objects POSTed before release are broken, so it will be checked again during release. - -6. If applicable you may need to update audits on the metadata. Please refer to [making_audits] - -7. To document all the schema changes that occurred between increments of the ```schema_version``` update the object changelogs the **schemas/changelogs** directory. Below is an example of the changelog for above upgrade: - - Schema version 2 - ---------------- - - * *property_1* values were changed to all lower case - - -[JSONSchema]: http://json-schema.org/ -[JSON-LD]: http://json-ld.org/ -[overview.rst]: ../../../docs/overview.rst -[object-lifecycle.rst]: ../../../docs/object-lifecycle.rst -[making_audits]: making_audits.md diff --git a/src/encoded/docs/updating_ontologies.md b/src/encoded/docs/updating_ontologies.md deleted file mode 100644 index a1648ac41b..0000000000 --- a/src/encoded/docs/updating_ontologies.md +++ /dev/null @@ -1,57 +0,0 @@ -Updating ontologies -========================= - -This document describes how to update the ontology versions used for searching and validation in the encoded application, ```ontology.json``` . - -Ontologies used ----------------- - -* [Uber anatomy ontology (Uberon)] -* [Cell Ontology (CL)] -* [Experimental Factor Ontology (EFO)] -* [Ontology for Biomedical Investigations (OBI)] - -How to update the ontology versions ----------------- - -1. Ontology files to use: - - * Uberon and CL: composite-metazoan.owl from [Uberon download] - * EFO: EFO_inferred.owl from [EFO src tree] - * OBI: obi.owl [OBI download] - -2. Run generate-ontology, an example is: - - $ bin/generate-ontology --uberon-url=http://ontologies.berkeleybop.org/uberon/composite-metazoan.owl --efo-url=https://github.com/EBISPOT/efo/raw/master/efo_inferred_all.owl?format=raw --obi-url=http://purl.obolibrary.org/obo/obi.owl - -3. Rename the ```ontology.json``` to one with the date that it was generated: - - $ cp ontology.json ontology-YYYY-MM-DD.json - -4. Load new ontology file into the encoded-build/ontology directory on S3 - - $ aws s3 cp ontology-YYYY-MM-DD.json s3://encoded-build/ontology - -5. Update the ontology version in the [buildout.cfg]: - - curl -o ontology.json https://s3-us-west-1.amazonaws.com/encoded-build/ontology ontology-YYYY-MM-DD.json - -6. Update the following information - - Site release version: 78 - ontology.json file: ontology-2018-11-12.json - [UBERON release date]: 2018-02-28 - [OBI release date]: 2018-08-27 - [EFO release date]: 2018-10-15 - -[Uber anatomy ontology (Uberon)]: http://uberon.org/ -[Cell Ontology (CL)]: http://cellontology.org/ -[Experimental Factor Ontology (EFO)]: http://www.ebi.ac.uk/efo -[Ontology for Biomedical Investigations (OBI)]: http://obi-ontology.org/ -[Uberon download]: http://uberon.github.io/downloads.html -[EFO src tree]: https://github.com/EBISPOT/efo/ -[OBI download]: http://www.ontobee.org/ontology/OBI -[buildout.cfg]: ../../../buildout.cfg -[UBERON release date]: http://uberon.github.io/ -[OBI release date]: http://www.ontobee.org/ontology/OBI -[EFO release date]: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt \ No newline at end of file diff --git a/src/encoded/static/components/StickyHeader.js b/src/encoded/static/components/StickyHeader.js deleted file mode 100644 index 040d2f5c44..0000000000 --- a/src/encoded/static/components/StickyHeader.js +++ /dev/null @@ -1,64 +0,0 @@ -import React from 'react'; -import PropTypes from 'prop-types'; -import offset from '../libs/offset'; - - -// Render the collection table header that sticks to the top of the browser window, or below the -// navigation bar of that’s position fixed (as it is if the browser window is wide enough). Note -// that this method makes the sticky header shudder up and down while scrolling. Better ways exist -// to do this without shudderingm, but they don't work on tables. -export default class StickyHeader extends React.Component { - constructor() { - super(); - - // Bind this to non-React components. - this.stickyHeader = this.stickyHeader.bind(this); - } - - componentDidMount() { - // Avoid shimming as ie8 does not support css transform - if (window.getComputedStyle === undefined) return; - this.stickyHeader(); - window.addEventListener('scroll', this.stickyHeader); - window.addEventListener('resize', this.stickyHeader); - } - - componentWillUnmount() { - if (window.getComputedStyle === undefined) return; - window.removeEventListener('scroll', this.stickyHeader); - window.removeEventListener('resize', this.stickyHeader); - } - - stickyHeader() { - // http://stackoverflow.com/a/6625189/199100 - // http://css-tricks.com/persistent-headers/ - const header = this.stickyHeaderComp; - if (header) { - const table = header.parentElement; - const offsetTop = offset(table).top; - const nb = document.querySelector('.navbar-fixed-top'); - let nbHeight = 0; - - if (window.getComputedStyle(nb).getPropertyValue('position') === 'fixed') { - nbHeight = nb.clientHeight; - } - const scrollTop = document.body.scrollTop + nbHeight; - let y = 0; - - if ((scrollTop > offsetTop) && (scrollTop < (offsetTop + table.clientHeight))) { - y = scrollTop - offsetTop - 3; // correction for borders - } - const transform = `translate(0px,${y}px)`; - header.style.transform = transform; - } - } - - render() { - const child = React.cloneElement(this.props.children, { ref: (comp) => { this.stickyHeaderComp = comp; } }); - return React.Children.only(child); - } -} - -StickyHeader.propTypes = { - children: PropTypes.object.isRequired, -}; diff --git a/src/encoded/static/components/__tests__/antibody-test.js b/src/encoded/static/components/__tests__/antibody-test.js deleted file mode 100644 index c0d779960e..0000000000 --- a/src/encoded/static/components/__tests__/antibody-test.js +++ /dev/null @@ -1,96 +0,0 @@ -import React from 'react'; -import { mount } from 'enzyme'; - -// Import test component and data. -import Antibody from '../antibody'; -import context from '../testdata/antibody/ENCAB000AUZ'; - - -describe('Antibody', () => { - beforeAll(() => { - // Set up context object to be rendered - context.host_organism = require('../testdata/organism/rabbit'); - context.source = require('../testdata/source/aviva'); - context.characterizations = [require('../testdata/characterization/antibody-367a6fdd0cef')]; - context.characterizations[0].submitted_by = require('../testdata/submitter'); - context.characterizations[0].documents = [require('../testdata/document/antibodyStandards')]; - context.characterizations[0].lab = require('../testdata/lab'); - context.characterizations[0].award = require('../testdata/award'); - context.characterizations[0].target = require('../testdata/target/HNRNPA1-human'); - context.characterizations[0].target.organism = require('../testdata/organism/human'); - context.lot_reviews = [require('../testdata/lot_review/EFO-0002791')]; - context.lot_reviews[0].organisms = [require('../testdata/organism/human')]; - context.lot_reviews[0].targets = [require('../testdata/target/HNRNPA1-human')]; - context.lot_reviews[0].targets[0].organisms = [require('../testdata/organism/human')]; - }); - - describe('Typical antibody', () => { - let antibody; - - beforeAll(() => { - // Render antibody into jsnode - antibody = mount( - - ); - }); - - test('has a good header', () => { - let headerLine = antibody.find('h2'); - expect(headerLine.text()).toEqual('ENCAB000AUZ'); - headerLine = antibody.find('h3'); - expect(headerLine.text()).toEqual('Antibody against Homo sapiens HNRNPA1'); - }); - - test('has a good status panel', () => { - const panel = antibody.find('.antibody-status'); - const row = panel.find('.antibody-status__group'); - const element = row.at(0).find('.antibody-status__status'); - expect(element).toHaveLength(1); - expect(element.text()).toEqual('awaiting characterization'); - expect(row.find('.antibody-status__organism').text()).toEqual('Homo sapiens'); - expect(row.find('.antibody-status__terms').text()).toEqual('HeLa-S3'); - }); - - test('has a good summary panel', () => { - const panel = antibody.find('.data-display'); - - let item = panel.find('[data-test="source"]'); - let itemDescription = item.find('dd'); - let anchor = itemDescription.at(0).find('a'); - expect(itemDescription.text()).toEqual('Aviva'); - expect(anchor.prop('href')).toEqual('http://www.avivasysbio.com'); - - item = panel.find('[data-test="productid"]'); - itemDescription = item.find('dd'); - anchor = itemDescription.find('a'); - expect(itemDescription.text()).toEqual('ARP40383_T100'); - expect(anchor.at(0).prop('href')).toEqual('http://www.avivasysbio.com/anti-hnrpa1-antibody-n-terminal-region-arp40383-t100.html'); - - item = panel.find('[data-test="lotid"]'); - itemDescription = item.find('dd'); - expect(itemDescription.text()).toEqual('QC9473-091124'); - - item = panel.find('[data-test="targets"]'); - itemDescription = item.find('dd'); - anchor = itemDescription.find('a'); - expect(itemDescription.text()).toEqual('HNRNPA1 (Homo sapiens)'); - expect(anchor.at(0).prop('href')).toEqual('/targets/HNRNPA1-human/'); - - item = panel.find('[data-test="host"]'); - itemDescription = item.find('dd'); - expect(itemDescription.text()).toEqual('rabbit'); - - item = panel.find('[data-test="clonality"]'); - itemDescription = item.find('dd'); - expect(itemDescription.text()).toEqual('polyclonal'); - - item = panel.find('[data-test="isotype"]'); - itemDescription = item.find('dd'); - expect(itemDescription.text()).toEqual('IgG'); - - item = panel.find('[data-test="antigensequence"]'); - itemDescription = item.find('dd'); - expect(itemDescription.text()).toEqual('MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN'); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/datacolor-test.js b/src/encoded/static/components/__tests__/datacolor-test.js deleted file mode 100644 index 84a08b1458..0000000000 --- a/src/encoded/static/components/__tests__/datacolor-test.js +++ /dev/null @@ -1,39 +0,0 @@ -import DataColors from '../datacolors'; - - -describe('DataColor Module', () => { - describe('Returns correct colors for keys', () => { - const testKeys = [ - 'cell line', - 'tissue', - 'primary cell', - 'whole organisms', - 'stem cell', - 'in vitro differentiated cells', - 'induced pluripotent stem cell line', - 'secondary cell', - ]; - const dataColorsInstance = new DataColors(testKeys); - - it('Returns correct colors for small array', () => { - const testColors = dataColorsInstance.colorList(['stem cell', 'primary cell']); - expect(testColors[0]).toEqual('#9b009b'); - expect(testColors[1]).toEqual('#ff9a00'); - }); - - it('Returns medium gray for a non-existent key', () => { - const testColors = dataColorsInstance.colorList(['stem DNA']); - expect(testColors[0]).toEqual('#808080'); - }); - - it('Wraps around the used color if more keys than colors', () => { - const testColors = dataColorsInstance.colorList(['secondary cell']); - expect(testColors[0]).toEqual('#2f62cf'); - }); - - it('Wraps around the used color if more keys than colors', () => { - const testColors = dataColorsInstance.colorList(['primary cell'], { tint: 0.1 }); - expect(testColors[0]).toEqual('#ffa419'); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/dataset-test.js b/src/encoded/static/components/__tests__/dataset-test.js deleted file mode 100644 index e52c6a7d16..0000000000 --- a/src/encoded/static/components/__tests__/dataset-test.js +++ /dev/null @@ -1,70 +0,0 @@ -import { mount } from 'enzyme'; - -// Import test component and data. -import { annotationBiosampleSummary } from '../dataset'; - - -describe('Annotation biosample summary', () => { - test('it works for just scientific name, life stage', () => { - const context = { - organism: { - scientific_name: 'Mus musculus', - }, - relevant_life_stage: 'adult', - }; - const summary = mount( - annotationBiosampleSummary(context) - ); - - const summaryOutput = summary.find('.biosample-summary'); - expect(summaryOutput.text()).toEqual('Mus musculus, adult'); - }); - - test('it works for just scientific name, unknown life stage', () => { - const context = { - organism: { - scientific_name: 'Mus musculus', - }, - relevant_life_stage: 'unknown', - }; - const summary = mount( - annotationBiosampleSummary(context) - ); - - const summaryOutput = summary.find('.biosample-summary'); - expect(summaryOutput.text()).toEqual('Mus musculus'); - }); - - test('it works for just scientific name, life stage, timepoint', () => { - const context = { - organism: { - scientific_name: 'Mus musculus', - }, - relevant_life_stage: 'adult', - relevant_timepoint: '11.5', - }; - const summary = mount( - annotationBiosampleSummary(context) - ); - - const summaryOutput = summary.find('.biosample-summary'); - expect(summaryOutput.text()).toEqual('Mus musculus, adult, 11.5'); - }); - - test('it works for just scientific name, life stage, timepoint, timepoint units', () => { - const context = { - organism: { - scientific_name: 'Mus musculus', - }, - relevant_life_stage: 'adult', - relevant_timepoint: '11.5', - relevant_timepoint_units: 'year', - }; - const summary = mount( - annotationBiosampleSummary(context) - ); - - const summaryOutput = summary.find('.biosample-summary'); - expect(summaryOutput.text()).toEqual('Mus musculus, adult, 11.5 year'); - }); -}); diff --git a/src/encoded/static/components/__tests__/dbxref-test.js b/src/encoded/static/components/__tests__/dbxref-test.js deleted file mode 100644 index 301f5c6848..0000000000 --- a/src/encoded/static/components/__tests__/dbxref-test.js +++ /dev/null @@ -1,631 +0,0 @@ -import React from 'react'; -import { mount } from 'enzyme'; - -// Import test component. -import { DbxrefList } from '../dbxref'; - - -describe('Test individual dbxref types', () => { - describe('Test UniProtKB', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Treatment'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://www.uniprot.org/uniprot/1234'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://www.uniprot.org/uniprot/5678'); - }); - }); - - describe('Test HGNC', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Target'], genes: [{ symbol: 'CXXC1' }] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://www.genecards.org/cgi-bin/carddisp.pl?gene=CXXC1'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://www.genecards.org/cgi-bin/carddisp.pl?gene=CXXC1'); - }); - }); - - describe('Test ENSEMBLE', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Target'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000101126'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000154832'); - }); - }); - - describe('Test mouse ENSEMBLE', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Gene'], organism: { scientific_name: 'Mus musculus' } }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://www.ensembl.org/Mus_musculus/Gene/Summary?g=ENSMUSG00000005698'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://www.ensembl.org/Mus_musculus/Gene/Summary?g=ENSMUSG00000017167'); - }); - }); - - describe('Test GeneID', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Target'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/gene/23394'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/gene/10664'); - }); - }); - - describe('Test GEO', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': 'UcscBrowserComposite' }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(3); - expect(dbxLinks.at(0).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1002657'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL9442'); - expect(dbxLinks.at(2).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/biosample/SAMN00003235'); - }); - }); - - describe('Test IHEC', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': 'ReferenceEpigenome' }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://www.ebi.ac.uk/vg/epirr/view/IHECRE00000004.3'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://www.ebi.ac.uk/vg/epirr/view/IHECRE00000129.3'); - }); - }); - - describe('Test Cellosaurus', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': 'Biosample' }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://web.expasy.org/cellosaurus/CVCL_0395'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://web.expasy.org/cellosaurus/CVCL_5486'); - }); - }); - - describe('Test FlyBase for targets and fly donors', () => { - let dbxLinksFlyDonor; - let dbxLinksTarget; - - beforeAll(() => { - const contextFly = { '@type': ['FlyDonor'] }; - const contextTarget = { '@type': ['Target'] }; - const wrapperFlyDonor = mount( - - ); - const wrapperTarget = mount( - - ); - - dbxLinksFlyDonor = wrapperFlyDonor.find('a'); - dbxLinksTarget = wrapperTarget.find('a'); - }); - - it('has the correct links for FlyBase', () => { - expect(dbxLinksFlyDonor.length).toBe(2); - expect(dbxLinksFlyDonor.at(0).prop('href')).toEqual('http://flybase.org/reports/FBst0038626.html'); - expect(dbxLinksFlyDonor.at(1).prop('href')).toEqual('http://flybase.org/reports/FBst0000005.html'); - }); - - it('has the correct links for Targets', () => { - expect(dbxLinksTarget.length).toBe(2); - const flybaseSearchUrl = 'http://flybase.org/search/symbol/'; - - expect(dbxLinksTarget.at(0).prop('href')).toEqual(`${flybaseSearchUrl}CG43860`); - expect(dbxLinksTarget.at(1).prop('href')).toEqual(`${flybaseSearchUrl}FBtr0332562`); - }); - }); - - describe('Test BDSC', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': 'Biosample' }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://flystocks.bio.indiana.edu/stocks/38626'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://flystocks.bio.indiana.edu/stocks/5'); - }); - }); - - describe('Test WormBase for targets and worm donors', () => { - let dbxLinksWormDonor; - let dbxLinksTarget; - - beforeAll(() => { - const contextWorm = { '@type': ['WormDonor'] }; - const contextTarget = { '@type': ['Target'] }; - const wrapperWormDonor = mount( - - ); - const wrapperTarget = mount( - - ); - - dbxLinksWormDonor = wrapperWormDonor.find('a'); - dbxLinksTarget = wrapperTarget.find('a'); - }); - - it('has the correct links for FlyBase', () => { - expect(dbxLinksWormDonor.length).toBe(2); - expect(dbxLinksWormDonor.at(0).prop('href')).toEqual('http://www.wormbase.org/species/c_elegans/strain/RB884'); - expect(dbxLinksWormDonor.at(1).prop('href')).toEqual('http://www.wormbase.org/species/c_elegans/strain/RB885'); - }); - - it('has the correct links for Targets', () => { - expect(dbxLinksTarget.length).toBe(2); - expect(dbxLinksTarget.at(0).prop('href')).toEqual('http://www.wormbase.org/species/c_elegans/gene/WBGene00003222'); - expect(dbxLinksTarget.at(1).prop('href')).toEqual('http://www.wormbase.org/species/c_elegans/gene/Y2H9A.1'); - }); - }); - - describe('Test CGC', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': 'WormDonor' }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://cgc.umn.edu/strain/RB884'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://cgc.umn.edu/strain/N5'); - }); - }); - - describe('Test DSSC', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': 'FlyDonor' }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://stockcenter.ucsd.edu/index.php?action=view&q=15181-2171.01&table=Species&submit=Search'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://stockcenter.ucsd.edu/index.php?action=view&q=14012-0141.05&table=Species&submit=Search'); - }); - }); - - describe('Test MGI.D', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': 'MouseDonor' }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://www.informatics.jax.org/inbred_strains/mouse/docs/RIII.shtml'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://www.informatics.jax.org/inbred_strains/mouse/docs/NOD.shtml'); - }); - }); - - describe('Test RBPImage', () => { - let dbxLinks; - - beforeAll(() => { - const context = { - '@type': ['Experiment'], - biosample_ontology: { - classification: 'cell line', - term_id: 'EFO:0001187', - term_name: 'HepG2', - }, - }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://rnabiology.ircm.qc.ca/RBPImage/gene.php?cells=HepG2&targets=DNAJC2'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://rnabiology.ircm.qc.ca/RBPImage/gene.php?cells=HepG2&targets=SRSF9'); - }); - }); - - describe('Test JAX', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['MouseDonor'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://www.jax.org/strain/002448'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://www.jax.org/strain/000646'); - }); - }); - - describe('Test NBRP', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['MouseDonor'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://shigen.nig.ac.jp/c.elegans/mutants/DetailsSearch?lang=english&seq=233'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://shigen.nig.ac.jp/c.elegans/mutants/DetailsSearch?lang=english&seq=292'); - }); - }); - - describe('Test UCSC-ENCODE-mm9', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Experiment'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://genome.ucsc.edu/cgi-bin/hgTracks?tsCurTab=advancedTab&tsGroup=Any&tsType=Any&hgt_mdbVar1=dccAccession&hgt_tSearch=search&hgt_tsDelRow=&hgt_tsAddRow=&hgt_tsPage=&tsSimple=&tsName=&tsDescr=&db=mm9&hgt_mdbVal1=wgEncodeEM002001'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://genome.ucsc.edu/cgi-bin/hgTracks?tsCurTab=advancedTab&tsGroup=Any&tsType=Any&hgt_mdbVar1=dccAccession&hgt_tSearch=search&hgt_tsDelRow=&hgt_tsAddRow=&hgt_tsPage=&tsSimple=&tsName=&tsDescr=&db=mm9&hgt_mdbVal1=wgEncodeEM002004'); - }); - }); - - describe('Test UCSC-ENCODE-hg19', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Experiment'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://genome.ucsc.edu/cgi-bin/hgTracks?tsCurTab=advancedTab&tsGroup=Any&tsType=Any&hgt_mdbVar1=dccAccession&hgt_tSearch=search&hgt_tsDelRow=&hgt_tsAddRow=&hgt_tsPage=&tsSimple=&tsName=&tsDescr=&db=hg19&hgt_mdbVal1=wgEncodeEH003317'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://genome.ucsc.edu/cgi-bin/hgTracks?tsCurTab=advancedTab&tsGroup=Any&tsType=Any&hgt_mdbVar1=dccAccession&hgt_tSearch=search&hgt_tsDelRow=&hgt_tsAddRow=&hgt_tsPage=&tsSimple=&tsName=&tsDescr=&db=hg19&hgt_mdbVal1=wgEncodeEH002546'); - }); - }); - - describe('Test UCSC-ENCODE-cv', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Experiment'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode%2Fcv.ra&term=%22IgG-Yale%22'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode%2Fcv.ra&term=%22Illumina_GA2e%22'); - }); - }); - - describe('Test UCSC-GB-mm9', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Experiment'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://genome.cse.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhHist'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://genome.cse.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodePsuRnaSeq'); - }); - }); - - describe('Test UCSC-GB-hg19', () => { - let dbxLinks; - - beforeAll(() => { - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://genome.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwAffyExonArray'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://genome.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUmassDekker5C'); - }); - }); - - describe('Test PMID', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Publication'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/pubmed/?term=22064851'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/pubmed/?term=19966280'); - }); - }); - - describe('Test PMCID', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Publication'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832824'); - }); - }); - - describe('Test doi', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['Publication'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://doi.org/doi:10.1038%2Fnphys1170'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://doi.org/doi:10.1006%2Fgeno.1998.5693'); - }); - }); - - describe('Test AR', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['AntibodyLot'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://antibodyregistry.org/search.php?q=AB_2615158'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://antibodyregistry.org/search.php?q=AB_2614941'); - }); - }); - - describe('Test NIH', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['HumanDonor'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://search.usa.gov/search?utf8=%E2%9C%93&affiliate=grants.nih.gov&query=NIHhESC-10-0062'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://search.usa.gov/search?utf8=%E2%9C%93&affiliate=grants.nih.gov&query=NIHhESC-10-0063'); - }); - }); - - describe('Test TRiP', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['FlyDonor'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('http://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl?gname=HMC04792'); - expect(dbxLinks.at(1).prop('href')).toEqual('http://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl?gname=HMC04793'); - }); - }); - - describe('Test DGGR', () => { - let dbxLinks; - - beforeAll(() => { - const context = { '@type': ['FlyDonor'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - }); - - it('has the correct links', () => { - expect(dbxLinks.length).toBe(2); - expect(dbxLinks.at(0).prop('href')).toEqual('https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=109027'); - expect(dbxLinks.at(1).prop('href')).toEqual('https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=101084'); - }); - }); - - describe('Test no matching dbxref prefix', () => { - let dbxLinks; - let dbxSpans; - - beforeAll(() => { - const context = { '@type': ['HumanDonor'] }; - const wrapper = mount( - - ); - - dbxLinks = wrapper.find('a'); - dbxSpans = wrapper.find('span'); - }); - - it('has the correct span contents', () => { - expect(dbxLinks.length).toBe(0); - expect(dbxSpans.length).toBe(1); - expect(dbxSpans.at(0).text()).toEqual('OK:NOT-REAL'); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/experiment-test.js b/src/encoded/static/components/__tests__/experiment-test.js deleted file mode 100644 index 6675557335..0000000000 --- a/src/encoded/static/components/__tests__/experiment-test.js +++ /dev/null @@ -1,102 +0,0 @@ -import React from 'react'; -import { mount } from 'enzyme'; -import configureStore from 'redux-mock-store'; -import { Provider } from 'react-redux'; -import _ from 'underscore'; - -// Import test component and data. -import Experiment from '../experiment'; -import context from '../testdata/experiment'; - -// Create the Redux mock store. -const initialCart = { cart: [], name: 'Untitled' }; -const mockStore = configureStore(); - - -describe('Experiment Page', () => { - describe('Minimal Experiment', () => { - let experiment; - let summary; - - beforeAll(() => { - const contextMin = _.clone(context); - contextMin.references = [require('../testdata/publication/PMID16395128'), require('../testdata/publication/PMID23000965')]; - const store = mockStore(initialCart); - experiment = mount( - - ); - - summary = experiment.find('.data-display'); - }); - - test('has proper links in dbxrefs key-value', () => { - const item = summary.at(0).find('[data-test="external-resources"]'); - const desc = item.find('dd'); - const dbxrefs = desc.at(0).find('a'); - expect(dbxrefs).toHaveLength(2); - expect(dbxrefs.at(0).prop('href')).toEqual('http://genome.ucsc.edu/cgi-bin/hgTracks?tsCurTab=advancedTab&tsGroup=Any&tsType=Any&hgt_mdbVar1=dccAccession&hgt_tSearch=search&hgt_tsDelRow=&hgt_tsAddRow=&hgt_tsPage=&tsSimple=&tsName=&tsDescr=&db=hg19&hgt_mdbVal1=wgEncodeEH003317'); - expect(dbxrefs.at(1).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1010811'); - }); - - test('has proper release date', () => { - const item = summary.at(0).find('[data-test="date-released"]'); - const desc = item.find('dd'); - expect(desc.at(0).text()).toEqual('October 29, 2011'); - }); - }); - - describe('Replicate Panels', () => { - let experiment; - let summary; - - beforeAll(() => { - const contextRep = _.clone(context); - contextRep.replicates = [require('../testdata/replicate/human'), require('../testdata/replicate/mouse')]; - contextRep.replicates[0].library = require('../testdata/library/sid38806'); - contextRep.replicates[1].library = require('../testdata/library/sid38807'); - contextRep.files = [require('../testdata/file/fastq')[0]]; - const store = mockStore(initialCart); - experiment = mount( - - ); - summary = experiment.find('.data-display'); - }); - - test('has proper treatment', () => { - const item = summary.find('[data-test="treatments"]'); - const desc = item.find('dd'); - expect(desc.text()).toEqual('97.2 nM doxycycline hyclate (CHEBI:34730) for 6 hour [1-1]'); - }); - - test('has proper strand specificity', () => { - const item = summary.find('[data-test="strandspecificity"]'); - const desc = item.find('dd'); - expect(desc.text()).toEqual('Strand-specific'); - }); - - test('has proper spikeins', () => { - const item = summary.find('[data-test="spikeins"]'); - const desc = item.find('dd'); - expect(desc.text()).toEqual('ENCSR000AJW [1-1]'); - }); - }); - - describe('Alternate accession display', () => { - let experiment; - let alt; - - beforeAll(() => { - const contextAlt = _.clone(context); - contextAlt.alternate_accessions = ['ENCSR000ACT', 'ENCSR999NOF']; - const store = mockStore(initialCart); - experiment = mount( - - ); - alt = experiment.find('.repl-acc'); - }); - - test('displays two alternate accessions', () => { - expect(alt.text()).toEqual('Alternate accessions: ENCSR000ACT, ENCSR999NOF'); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/graph-test.js b/src/encoded/static/components/__tests__/graph-test.js deleted file mode 100644 index 0325280653..0000000000 --- a/src/encoded/static/components/__tests__/graph-test.js +++ /dev/null @@ -1,324 +0,0 @@ -import _ from 'underscore'; - - -// Import test component and data. -import { assembleGraph } from '../filegallery'; -import context from '../testdata/experiment'; - - -describe('Experiment Graph', () => { - // Collects all the IDs of all nodes in the given node array and returns it in object keyed by node ID - function collectNodes(graphId, nodes) { - let allNodes = {}; - - nodes.forEach((node) => { - allNodes[node.id] = node; - if (node.nodes.length) { - allNodes = _.extend(allNodes, collectNodes(graphId, node.nodes)); - } - }); - return allNodes; - } - - // Utility to check whether the node ids in the "ids" array are all in the graph given in "graph" - function containsNodes(graph, ids) { - let allNodes; - - // Make an object of all nodes in graph - if (graph.nodes.length) { - allNodes = collectNodes(graph.id, graph.nodes); - } - - // See if all the given ids are in the nodes - return _(ids).all(id => id in allNodes); - } - - // Utility returns true if child ID has all parents in "parent" IDs - function hasParents(graph, child, parents) { - const matchingTargets = _(graph.edges).where({ target: child }); - if (matchingTargets.length) { - return _(parents).all(parent => _(matchingTargets).any(target => parent === target.source)); - } - return null; - } - - // One file derived from two files, through one step. - describe('Basic graph display', () => { - let graph; - let files; - - beforeAll(() => { - const contextGraph = _.clone(context); - contextGraph.accession = 'ENCTS000BGR'; - files = [require('../testdata/file/bam-vuq'), require('../testdata/file/bam-vus'), require('../testdata/file/bed-2cos')]; - contextGraph.files = files; - graph = assembleGraph(files, contextGraph, { selectedAssembly: 'hg19', selectedAnnotation: '' }); - }); - - it('Has the correct number of nodes and edges', () => { - expect(graph.nodes).toHaveLength(4); - expect(graph.edges).toHaveLength(3); - }); - - it('has the right nodes', () => { - expect(containsNodes(graph, ['file:/files/ENCFF000VUQ/', 'file:/files/ENCFF000VUS/', 'file:/files/ENCFF002COS/', 'step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - - it('has the right relationships between edges and nodes', () => { - expect(hasParents(graph, 'step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUS/', 'file:/files/ENCFF000VUQ/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF002COS/', ['step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - }); - - // Two files each deriving from one file each; share a step. - // There should be two copies of the step with different file - // accessions in their IDs. - describe('Basic graph step duplication display', () => { - let graph; - let files; - - beforeAll(() => { - const contextGraph = _.clone(context); - contextGraph.accession = 'ENCTS000BDD'; - files = [require('../testdata/file/bam-vuq'), require('../testdata/file/bam-vus'), require('../testdata/file/bed-3cos'), require('../testdata/file/bed-4cos')]; - graph = assembleGraph(files, contextGraph, { selectedAssembly: 'hg19', selectedAnnotation: '' }); - }); - - it('Has the correct number of nodes and edges', () => { - expect(graph.nodes.length).toEqual(6); - expect(graph.edges.length).toEqual(4); - }); - - it('has the right nodes', () => { - expect(containsNodes(graph, ['file:/files/ENCFF000VUQ/', 'file:/files/ENCFF000VUS/', 'file:/files/ENCFF003COS/', 'file:/files/ENCFF004COS/', 'step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', 'step:/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - - it('has the right relationships between edges and nodes', () => { - expect(hasParents(graph, 'step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUQ/'])).toBeTruthy(); - expect(hasParents(graph, 'step:/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUS/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF003COS/', ['step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF004COS/', ['step:/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - }); - - // Two files each deriving from one file they share; and they share a step. - // There should be one copy of the step. - describe('Basic graph step no duplication display', () => { - let graph; - let files; - - beforeAll(() => { - const contextGraph = _.clone(context); - contextGraph.accession = 'ENCTS000NDD'; - files = [require('../testdata/file/bam-vuq'), require('../testdata/file/bed-5cos'), require('../testdata/file/bed-6cos')]; - graph = assembleGraph(files, contextGraph, { selectedAssembly: 'hg19', selectedAnnotation: '' }); - }); - - it('Has the correct number of nodes and edges', () => { - expect(graph.nodes.length).toEqual(4); - expect(graph.edges.length).toEqual(3); - }); - - it('has the right nodes', () => { - expect(containsNodes(graph, ['file:/files/ENCFF000VUQ/', 'file:/files/ENCFF005COS/', 'file:/files/ENCFF006COS/', 'step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - - it('has the right relationships between edges and nodes', () => { - expect(hasParents(graph, 'step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUQ/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF005COS/', ['step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF006COS/', ['step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - }); - - // Two files derive from the same two files and share a step. - // There should be one copy of the step. - describe('Two files derived from same two files', () => { - let graph; - let files; - - beforeAll(() => { - const contextGraph = _.clone(context); - contextGraph.accession = 'ENCTS000TFS'; - files = [require('../testdata/file/bam-vuq'), require('../testdata/file/bam-vus'), require('../testdata/file/bed-7cos'), require('../testdata/file/bed-8cos')]; - graph = assembleGraph(files, contextGraph, { selectedAssembly: 'hg19', selectedAnnotation: '' }); - }); - - it('Has the correct number of nodes and edges', () => { - expect(graph.nodes.length).toEqual(5); - expect(graph.edges.length).toEqual(4); - }); - - it('has the right nodes', () => { - expect(containsNodes(graph, ['file:/files/ENCFF000VUQ/', 'file:/files/ENCFF000VUS/', 'file:/files/ENCFF008COS/', 'file:/files/ENCFF008COS/', 'step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - - it('has the right relationships between edges and nodes', () => { - expect(hasParents(graph, 'step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUQ/', 'file:/files/ENCFF000VUS/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF007COS/', ['step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF008COS/', ['step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - }); - - // Two files derive from two overlapping sets of files. The analysis - // step should get duplicated, one for each set of derived_from files. - describe('Two files derived from overlapping set of files', () => { - let graph; - let files; - - beforeAll(() => { - const contextGraph = _.clone(context); - contextGraph.accession = 'ENCTS000TOV'; - files = [require('../testdata/file/bam-vuq'), require('../testdata/file/bam-vus'), require('../testdata/file/bam-vuz'), require('../testdata/file/bed-10cos'), require('../testdata/file/bed-11cos')]; - graph = assembleGraph(files, contextGraph, { selectedAssembly: 'hg19', selectedAnnotation: '' }); - }); - - it('Has the correct number of nodes and edges', () => { - expect(graph.nodes.length).toEqual(7); - expect(graph.edges.length).toEqual(6); - }); - - it('has the right nodes', () => { - expect(containsNodes(graph, ['file:/files/ENCFF000VUQ/', 'file:/files/ENCFF000VUS/', 'file:/files/ENCFF000VUZ/', 'file:/files/ENCFF010COS/', 'file:/files/ENCFF011COS/', 'step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', 'step:/files/ENCFF000VUS/,/files/ENCFF000VUZ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - - it('has the right relationships between edges and nodes', () => { - expect(hasParents(graph, 'step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUQ/', 'file:/files/ENCFF000VUS/'])).toBeTruthy(); - expect(hasParents(graph, 'step:/files/ENCFF000VUS/,/files/ENCFF000VUZ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUS/', 'file:/files/ENCFF000VUZ/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF010COS/', ['step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF011COS/', ['step:/files/ENCFF000VUS/,/files/ENCFF000VUZ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - }); - - // One file derived from two files, through one step. - // Another file not derived from, and doesn't derive from others; it should vanish. - describe('Basic graph with detached node', () => { - let graph; - let files; - - beforeAll(() => { - const contextGraph = _.clone(context); - contextGraph.accession = 'ENCTS000DET'; - files = [require('../testdata/file/bam-vuq'), require('../testdata/file/bam-vus'), require('../testdata/file/bam-vuz'), require('../testdata/file/bed-2cos')]; - graph = assembleGraph(files, contextGraph, { selectedAssembly: 'hg19', selectedAnnotation: '' }); - }); - - it('Has the correct number of nodes and edges', () => { - expect(graph.nodes.length).toEqual(4); - expect(graph.edges.length).toEqual(3); - }); - - // VUZ should be missing. - it('has the right nodes', () => { - expect(containsNodes(graph, ['file:/files/ENCFF000VUQ/', 'file:/files/ENCFF000VUS/', 'file:/files/ENCFF002COS/', 'step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - expect(containsNodes(graph, ['file:/files/ENCFF000VUZ/'])).toBeFalsy(); - }); - - it('has the right relationships between edges and nodes', () => { - expect(hasParents(graph, 'step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUS/', 'file:/files/ENCFF000VUQ/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF002COS/', ['step:/files/ENCFF000VUQ/,/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - }); - - // Two files derive from one file each through a shared step. Each file and derived from files in a replicate. - // Total of two replicates with three nodes each - describe('Two graphs in two replicates', () => { - let graph; - let files; - - beforeAll(() => { - const contextGraph = _.clone(context); - contextGraph.accession = 'ENCTS000REP'; - files = [require('../testdata/file/bam-vuq'), require('../testdata/file/bam-vus'), require('../testdata/file/bed-3cos'), require('../testdata/file/bed-4cos')]; - files[0].biological_replicates = [1]; - files[1].biological_replicates = [2]; - files[2].biological_replicates = [1]; - files[3].biological_replicates = [2]; - - graph = assembleGraph(files, contextGraph, { selectedAssembly: 'hg19', selectedAnnotation: '' }); - }); - - it('Has the correct number of nodes and edges', () => { - let subNodes = 0; - - expect(graph.nodes.length).toEqual(2); - graph.nodes.forEach((node) => { - subNodes += node.nodes.length; - }); - expect(subNodes).toEqual(6); - expect(graph.edges.length).toEqual(4); - }); - - it('has the right nodes', () => { - expect(containsNodes(graph, ['rep:1', 'rep:2', 'file:/files/ENCFF000VUQ/', 'file:/files/ENCFF000VUS/', 'file:/files/ENCFF003COS/', 'file:/files/ENCFF004COS/', - 'step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', 'step:/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - - it('has the right relationships between edges and nodes', () => { - expect(hasParents(graph, 'step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUQ/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF003COS/', ['step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - expect(hasParents(graph, 'step:/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUS/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF004COS/', ['step:/files/ENCFF000VUS//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - }); - - // Two files derive from one file each through a shared step. Each file and derived from files in a replicate. - // Total of two replicates with three nodes each - describe('Two graphs in two replicates; one derived-from missing', () => { - let graph; - let files; - - beforeEach(() => { - const contextGraph = _.clone(context); - contextGraph.accession = 'ENCTS000RPM'; - files = [require('../testdata/file/bam-vuq'), require('../testdata/file/bed-3cos'), require('../testdata/file/bed-4cos')]; - files[0].biological_replicates = [1]; - files[1].biological_replicates = [1]; - files[2].derived_from = [require('../testdata/file/bam-vus')['@id']]; - files[2].biological_replicates = [2]; - graph = assembleGraph(files, contextGraph, { selectedAssembly: 'hg19', selectedAnnotation: '' }); - }); - - it('Has the correct number of nodes and edges', () => { - let subNodes = 0; - - expect(graph.nodes.length).toEqual(3); - graph.nodes.forEach((node) => { - subNodes += node.nodes.length; - }); - expect(subNodes).toEqual(5); - expect(graph.edges.length).toEqual(4); - }); - - it('has the right nodes', () => { - expect(containsNodes(graph, ['rep:1', 'file:/files/ENCFF000VUQ/', 'file:/files/ENCFF003COS/', - 'step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - expect(containsNodes(graph, ['rep:2'])).toBeTruthy(); - }); - - it('has the right relationships between edges and nodes', () => { - expect(hasParents(graph, 'step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/', ['file:/files/ENCFF000VUQ/'])).toBeTruthy(); - expect(hasParents(graph, 'file:/files/ENCFF003COS/', ['step:/files/ENCFF000VUQ//analysis-steps/1b7bec83-dd21-4086-8673-2e08cf8f1c0f/'])).toBeTruthy(); - }); - }); - - // A processed file derives from a fastq that derives from an sra file. - describe('fastq derives from an sra in the same dataset, ', () => { - let graph; - let files; - - beforeEach(() => { - const contextGraph = _.clone(context); - contextGraph.accession = 'ENCSR000RPM'; - files = [require('../testdata/file/sra'), require('../testdata/file/fastq')[1], require('../testdata/file/bed-3cos')]; - files[1].derived_from = [files[0]['@id']]; - files[2].derived_from = [files[1]['@id']]; - files[2].biological_replicates = []; - graph = assembleGraph(files, contextGraph, { selectedAssembly: 'hg19', selectedAnnotation: '' }); - }); - - it('Has the correct number of nodes and edges', () => { - expect(graph.nodes.length).toEqual(5); - expect(graph.edges.length).toEqual(4); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/objectutils-test.js b/src/encoded/static/components/__tests__/objectutils-test.js deleted file mode 100644 index 78e1b91e0f..0000000000 --- a/src/encoded/static/components/__tests__/objectutils-test.js +++ /dev/null @@ -1,38 +0,0 @@ -import React from 'react'; -import { mount } from 'enzyme'; - -// Import test component and data. -import { InternalTags } from '../objectutils'; - - -describe('InternalTags', () => { - let context; - let wrapper; - const testTags = ['ENTEx', 'SESCC']; - - beforeAll(() => { - context = { - '@type': ['HumanDonor', 'Donor', 'Item'], - internal_tags: testTags, - }; - wrapper = mount( - - ); - }); - - test('generates two links', () => { - const internalTagLinks = wrapper.find('a'); - expect(internalTagLinks).toHaveLength(2); - }); - - - test('generates the right images in each link', () => { - const uris = testTags.map(tag => `/static/img/tag-${tag}.png`); - wrapper.find('a').forEach((link, i) => { - const image = link.find('img'); - expect(image).toHaveLength(1); - expect(image.prop('src')).toEqual(uris[i]); - expect(image.prop('alt')).toContain(testTags[i]); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/platform-test.js b/src/encoded/static/components/__tests__/platform-test.js deleted file mode 100644 index 212800a4c1..0000000000 --- a/src/encoded/static/components/__tests__/platform-test.js +++ /dev/null @@ -1,65 +0,0 @@ -import React from 'react'; -import { mount } from 'enzyme'; - -// Import test component and data. -import Platform from '../platform'; -import context from '../testdata/platform'; - - -describe('Platform', () => { - let platformPanel; - let defTerms; - let defDescs; - - beforeAll(() => { - // Render platform panel into jsnode - platformPanel = mount( - - ); - - // Get the
and
terms needed for all tests - defTerms = platformPanel.find('dt'); - defDescs = platformPanel.find('dd'); - }); - - test('has three
and
elements', () => { - expect(defTerms).toHaveLength(3); - expect(defDescs).toHaveLength(3); - }); - - describe('External References (third key-value) Item', () => { - let defDescNode; - let unorderedList; - let listItems; - let anchors; - - beforeAll(() => { - defDescNode = defDescs.at(2); - unorderedList = defDescNode.children().childAt(0); - listItems = unorderedList.children(); - anchors = unorderedList.find('a'); - }); - - test('has an unordered list with three items', () => { - expect(defDescNode.children().exists()).toBeTruthy(); - expect(defDescNode.children()).toHaveLength(1); - expect(unorderedList.children().exists()).toBeTruthy(); - expect(unorderedList.children()).toHaveLength(3); - }); - - test('has proper link text', () => { - expect(listItems.at(0).text()).toEqual('UCSC-ENCODE-cv:Illumina_HiSeq_2000'); - expect(listItems.at(1).text()).toEqual('GEO:GPL11154'); - expect(listItems.at(2).text()).toEqual('GEO:GPL13112'); - }); - - test('has links to the proper places', () => { - expect(listItems.at(0).children().exists()).toBeTruthy(); - expect(listItems.at(0).children()).toHaveLength(1); - expect(listItems.at(1).children().exists()).toBeTruthy(); - expect(listItems.at(1).children()).toHaveLength(1); - expect(anchors.at(0).prop('href')).toEqual('http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode%2Fcv.ra&term=%22Illumina_HiSeq_2000%22'); - expect(anchors.at(1).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154'); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/publication-test.js b/src/encoded/static/components/__tests__/publication-test.js deleted file mode 100644 index f6644968ec..0000000000 --- a/src/encoded/static/components/__tests__/publication-test.js +++ /dev/null @@ -1,141 +0,0 @@ -import React from 'react'; -import { mount } from 'enzyme'; -import _ from 'underscore'; - -// Import test component and data. -import Publication from '../publication'; -import context from '../testdata/publication/publication'; - - -describe('Publication', () => { - describe('Publication without references', () => { - let publication; - - beforeAll(() => { - // Render publication panel into jsnode - publication = mount( - - ); - }); - - test('has a good author line', () => { - const authors = publication.find('.authors'); - expect(authors).toHaveLength(1); - expect(authors.text()).toEqual('ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M.'); - }); - - test('has a good citation line', () => { - const journal = publication.find('.journal'); - expect(journal.text()).toEqual('Nature. 2012 Sep;489(7414):57-74.'); - }); - - test('has a journal name in italics', () => { - const journal = publication.find('.journal'); - const italicTexts = journal.find('i'); - expect(italicTexts).toHaveLength(1); - expect(italicTexts.text()).toEqual('Nature. '); - }); - - test('has a good abstract with an h2 and a p', () => { - const panel = publication.find('.panel'); - const item = panel.find('[data-test="abstract"]'); - expect(item).toHaveLength(1); - let abstractPart = item.find('dt'); - expect(abstractPart).toHaveLength(1); - abstractPart = item.find('dd'); - expect(abstractPart).toHaveLength(1); - expect(abstractPart.text()).toContain('The human genome encodes the blueprint of life,'); - }); - }); - - describe('Publication with references', () => { - let publication; - - beforeAll(() => { - // Render publication panel into jsnode - const contextRef = _.clone(context); - contextRef.identifiers = ['PMID:19352372', 'PMCID:PMC3062402']; - publication = mount( - - ); - }); - - test('has two references', () => { - const pubdata = publication.find('.key-value'); - const item = pubdata.find('[data-test="references"]'); - const ul = item.find('ul'); - const li = ul.find('li'); - - // Should have two
  • within the
      for references. - expect(li).toHaveLength(2); - - // Make sure is correct for both
    • . - let anchor = li.at(0).find('a'); - expect(anchor.at(0).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/pubmed/?term=19352372'); - anchor = li.at(1).find('a'); - expect(anchor.at(0).prop('href')).toEqual('https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062402'); - }); - }); - - describe('Publication with data_used', () => { - let publication; - - beforeAll(() => { - const contextDu = _.clone(context); - contextDu.data_used = 'ENCODE main paper'; - publication = mount( - - ); - }); - - test('has a data-used field', () => { - const dataused = publication.find('.key-value'); - const item = dataused.find('[data-test="dataused"]'); - const dd = item.find('dd'); - expect(dd.at(0).text()).toEqual('ENCODE main paper'); - }); - }); - - describe('Publication with datasets', () => { - let publication; - - beforeAll(() => { - const contextDs = _.clone(context); - contextDs.datasets = [require('../testdata/dataset/ENCSR000AJW.js'), require('../testdata/dataset/ENCSR999BLA.js')]; - publication = mount( - - ); - }); - - test('has two dataset links', () => { - const pubdata = publication.find('.key-value'); - const item = pubdata.find('[data-test="datasets"]'); - const itemDescription = item.find('dd'); - const anchors = itemDescription.find('a'); - expect(anchors).toHaveLength(2); - expect(anchors.at(0).prop('href')).toEqual('/datasets/ENCSR000AJW/'); - expect(anchors.at(0).text()).toEqual('ENCSR000AJW'); - expect(anchors.at(1).prop('href')).toEqual('/datasets/ENCSR999BLA/'); - expect(anchors.at(1).text()).toEqual('ENCSR999BLA'); - }); - }); - - describe('Publication with supplementary data', () => { - let publication; - - beforeAll(() => { - const contextSd = _.clone(context); - contextSd.supplementary_data = [require('../testdata/publication/supplementary-data-1.js'), require('../testdata/publication/supplementary-data-2.js')]; - publication = mount( - - ); - }); - - test('has a supplementary data panel with two items', () => { - const supdata = publication.find('.type-Publication'); - const item = supdata.find('[data-test="supplementarydata"]'); - const itemSection = item.find('section'); - expect(itemSection).toHaveLength(2); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/regulome-help-test.js b/src/encoded/static/components/__tests__/regulome-help-test.js new file mode 100644 index 0000000000..86de0bfeb1 --- /dev/null +++ b/src/encoded/static/components/__tests__/regulome-help-test.js @@ -0,0 +1,25 @@ +import React from 'react'; +import { mount } from 'enzyme'; + + +// Import test component +import RegulomeHelp from '../regulome_help'; + + +describe('Help', () => { + describe('Help page', () => { + let help; + + beforeAll(() => { + help = mount( + + ); + }); + + it('Has correct title', () => { + const item = help.find('.page-title'); + expect(item.at(0).text()).toEqual('Help'); + help.unmount(); + }); + }); +}); diff --git a/src/encoded/static/components/__tests__/regulome-summary-test.js b/src/encoded/static/components/__tests__/regulome-summary-test.js new file mode 100644 index 0000000000..25ab01179f --- /dev/null +++ b/src/encoded/static/components/__tests__/regulome-summary-test.js @@ -0,0 +1,39 @@ +import React from 'react'; +import { mount } from 'enzyme'; + + +// Import test component and data +import RegulomeSummary from '../regulome_summary'; +import context from '../testdata/regulome_summary'; + + +describe('Summary', () => { + describe('Summary page', () => { + let summary; + + beforeAll(() => { + summary = mount( + + ); + }); + + it('Has a summary of variants found', () => { + const item = summary.find('.notification-summary'); + const itemCount = item.find('b'); + expect(itemCount.text()).toEqual('2'); + }); + + it('Has two download links', () => { + const downloadBed = summary.find('[data-test="download-bed"]'); + expect(downloadBed.text()).toEqual('Download BED'); + const downloadTsv = summary.find('[data-test="download-tsv"]'); + expect(downloadTsv.text()).toEqual('Download TSV'); + }); + + it('Has summary table', () => { + const table = summary.find('.summary-table-hoverable'); + const tableHeader = table.find('th'); + expect(tableHeader.at(0).text()).toEqual('Chromosome location'); + }); + }); +}); diff --git a/src/encoded/static/components/__tests__/server-render-test.js b/src/encoded/static/components/__tests__/server-render-test.js index df5dc1e128..b7e521eb39 100644 --- a/src/encoded/static/components/__tests__/server-render-test.js +++ b/src/encoded/static/components/__tests__/server-render-test.js @@ -11,37 +11,21 @@ jest.mock('../browserfeat'); describe('Server rendering', () => { let document; - const homeUrl = 'http://localhost/'; + const homeUrl = 'http://localhost/regulome-search'; const home = { - '@id': '/', - '@type': ['Portal'], - portal_title: 'RegulomeDB', - title: 'Home', + '@id': '/regulome-search', + '@type': ['regulome-search'], + portal_title: 'RegulomeDB Search – RegulomeDB', + title: 'RegulomeDB Search', + query_coordinates: [], + total: 0, + variants: [], + notifications: { + Failed: 'Received 0 region queries. Exact one region or one variant can be processed by regulome-search', + }, }; beforeEach(() => { - // Mock the node fetch() call within App.fetch(). - global.fetch = jest.fn().mockImplementation(() => ( - new Promise((resolve) => { - resolve({ - ok: true, - headers: { - get: () => null, - }, - json: () => ( - ({ - '@type': [ - 'JSONSchemas', - ], - AntibodyLot: 'Antibody lot', - CpgCorrelationQualityMetric: 'CpG correlation quality metric', - PublicationData: 'Publication data', - }) - ), - }); - }) - )); - const serverApp = ; const markup = `\n${ReactDOMServer.renderToString(serverApp)}`; const parser = new DOMParser(); diff --git a/src/encoded/static/components/__tests__/software-test.js b/src/encoded/static/components/__tests__/software-test.js deleted file mode 100644 index 53571cef68..0000000000 --- a/src/encoded/static/components/__tests__/software-test.js +++ /dev/null @@ -1,78 +0,0 @@ -import React from 'react'; -import { mount } from 'enzyme'; -import _ from 'underscore'; - -// Import test component and data. -import { Software } from '../software'; -import context from '../testdata/software'; - - -describe('Software', () => { - describe('Software object with no references', () => { - let software; - let summary; - - beforeAll(() => { - software = mount( - - ); - - summary = software.find('.key-value'); - }); - - it('has a title with link to software source', () => { - const item = summary.find('[data-test="title"]'); - const itemDescription = item.find('dd'); - const anchor = itemDescription.find('a'); - expect(itemDescription.text()).toEqual('HaploReg'); - expect(anchor.prop('href')).toEqual('http://www.broadinstitute.org/mammals/haploreg/haploreg.php'); - }); - - it('has a good description, software type, and used for', () => { - let item = summary.find('[data-test="description"]'); - let itemDescription = item.find('dd'); - expect(itemDescription.text()).toContain('Explores annotations of the noncoding genome'); - - item = summary.find('[data-test="type"]'); - itemDescription = item.find('dd'); - expect(itemDescription.text()).toEqual('database, variant annotation'); - - item = summary.find('[data-test="purpose"]'); - itemDescription = item.find('dd'); - expect(itemDescription.text()).toEqual('community resource'); - }); - }); - - describe('Software object with a single reference', () => { - let software; - let summary; - - beforeAll(() => { - const contextRef = _.clone(context); - contextRef.references = [require('../testdata/publication/publication')]; - contextRef.references[0].identifiers = ['PMID:19352372', 'PMCID:PMC3062402']; - - software = mount( - - ); - - summary = software.find('.key-value'); - }); - - it('has two references with proper links', () => { - const item = summary.find('[data-test="references"]'); - const itemDescription = item.find('dd'); - const ul = itemDescription.find('ul'); - const lis = ul.find('li'); - expect(lis).toHaveLength(2); - - let anchor = lis.at(0).find('a'); - expect(anchor.at(0).text()).toEqual('PMID:19352372'); - expect(anchor.at(0).prop('href')).toEqual('/publications/52e85c70-fe2d-11e3-9191-0800200c9a66/'); - - anchor = lis.at(1).find('a'); - expect(anchor.at(0).text()).toEqual('PMCID:PMC3062402'); - expect(anchor.at(0).prop('href')).toEqual('/publications/52e85c70-fe2d-11e3-9191-0800200c9a66/'); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/sorttable-test.js b/src/encoded/static/components/__tests__/sorttable-test.js deleted file mode 100644 index 1dd2ba9642..0000000000 --- a/src/encoded/static/components/__tests__/sorttable-test.js +++ /dev/null @@ -1,118 +0,0 @@ -import React from 'react'; -import { mount } from 'enzyme'; -import moment from 'moment'; - -// Import test component. -import { SortTablePanel, SortTable } from '../sorttable'; - - -describe('Software', () => { - const tableConfig = { - accession: { - title: 'Accession', - }, - file_type: { - title: 'File type', - }, - output_type: { - title: 'Output type', - }, - biological_replicates: { - title: 'Biological replicates', - getValue: item => (item.biological_replicates ? item.biological_replicates.sort((a, b) => a - b).join(', ') : ''), - }, - technical_replicate_number: { - title: 'Technical replicate', - getValue: item => (item.replicate ? item.replicate.technical_replicate_number : null), - }, - assembly: { - title: 'Mapping assembly', - }, - genome_annotation: { - title: 'Genome annotation', - }, - title: { - title: 'Lab', - getValue: item => (item.lab && item.lab.title ? item.lab.title : null), - }, - date_created: { - title: 'Date added', - getValue: item => moment.utc(item.date_created).format('YYYY-MM-DD'), - sorter: (a, b) => { - if (a.date_created && b.date_created) { - return Date.parse(a.date_created) - Date.parse(b.date_created); - } - // Arguably better as a nested ternary with parens, but eslint currently has no - // option for this. - // https://github.com/eslint/eslint/issues/3480 - if (a.date_created) { - return -1; - } - if (b.date_created) { - return 1; - } - return 0; - }, - }, - }; - - describe('Make a table with no footer and verify row and column counts', () => { - let table; - let tableOutput; - let rows; - - beforeAll(() => { - const file0 = require('../testdata/file/fastq.js')[0]; - file0.replicate = require('../testdata/replicate/human.js'); - const files = [file0]; - table = mount( - - - - ); - - tableOutput = table.find('table'); - rows = tableOutput.find('tr'); - }); - - it('has the correct number of rows', () => { - expect(tableOutput).toHaveLength(1); - expect(rows).toHaveLength(2); - }); - - it('has the correct number of columns', () => { - const cells = rows.at(1).find('td'); - expect(cells).toHaveLength(9); - }); - }); - - describe('Make a table with footer and verify row and column counts', () => { - let table; - let tableOutput; - let rows; - - beforeAll(() => { - const file0 = require('../testdata/file/fastq.js')[0]; - file0.replicate = require('../testdata/replicate/human.js'); - const files = [file0]; - table = mount( - - - - ); - - tableOutput = table.find('table'); - rows = tableOutput.find('tr'); - }); - - it('has the correct number of rows', () => { - expect(tableOutput).toHaveLength(1); - expect(rows).toHaveLength(3); - }); - - it('has the correct number of columns', () => { - const cells = rows.at(1).find('td'); - expect(cells).toHaveLength(9); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/status-test.js b/src/encoded/static/components/__tests__/status-test.js deleted file mode 100644 index bb50b19884..0000000000 --- a/src/encoded/static/components/__tests__/status-test.js +++ /dev/null @@ -1,105 +0,0 @@ -import React from 'react'; -import { shallow } from 'enzyme'; -import Status, { getObjectStatuses } from '../status'; - - -describe('Status utility and component tests', () => { - // Test getObjectStatuses function for success cases. - describe('getObjectStatuses successful', () => { - test('has the proper number of statuses at each access level for Datasets', () => { - let statuses = getObjectStatuses('Dataset', 'external'); - expect(statuses).toHaveLength(3); - statuses = getObjectStatuses('Dataset', 'consortium'); - expect(statuses).toHaveLength(5); - statuses = getObjectStatuses('Dataset', 'administrator'); - expect(statuses).toHaveLength(7); - statuses = getObjectStatuses('Dataset'); - expect(statuses).toHaveLength(3); - }); - }); - - // Make sure getObjectStatuses function fails properly. - describe('getObjectStatuses failures', () => { - test('fails by returning empty array', () => { - let statuses = getObjectStatuses('Assay', 'public'); - expect(statuses).toHaveLength(0); - statuses = getObjectStatuses('Dataset', 'faculty'); - expect(statuses).toHaveLength(0); - }); - }); - - // Test the component. - describe('Generate correct status badge components', () => { - let context; - - beforeAll(() => { - context = { - '@type': ['FlyDonor', 'Donor', 'Item'], - status: 'in progress', - }; - }); - - test('has an SVG, correct label, and correct status CSS class', () => { - const status = shallow( - - ); - const statusWrapper = status.find('.status'); - expect(statusWrapper.length).toBe(1); - expect(status.find('.status--in-progress').length).toBe(1); - - // Make sure the Status component has an icon with an svg in it. - const statusIcon = statusWrapper.find('.status__icon'); - expect(statusIcon.length).toBe(1); - expect(statusIcon.find('svg').length).toBe(1); - - const statusLabel = statusWrapper.find('.status__label'); - expect(statusLabel.length).toBe(1); - expect(statusLabel.text()).toEqual('in progress'); - }); - - test('has optional tooltip', () => { - const status = shallow( - - ); - expect(status.find({ title: 'This is a tooltip' }).length).toEqual(1); - }); - - test('has optional added CSS classes', () => { - const status = shallow( - - ); - expect(status.find('.class1').length).toEqual(1); - expect(status.find('.class2').length).toEqual(1); - }); - - test('missing label when requested', () => { - const status = shallow( - - ); - const statusWrapper = status.find('.status'); - expect(statusWrapper.find('.status__label').length).toEqual(0); - }); - - test('missing icon when requested', () => { - const status = shallow( - - ); - const statusWrapper = status.find('.status'); - expect(statusWrapper.find('.status__icon').length).toEqual(0); - }); - }); -}); diff --git a/src/encoded/static/components/__tests__/store-test.js b/src/encoded/static/components/__tests__/store-test.js deleted file mode 100644 index 8e7fd60093..0000000000 --- a/src/encoded/static/components/__tests__/store-test.js +++ /dev/null @@ -1,144 +0,0 @@ -import 'whatwg-fetch'; -import ItemStore from '../lib/store'; - - -/* eslint no-underscore-dangle: ["error", { "allow": ["_items"] }] */ - -describe('ItemStore', () => { - let items; - let view; - let fetch; - - beforeEach(() => { - fetch = jest.fn(); - fetch.mockResponse = function mockResponse(data, options) { - this.mockReturnValue(Promise.resolve(new Response(JSON.stringify(data), options || { status: 200 }))); - }; - items = [{ '@id': '/items/foo/' }]; - view = { - context: { fetch }, - setState: jest.fn(), - }; - }); - - describe('Instantiating a store', () => { - let store; - - beforeEach(() => { - store = new ItemStore(items, view, 'items'); - }); - - test('holds the initial items', () => { - expect(store._items).toHaveLength(1); - }); - }); - - describe('Creating an item', () => { - let store; - let done; - - beforeEach(() => { - view.onCreate = jest.fn(); - fetch.mockResponse({ - '@graph': [{ '@id': '/items/bar/' }], - }); - - store = new ItemStore(items, view, 'items'); - done = store.create('/items/', { '@id': 'bar' }); - }); - - it('posts the item to the backend', () => - done.then(() => expect(fetch.mock.calls.length).toEqual(1)) - ); - - it('updates the internal list of items', () => - done.then(() => expect(store._items.length).toEqual(2)) - ); - - it('calls the view onCreate callback with the response', () => - done.then(() => { - expect(view.onCreate).toBeCalledWith({ '@graph': [{ '@id': '/items/bar/' }] }); - }) - ); - - it('notifies the view of its new state', () => - done.then(() => expect(view.setState.mock.calls[0][0].items.length).toEqual(2)) - ); - }); - - describe('Updating an item', () => { - let store; - let done; - - beforeEach(() => { - view.onUpdate = jest.fn(); - fetch.mockResponse({}); - - store = new ItemStore(items, view, 'items'); - done = store.update({ '@id': '/items/foo/', updated: true }); - }); - - it('puts the item to the backend', () => - done.then(() => { - expect(fetch.mock.calls.length).toEqual(1); - const args = fetch.mock.calls[0]; - expect(args[1].method).toEqual('PUT'); - }) - ); - - it('updates the internal list of items', () => - done.then(() => expect(store._items[0].updated).toBe(true)) - ); - - it('calls the view onUpdate callback with the response', () => - done.then(() => { - expect(view.onUpdate).toBeCalledWith({ '@id': '/items/foo/', updated: true }); - }) - ); - }); - - describe('Deleting an item', () => { - let store; - let done; - - beforeEach(() => { - view.onDelete = jest.fn(); - fetch.mockResponse({}); - - store = new ItemStore(items, view, 'items'); - done = store.delete('/items/foo/'); - }); - - it('updates the status on the backend', () => - done.then(() => { - expect(fetch.mock.calls.length).toEqual(1); - const args = fetch.mock.calls[0]; - expect(args[1].method).toEqual('PATCH'); - const body = JSON.parse(args[1].body); - expect(body).toEqual({ status: 'deleted' }); - }) - ); - - it('updates the internal list of items', () => - done.then(() => expect(store._items.length).toEqual(0)) - ); - - it('calls the view onDelete callback with the removed item', () => - done.then(() => { - expect(view.onDelete).toBeCalledWith({ '@id': '/items/foo/' }); - }) - ); - }); - - describe('Reporting errors', () => { - it('calls the view onError callback in case of HTTP errors', () => { - view.onError = jest.genMockFunction(); - fetch.mockResponse({ message: 'failure' }, { status: 500, headers: new Headers({ 'Content-Type': 'application/json' }) }); - - const store = new ItemStore(items, view, 'items'); - return store.create('/items/', {}).then(() => { - expect(view.onError.mock.calls[0][0].message).toEqual('failure'); - }); - }); - }); -}); diff --git a/src/encoded/static/components/antibody.js b/src/encoded/static/components/antibody.js deleted file mode 100644 index 0db197b47a..0000000000 --- a/src/encoded/static/components/antibody.js +++ /dev/null @@ -1,700 +0,0 @@ -import React from 'react'; -import PropTypes from 'prop-types'; -import url from 'url'; -import _ from 'underscore'; -import { auditDecor } from './audit'; -import { Panel, PanelBody } from '../libs/bootstrap/panel'; -import { collapseIcon } from '../libs/svg-icons'; -import * as globals from './globals'; -import { Breadcrumbs } from './navigation'; -import { DbxrefList } from './dbxref'; -import { DocumentsPanel, Document, DocumentPreview, CharacterizationDocuments } from './doc'; -import { RelatedItems } from './item'; -import { AlternateAccession, DisplayAsJson } from './objectutils'; -import { PickerActions } from './search'; -import Status, { getObjectStatuses, sessionToAccessLevel } from './status'; -import { ExperimentTable } from './typeutils'; - - -// Order that antibody statuses should be displayed. -const antibodyStatusOrder = [ - 'characterized to standards', - 'characterized to standards with exemption', - 'awaiting characterization', - 'partially characterized', - 'not pursued', - 'not characterized to standards', -]; - - -const LotComponent = (props, reactContext) => { - const context = props.context; - - // Sort characterization arrays, filtering for the current logged-in and administrative status. - const accessLevel = sessionToAccessLevel(reactContext.session, reactContext.session_properties); - const viewableStatuses = getObjectStatuses('AntibodyCharacterization', accessLevel); - let characterizations = context.characterizations.filter(characterization => viewableStatuses.indexOf(characterization.status) !== -1); - characterizations = _(characterizations).sortBy(characterization => ([ - characterization.target.label, - characterization.target.organism ? characterization.target.organism.name : characterization.target.investigated_as[0], - ])); - - // Compile the document list - const documentSpecs = [ - { documents: characterizations }, - ]; - - // Build antibody status panel - const PanelView = globals.panelViews.lookup(context); - const antibodyStatuses = ; - - // Make an array of targets with no falsy entries and no repeats - const targets = {}; - if (context.lot_reviews && context.lot_reviews.length) { - context.lot_reviews.forEach((lotReview) => { - lotReview.targets.forEach((target) => { - targets[target['@id']] = target; - }); - }); - } - const targetKeys = Object.keys(targets); - - // Build lists of organism names and gene symbols from the target objects. We have to remember - // whether the organism name comes from the organism object or from `investigated_as`, so the - // list of organism names uses an object for each element including a boolean indicating its - // source. - let organisms = []; - let genes = []; - targetKeys.forEach((key) => { - if (targets[key].organism) { - organisms.push({ name: targets[key].organism.scientific_name, noOrganism: false }); - if (targets[key].genes && targets[key].genes.length > 0) { - genes.push(...targets[key].genes.map(gene => gene.symbol)); - } - } else { - organisms.push({ name: targets[key].investigated_as[0], noOrganism: true }); - } - }); - - // Build up the organism breadcrumb components. - let organismComponents = null; - let organismQuery = ''; - if (organisms.length > 0) { - // Remove duplicates from organism list. Concat with `noOrganism` flag in case of a - // organism/non-organism name clash. - organisms = _.uniq(organisms, organism => `${organism.name}${organism.noOrganism}`); - organismComponents = organisms.map((organism, i) => { - const organismName = organism.noOrganism ? {organism.name} : {organism.name}; - return {i > 0 ? + {organismName} : {organismName}}; - }); - organismQuery = organisms.map(organism => `${organism.noOrganism ? 'targets.investigated_as' : 'targets.organism.scientific_name'}=${globals.encodedURIComponent(organism.name)}`).join('&'); - } - - // Build up the gene breadcrumb components. - let geneComponents = null; - let geneQuery = ''; - if (genes.length > 0) { - genes = _.uniq(genes); - geneComponents = genes.map((gene, i) => {i > 0 ? + {gene} : {gene}}); - geneQuery = genes.map(gene => `targets.genes.symbol=${globals.encodedURIComponent(gene)}`).join('&'); - } - - // Build the breadcrumb object with option gene component. - const crumbs = [ - { id: 'Antibodies' }, - { id: organismComponents, query: organismQuery, tip: organisms.map(organism => organism.name).join(' + ') }, - { id: geneComponents, query: geneQuery, tip: genes.join(' + ') }, - ]; - - const crumbsReleased = (context.status === 'released'); - - return ( -
      -
      -
      - -

      {context.accession}

      - -

      - {targetKeys.length ? - - Antibody against {Object.keys(targets).map((target, i) => { - const targetObj = targets[target]; - return {i !== 0 ? ', ' : ''}{targetObj.organism ? {targetObj.organism.scientific_name} : {targetObj.investigated_as[0]}}{` ${targetObj.label}`}; - })} - - : - Antibody - } -

      - {props.auditIndicators(context.audit, 'antibody-audit', { session: reactContext.session })} - -
      -
      - {props.auditDetail(context.audit, 'antibody-audit', { except: context['@id'], session: reactContext.session })} - -
      - {antibodyStatuses} -
      - - - -
      -
      -
      Status
      -
      -
      - -
      - -
      -
      Product ID
      -
      {context.product_id}
      -
      - -
      -
      Lot ID
      -
      {context.lot_id}
      -
      - - {Object.keys(targets).length ? -
      -
      Characterized targets
      -
      - {targetKeys.map((target, i) => { - const targetObj = targets[target]; - return {i !== 0 ? ', ' : ''}{targetObj.label}{' ('}{targetObj.organism ? {targetObj.organism.scientific_name} : {targetObj.investigated_as[0]}}{')'}; - })} -
      -
      - : null} - - {context.lot_id_alias && context.lot_id_alias.length ? -
      -
      Lot ID aliases
      -
      {context.lot_id_alias.join(', ')}
      -
      - : null} - -
      -
      Host
      -
      {context.host_organism.name}
      -
      - - {context.clonality ? -
      -
      Clonality
      -
      {context.clonality}
      -
      - : null} - - {context.purifications && context.purifications.length ? -
      -
      Purification
      -
      {context.purifications.join(', ')}
      -
      - : null} - - {context.isotype ? -
      -
      Isotype
      -
      {context.isotype}
      -
      - : null} - - {context.antigen_description ? -
      -
      Antigen description
      -
      {context.antigen_description}
      -
      - : null} - - {context.antigen_sequence ? -
      -
      Antigen sequence
      -
      {context.antigen_sequence}
      -
      - : null} - - {context.aliases && context.aliases.length ? -
      -
      Aliases
      -
      {context.aliases.join(', ')}
      -
      - : null} - - {context.dbxrefs && context.dbxrefs.length ? -
      -
      External resources
      -
      -
      - : null} -
      - - - - - - -
      - ); -}; - -LotComponent.propTypes = { - context: PropTypes.object.isRequired, - auditIndicators: PropTypes.func.isRequired, // Audit decorator function - auditDetail: PropTypes.func.isRequired, // Audit decorator function -}; - -LotComponent.contextTypes = { - session: PropTypes.object, // Login session information - session_properties: PropTypes.object, // Logged-in user information -}; - -const Lot = auditDecor(LotComponent); - -globals.contentViews.register(Lot, 'AntibodyLot'); - -// Must export for Jest testing. -export default Lot; - - -const AntibodyStatus = (props) => { - const context = props.context; - - // Sort the lot reviews by their status according to our predefined order - // given in the statusOrder array we imported from globals.js. - const lotReviews = _.sortBy(context.lot_reviews, (lotReview => - antibodyStatusOrder.indexOf(lotReview.status) - )); - - // Build antibody display object as a hierarchy: status=>organism=>biosample_term_name - const statusTree = {}; - lotReviews.forEach((lotReview) => { - // Status at top of hierarchy. If haven’t seen this status before, remember it - if (!statusTree[lotReview.status]) { - statusTree[lotReview.status] = {}; - } - - // Look at all organisms in current lot_review. They go under this lot_review's status - const statusNode = statusTree[lotReview.status]; - if (lotReview.organisms.length === 0) { - lotReview.organisms = [null]; - } - lotReview.organisms.forEach((organism) => { - const source = organism ? organism.scientific_name : lotReview.targets[0].investigated_as[0]; - // If haven’t seen this source (organism) with this status before, remember it - if (!statusNode[source]) { - statusNode[source] = {}; - } - - // If haven't seen this biosample term name for this organism, remember it - const organismNode = statusNode[source]; - if (!organismNode[lotReview.biosample_term_name]) { - organismNode[lotReview.biosample_term_name] = true; - } - }); - }); - - return ( - - - {Object.keys(statusTree).map((status) => { - const organisms = statusTree[status]; - return ( -
      - {Object.keys(organisms).map((organism, i) => { - const terms = Object.keys(organisms[organism]); - return ( -
      -
      - {organism} -
      -
      - {terms.length === 1 && terms[0] === 'not specified' ? '' : terms.join(', ')} -
      -
      - {i === 0 ? : null} -
      -
      - ); - })} -
      - ); - })} -
      -
      - ); -}; - -AntibodyStatus.propTypes = { - context: PropTypes.object.isRequired, -}; - -globals.panelViews.register(AntibodyStatus, 'AntibodyLot'); - - -// Antibody characterization documents - -const EXCERPT_LENGTH = 80; // Maximum number of characters in an excerpt - -// Document header component -- antibody characterization -const CharacterizationHeader = (props) => { - const doc = props.doc; - - return ( -
      -
      - {doc.target.label} {' ('}{doc.target.organism ? {doc.target.organism.scientific_name} : {doc.target.investigated_as[0]}}{')'} -
      - {doc.characterization_reviews && doc.characterization_reviews.length ? -
      - {doc.characterization_reviews.map(review => ( - {review.biosample_term_name} - ))} -
      - : null} -
      - ); -}; - -CharacterizationHeader.propTypes = { - doc: PropTypes.object.isRequired, // Document object to render -}; - - -// Document caption component -- antibody characterization -const CharacterizationCaption = (props) => { - const doc = props.doc; - - return ( -
      - {doc.characterization_method ? -
      - Method: - {doc.characterization_method} -
      - : null} -
      - ); -}; - -CharacterizationCaption.propTypes = { - doc: PropTypes.object.isRequired, // Document object to render -}; - - -const CharacterizationFile = (props) => { - const { doc, detailOpen, detailSwitch } = props; - - return ( -
      -
      - {detailSwitch ? - - : null} -
      - ); -}; - -CharacterizationFile.propTypes = { - doc: PropTypes.object.isRequired, // Document object to render - detailOpen: PropTypes.bool, // True if detail panel is visible - detailSwitch: PropTypes.func, // Parent component function to call when detail switch clicked -}; - -CharacterizationFile.defaultProps = { - detailOpen: false, - detailSwitch: null, -}; - - -const CharacterizationDetail = (props) => { - const { doc, detailOpen, id } = props; - const keyClass = `document__detail${detailOpen ? ' active' : ''}`; - const excerpt = doc.caption && doc.caption.length > EXCERPT_LENGTH; - - let download; - let attachmentHref; - if (doc.attachment && doc.attachment.href && doc.attachment.download) { - attachmentHref = url.resolve(doc['@id'], doc.attachment.href); - download = ( -
      -   - - {doc.attachment.download} - -
      - ); - } else { - download = ( - Document not available - ); - } - - return ( -
      -
      - {excerpt ? -
      -
      Caption
      -
      {doc.caption}
      -
      - : null} - - {doc.submitter_comment ? -
      -
      Submitter comment
      -
      {doc.submitter_comment}
      -
      - : null} - - {doc.notes ? -
      -
      Reviewer comment
      -
      {doc.notes}
      -
      - : null} - - {doc.submitted_by && doc.submitted_by.title ? -
      -
      Submitted by
      -
      {doc.submitted_by.title}
      -
      - : null} - -
      -
      Lab
      -
      {doc.lab.title}
      -
      - -
      -
      Grant
      -
      {doc.award.name}
      -
      - -
      -
      Download
      - {download} -
      - - {doc.documents && doc.documents.length ? -
      -
      Documents
      - -
      - : null} -
      -
      - ); -}; - -CharacterizationDetail.propTypes = { - doc: PropTypes.object.isRequired, // Document object to render - detailOpen: PropTypes.bool, // True if detail panel is visible - id: PropTypes.string, // Unique key for identification -}; - -CharacterizationDetail.defaultProps = { - detailOpen: false, - id: '', -}; - - -// Parts of individual document panels -globals.panelViews.register(Document, 'AntibodyCharacterization'); -globals.documentViews.header.register(CharacterizationHeader, 'AntibodyCharacterization'); -globals.documentViews.caption.register(CharacterizationCaption, 'AntibodyCharacterization'); -globals.documentViews.preview.register(DocumentPreview, 'AntibodyCharacterization'); -globals.documentViews.file.register(CharacterizationFile, 'AntibodyCharacterization'); -globals.documentViews.detail.register(CharacterizationDetail, 'AntibodyCharacterization'); - - -// Display one antibody status indicator -class StatusIndicator extends React.Component { - constructor() { - super(); - - // Set initial React component state. - this.state = { - tipOpen: false, - tipStyles: {}, - }; - - // Bind `this` to non-React methods. - this.onMouseEnter = this.onMouseEnter.bind(this); - this.onMouseLeave = this.onMouseLeave.bind(this); - } - - // Display tooltip on hover - onMouseEnter() { - function getNextElementSibling(el) { - // IE8 doesn't support nextElementSibling - return el.nextElementSibling ? el.nextElementSibling : el.nextSibling; - } - - // Get viewport bounds of result table and of this tooltip - let whiteSpace = 'nowrap'; - const resultBounds = document.getElementById('result-table').getBoundingClientRect(); - const resultWidth = resultBounds.right - resultBounds.left; - const tipBounds = _.clone(getNextElementSibling(this.indicator).getBoundingClientRect()); - const tipWidth = tipBounds.right - tipBounds.left; - let width = tipWidth; - if (tipWidth > resultWidth) { - // Tooltip wider than result table; set tooltip to result table width and allow text to wrap - tipBounds.right = (tipBounds.left + resultWidth) - 2; - whiteSpace = 'normal'; - width = tipBounds.right - tipBounds.left - 2; - } - - // Set an inline style to move the tooltip if it runs off right edge of result table - const leftOffset = resultBounds.right - tipBounds.right; - if (leftOffset < 0) { - // Tooltip goes outside right edge of result table; move it to the left - this.setState({ tipStyles: { left: `${leftOffset + 10}px`, maxWidth: `${resultWidth}px`, whiteSpace, width: `${width}px` } }); - } else { - // Tooltip fits inside result table; move it to native position - this.setState({ tipStyles: { left: '10px', maxWidth: `${resultWidth}px`, whiteSpace, width: `${width}px` } }); - } - - this.setState({ tipOpen: true }); - } - - // Close tooltip when not hovering - onMouseLeave() { - this.setState({ tipStyles: { maxWidth: 'none', whiteSpace: 'nowrap', width: 'auto', left: '15px' } }); // Reset position and width - this.setState({ tipOpen: false }); - } - - render() { - const classes = `tooltip-status sentence-case${this.state.tipOpen ? ' tooltipopen' : ''}`; - - return ( - - { this.indicator = indicator; }} onMouseEnter={this.onMouseEnter} onMouseLeave={this.onMouseLeave}> - - -
      - {this.props.status}
      {this.props.terms.join(', ')} -
      -
      - ); - } -} - -StatusIndicator.propTypes = { - status: PropTypes.string, - terms: PropTypes.array.isRequired, -}; - -StatusIndicator.defaultProps = { - status: '', -}; - - -// Display the status indicators for one target -const StatusIndicators = (props) => { - const { targetTree, target } = props; - - return ( - - {Object.keys(targetTree[target]).map((status, i) => { - if (status !== 'target') { - return ; - } - return null; - })} - - ); -}; - -StatusIndicators.propTypes = { - targetTree: PropTypes.object.isRequired, - target: PropTypes.string.isRequired, -}; - - -const ListingComponent = (props, reactContext) => { - const result = props.context; - - // Sort the lot reviews by their status according to our predefined order - // given in the statusOrder array. - const lotReviews = _.sortBy(result.lot_reviews, lotReview => antibodyStatusOrder.indexOf(lotReview.status)); - - // Build antibody display object as a hierarchy: target=>status=>biosample_term_names - const targetTree = {}; - lotReviews.forEach((lotReview) => { - lotReview.targets.forEach((target) => { - // If we haven't seen this target, save it in targetTree along with the - // corresponding target and organism structures. - if (!targetTree[target.name]) { - targetTree[target.name] = { target }; - } - const targetNode = targetTree[target.name]; - - // If we haven't seen the status, save it in the targetTree target - if (!targetNode[lotReview.status]) { - targetNode[lotReview.status] = []; - } - const statusNode = targetNode[lotReview.status]; - - // If we haven't seen the biosample term name, save it in the targetTree target status - if (statusNode.indexOf(lotReview.biosample_term_name) === -1) { - statusNode.push(lotReview.biosample_term_name); - } - }); - }); - - return ( -
    • -
      - -
      -

      Antibody

      -

      {` ${result.accession}`}

      - - {props.auditIndicators(result.audit, result['@id'], { session: reactContext.session, search: true })} -
      - -
      -
      Source: {result.source.title}
      -
      Product ID / Lot ID: {result.product_id} / {result.lot_id}
      -
      -
      - {props.auditDetail(result.audit, result['@id'], { session: reactContext.session, except: result['@id'], forcedEditLink: true })} -
    • - ); -}; - -ListingComponent.propTypes = { - context: PropTypes.object.isRequired, // Antibody search results - auditIndicators: PropTypes.func.isRequired, // Audit decorator function - auditDetail: PropTypes.func.isRequired, // Audit decorator function -}; - -ListingComponent.contextTypes = { - session: PropTypes.object, // Login information from -}; - -const Listing = auditDecor(ListingComponent); - -globals.listingViews.register(Listing, 'AntibodyLot'); diff --git a/src/encoded/static/components/app.js b/src/encoded/static/components/app.js index aed6c84381..5b6a84a26c 100644 --- a/src/encoded/static/components/app.js +++ b/src/encoded/static/components/app.js @@ -2,18 +2,14 @@ import React from 'react'; import PropTypes from 'prop-types'; import serialize from 'form-serialize'; import ga from 'google-analytics'; -import { Provider } from 'react-redux'; import _ from 'underscore'; import url from 'url'; import jsonScriptEscape from '../libs/jsonScriptEscape'; import origin from '../libs/origin'; -import initializeCart, { cartAddElements, cartCacheSaved, cartSave } from './cart'; import { BrowserFeat } from './browserfeat'; import * as globals from './globals'; import Navigation from './navigation'; import Footer from './footer'; -import Home from './home'; -import newsHead from './page'; const portal = { @@ -155,12 +151,6 @@ class App extends React.Component { promisePending: false, }; - this.cartStore = initializeCart(); - - this.triggers = { - profile: 'triggerProfile' - }; - // Bind this to non-React methods. this.fetch = this.fetch.bind(this); this.fetchSessionProperties = this.fetchSessionProperties.bind(this); @@ -172,7 +162,6 @@ class App extends React.Component { this.handleSubmit = this.handleSubmit.bind(this); this.handlePopState = this.handlePopState.bind(this); this.confirmNavigation = this.confirmNavigation.bind(this); - this.handleBeforeUnload = this.handleBeforeUnload.bind(this); this.navigate = this.navigate.bind(this); this.receiveContextResponse = this.receiveContextResponse.bind(this); this.listActionsFor = this.listActionsFor.bind(this); @@ -208,20 +197,10 @@ class App extends React.Component { session_cookie: sessionCookie, session, }); - + // Set browser features in the CSS class. BrowserFeat.setHtmlFeatClass(); - // Make a URL for the logo. - const hrefInfo = url.parse(this.state.href); - const logoHrefInfo = { - hostname: hrefInfo.hostname, - port: hrefInfo.port, - protocol: hrefInfo.protocol, - pathname: '/static/img/RegulomeLogoFinal.gif', - }; - const logoUrl = url.format(logoHrefInfo); - // Initialize browesr history mechanism if (this.constructor.historyEnabled()) { const data = this.props.context; @@ -261,7 +240,6 @@ class App extends React.Component { } else { window.onhashchange = this.onHashChange; } - window.onbeforeunload = this.handleBeforeUnload; } shouldComponentUpdate(nextProps, nextState) { @@ -363,7 +341,6 @@ class App extends React.Component { return response.json(); }).then((sessionProperties) => { this.setState({ session_properties: sessionProperties }); - return this.initializeCartFromSessionProperties(sessionProperties); }); } @@ -401,75 +378,6 @@ class App extends React.Component { }); } - // Retrieve the cart contents for the current logged-in user and add them to the in-memory cart. - initializeCartFromSessionProperties(sessionProperties) { - // Retrieve the logged-in user's cart. - cartCacheSaved({}, this.cartStore.dispatch); - const savedCartObjPromise = this.fetch('/carts/@@get-cart', { - method: 'GET', - headers: { - Accept: 'application/json', - }, - }).then((response) => { - if (response.ok) { - return response.json(); - } - throw new Error(response); - }).then((userCart) => { - const userCartAtId = userCart['@graph'].length > 0 ? userCart['@graph'][0] : null; - if (userCartAtId) { - return this.fetch(`${userCartAtId}?datastore=database`, { - method: 'GET', - headers: { - Accept: 'application/json', - }, - }); - } - return Promise.resolve(null); - }).then((response) => { - if (!response) { - // No saved cart for the user. - return null; - } - if (response.ok) { - // Decode the user's saved cart. - return response.json(); - } - throw new Error(response); - }); - - // Once we have the user's first saved cart object, see if we need to merge it into the - // user's in-memory cart, and whether we then have to save the updated cart. - savedCartObjPromise.then((savedCartObj) => { - const savedCart = (savedCartObj && savedCartObj.elements) || []; - let memoryCart = this.cartStore.getState().cart; - if (memoryCart.length !== savedCart.length || !_.isEqual(memoryCart, savedCart)) { - // We now know the saved and in-memory carts are different somehow. If the user has - // a saved cart, merge its contents with the in-memory cart. - if (savedCartObj) { - cartAddElements(savedCart, this.cartStore.dispatch); - cartCacheSaved(savedCartObj, this.cartStore.dispatch); - } - - // Save the (updated if it got merged with the saved cart) in-memory cart if it had - // anything in it on page load. - if (memoryCart.length > 0) { - memoryCart = this.cartStore.getState().cart; - return cartSave(memoryCart, savedCartObj, sessionProperties.user, this.fetch).then((updatedSavedCartObj) => { - cartCacheSaved(updatedSavedCartObj, this.cartStore.dispatch); - }); - } - } else if (savedCartObj) { - // User has a cart object from before. Cache the user's cart so we know what cart - // to save to. - cartCacheSaved(savedCartObj, this.cartStore.dispatch); - } - return savedCartObj; - }).catch((err) => { - globals.parseAndLogError('Load savedCartObj on page load', err); - }); - } - /* eslint no-script-url: 0 */ // We're not *using* a javascript: link -- just checking them. handleClick(event) { // https://github.com/facebook/react/issues/1691 @@ -567,7 +475,6 @@ class App extends React.Component { } const options = {}; - const actionUrl = url.parse(url.resolve(this.state.href, target.action)); let search = serialize(target); if (target.getAttribute('data-removeempty')) { @@ -632,17 +539,6 @@ class App extends React.Component { return true; } - handleBeforeUnload() { - // Determine if the cart has items in it but no saved cart object exists. - const cartState = this.cartStore.getState(); - const unsavedCart = cartState.cart.length > 0 && Object.keys(cartState.savedCartObj).length === 0; - - if (this.state.unsavedChanges.length || unsavedCart) { - return 'You have unsaved changes.'; - } - return undefined; - } - navigate(href, options) { const mutatableOptions = options || {}; if (!this.confirmNavigation()) { @@ -837,20 +733,14 @@ class App extends React.Component { // Switching between collections may leave component in place const key = context && context['@id'] && context['@id'].split('?')[0]; const currentAction = this.currentAction(); - const isHomePage = context.default_page && context.default_page.name === 'homepage' && (!hrefUrl.hash || hrefUrl.hash === '#logged-out'); - if (isHomePage) { + const isHomePage = null; + if (!currentAction && context.default_page) { context = context.default_page; - content = ; - containerClass = 'container-homepage'; - } else { - if (!currentAction && context.default_page) { - context = context.default_page; - } - if (context) { - const ContentView = globals.contentViews.lookup(context, currentAction); - content = ; - containerClass = 'container'; - } + } + if (context) { + const ContentView = globals.contentViews.lookup(context, currentAction); + content = ; + containerClass = 'container'; } const errors = this.state.errors.map(i =>
      ); @@ -897,7 +787,6 @@ class App extends React.Component { {this.props.inline ?