From f676bd44ae22b272bea87d0563f30aba26882e50 Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Tue, 13 Feb 2018 12:16:25 -0800 Subject: [PATCH 01/10] Reorganize Features tab components into separate files --- static/js/components/Features.jsx | 266 ++------------------ static/js/components/FeaturesetsTable.jsx | 63 +++++ static/js/components/FeaturizeForm.jsx | 162 ++++++++++++ static/js/components/UploadFeaturesForm.jsx | 13 + 4 files changed, 253 insertions(+), 251 deletions(-) create mode 100644 static/js/components/FeaturesetsTable.jsx create mode 100644 static/js/components/FeaturizeForm.jsx create mode 100644 static/js/components/UploadFeaturesForm.jsx diff --git a/static/js/components/Features.jsx b/static/js/components/Features.jsx index c574f8e..51d5d44 100644 --- a/static/js/components/Features.jsx +++ b/static/js/components/Features.jsx @@ -5,175 +5,16 @@ import { reduxForm } from 'redux-form'; import ReactTabs from 'react-tabs'; import { FormComponent, Form, TextInput, TextareaInput, SubmitButton, - CheckBoxInput, SelectInput } from './Form'; + CheckBoxInput, SelectInput } from './Form'; import * as Validate from '../validate'; import Expand from './Expand'; import * as Action from '../actions'; import Plot from './Plot'; import FoldableRow from './FoldableRow'; import { reformatDatetime, contains } from '../utils'; -import Delete from './Delete'; -import Download from './Download'; - -const { Tab, Tabs, TabList, TabPanel } = { ...ReactTabs }; - - -let FeaturizeForm = (props) => { - const { fields, fields: { datasetID, featuresetName, customFeatsCode }, - handleSubmit, submitting, resetForm, error, featuresList, - featureDescriptions } = props; - const datasets = props.datasets.map(ds => ( - { id: ds.id, - label: ds.name } - )); - - return ( -
-
- - - - Select Features to Compute
- - Features associated with at least one checked tag will be shown below - { - props.tagList.map(tag => ( - { props.dispatch(Action.clickFeatureTagCheckbox(tag)); }} - /> - )) - } - - - - { - Object.keys(props.featuresByCategory).map((ctgy, idx) => ( - {ctgy} - )) - } - Custom Features - - { - Object.keys(props.featuresByCategory).map((ctgy, idx) => ( - - { - props.dispatch(Action.groupToggleCheckedFeatures( - props.featuresByCategory[ctgy] -)); -}} - > - Check/Uncheck All - - - - { - props.featuresByCategory[ctgy].filter(feat => ( - contains(featuresList, feat) - )).map((feature, idx2) => ( - - - - - )) - } - -
- - - {featureDescriptions[feature]} -
- - )) - } - - - - - -
- ); -}; -FeaturizeForm.propTypes = { - fields: PropTypes.object.isRequired, - datasets: PropTypes.arrayOf(PropTypes.object).isRequired, - error: PropTypes.string, - handleSubmit: PropTypes.func.isRequired, - submitting: PropTypes.bool.isRequired, - resetForm: PropTypes.func.isRequired, - selectedProject: PropTypes.object, - featuresByCategory: PropTypes.object, - tagList: PropTypes.arrayOf(PropTypes.string).isRequired, - featuresList: PropTypes.array, - featureDescriptions: PropTypes.object -}; -FeaturizeForm.defaultProps = { - error: "", - selectedProject: {}, - featuresByCategory: {}, - featuresList: [], - featureDescriptions: {} -}; - - -const mapStateToProps = (state, ownProps) => { - const featuresList = state.features.featsWithCheckedTags; - - const initialValues = { }; - featuresList.map((f, idx) => { initialValues[f] = true; return null; }); - - const filteredDatasets = state.datasets.filter(dataset => - (dataset.project_id === ownProps.selectedProject.id)); - const zerothDataset = filteredDatasets[0]; - - return { - featuresByCategory: state.features.features_by_category, - tagList: state.features.tagList, - featuresList, - featureDescriptions: state.features.descriptions, - datasets: filteredDatasets, - fields: featuresList.concat( - ['datasetID', 'featuresetName', 'customFeatsCode'] - ), - initialValues: { ...initialValues, - datasetID: zerothDataset ? zerothDataset.id.toString() : "", - customFeatsCode: "" } - }; -}; - -const validate = Validate.createValidator({ - datasetID: [Validate.required], - featuresetName: [Validate.required] -}); - -FeaturizeForm = reduxForm({ - form: 'featurize', - fields: [''], - validate -}, mapStateToProps)(FeaturizeForm); +import UploadFeaturesForm from './UploadFeaturesForm'; +import FeaturizeForm from './FeaturizeForm'; +import FeaturesetsTable from './FeaturesetsTable'; let FeaturesTab = (props) => { @@ -181,7 +22,7 @@ let FeaturesTab = (props) => { return (
- + {
- + + + +
+ + @@ -214,90 +64,4 @@ const ftMapDispatchToProps = dispatch => ( FeaturesTab = connect(null, ftMapDispatchToProps)(FeaturesTab); -export let FeatureTable = props => ( -
- - - - - - - - - - - { - props.featuresets.map((featureset, idx) => { - const done = featureset.finished; - const foldedContent = done && ( - - - ); - - let elapsed = ""; - let percent = ""; - if (featureset.progress) { - ({ elapsed, percent } = { ...featureset.progress }); - } - - let status; - if (done) { - status = ; - } else if (elapsed == "") { - status = ; - } else { - status = ; - } - - return ( - - - - - {status} - - - {foldedContent} - - ); -}) - } - -
NameCreatedStatusActions{ /* extra column for spacing */ } -
- -
Completed { reformatDatetime(featureset.finished) }In progress...In progress: { percent }%, { elapsed }s
{featureset.name}{reformatDatetime(featureset.created_at)} - { - done && - - } -    - -
-
-); -FeatureTable.propTypes = { - featuresets: PropTypes.arrayOf(PropTypes.object).isRequired, - featurePlotURL: PropTypes.string -}; -FeatureTable.defaultProps = { - featurePlotURL: null -}; - - -const ftMapStateToProps = (state, ownProps) => ( - { - featuresets: state.featuresets.filter( - fs => (fs.project_id === ownProps.selectedProject.id) - ) - } -); - -FeatureTable = connect(ftMapStateToProps)(FeatureTable); - -const mapDispatchToProps = dispatch => ( - { delete: id => dispatch(Action.deleteFeatureset(id)) } -); -const DeleteFeatureset = connect(null, mapDispatchToProps)(Delete); - export default FeaturesTab; diff --git a/static/js/components/FeaturesetsTable.jsx b/static/js/components/FeaturesetsTable.jsx new file mode 100644 index 0000000..bcdfed6 --- /dev/null +++ b/static/js/components/FeaturesetsTable.jsx @@ -0,0 +1,63 @@ +import React from 'react'; +import { connect } from 'react-redux'; + +import { reformatDatetime } from '../utils'; + + +const FeaturesetsTable = props => ( +
+

Feature Sets

+ + + + + + + + + + + { + props.featuresets.map((featureset, idx) => { + const done = featureset.finished; + const foldedContent = done && ( + + + ); + + const status = done ? : ; + + return ( + + + + + {status} + + + {foldedContent} + + ); }) + } + +
NameCreatedStatusActions{ /* extra column for spacing */ } +
+ +
Completed {reformatDatetime(featureset.finished)}In progress
{featureset.name}{reformatDatetime(featureset.created_at)}
+
+); +FeaturesetsTable.propTypes = { + featuresets: React.PropTypes.arrayOf(React.PropTypes.object), + featurePlotURL: React.PropTypes.string +}; + + +const ftMapStateToProps = (state, ownProps) => ( + { + featuresets: state.featuresets.filter( + fs => (fs.project_id === ownProps.selectedProject.id) + ) + } +); + +export default connect(ftMapStateToProps)(FeaturesetsTable); diff --git a/static/js/components/FeaturizeForm.jsx b/static/js/components/FeaturizeForm.jsx new file mode 100644 index 0000000..45a6001 --- /dev/null +++ b/static/js/components/FeaturizeForm.jsx @@ -0,0 +1,162 @@ +import React from 'react'; +import { reduxForm } from 'redux-form'; +import ReactTabs from 'react-tabs'; + +import * as Validate from '../validate'; +import { FormComponent, Form, TextInput, TextareaInput, SubmitButton, + CheckBoxInput, SelectInput } from './Form'; +import Expand from './Expand'; +import { contains } from '../utils'; + + +const Tab = ReactTabs.Tab; +const Tabs = ReactTabs.Tabs; +const TabList = ReactTabs.TabList; +const TabPanel = ReactTabs.TabPanel; + + +const FeaturizeForm = (props) => { + const { fields, fields: { datasetID, featuresetName, customFeatsCode }, + handleSubmit, submitting, resetForm, error, featuresList, + featureDescriptions } = props; + const datasets = props.datasets.map(ds => ( + { id: ds.id, + label: ds.name } + )); + + return ( +
+
+ + + + Select Features to Compute
+ + Features associated with at least one checked tag will be shown below + { + props.tagList.map(tag => ( + { props.dispatch(Action.clickFeatureTagCheckbox(tag)); }} + /> + )) + } + + + + { + Object.keys(props.featuresByCategory).map(ctgy => ( + {ctgy} + )) + } + Custom Features + + { + Object.keys(props.featuresByCategory).map(ctgy => ( + + { + props.dispatch(Action.groupToggleCheckedFeatures( + props.featuresByCategory[ctgy])); }} + > + Check/Uncheck All + + + + { + props.featuresByCategory[ctgy].filter(feat => ( + contains(featuresList, feat) + )).map((feature, idx) => ( + + + + + )) + } + +
+ + + {featureDescriptions[feature]} +
+ + )) + } + + + + + +
+ ); +}; +FeaturizeForm.propTypes = { + fields: React.PropTypes.object.isRequired, + datasets: React.PropTypes.arrayOf(React.PropTypes.object).isRequired, + error: React.PropTypes.string, + handleSubmit: React.PropTypes.func.isRequired, + submitting: React.PropTypes.bool.isRequired, + resetForm: React.PropTypes.func.isRequired, + selectedProject: React.PropTypes.object, + featuresByCategory: React.PropTypes.object, + tagList: React.PropTypes.arrayOf(React.PropTypes.string).isRequired, + featuresList: React.PropTypes.array, + featureDescriptions: React.PropTypes.object +}; + + +const mapStateToProps = (state, ownProps) => { + const featuresList = state.features.featsWithCheckedTags; + + const initialValues = { }; + featuresList.map((f, idx) => { initialValues[f] = true; return null; }); + + const filteredDatasets = state.datasets.filter(dataset => + (dataset.project_id === ownProps.selectedProject.id)); + const zerothDataset = filteredDatasets[0]; + + return { + featuresByCategory: state.features.features_by_category, + tagList: state.features.tagList, + featuresList, + featureDescriptions: state.features.descriptions, + datasets: filteredDatasets, + fields: featuresList.concat( + ['datasetID', 'featuresetName', 'customFeatsCode']), + initialValues: { ...initialValues, + datasetID: zerothDataset ? zerothDataset.id.toString() : "", + customFeatsCode: "" } + }; +}; + +const validate = Validate.createValidator({ + datasetID: [Validate.required], + featuresetName: [Validate.required] +}); + +export default reduxForm({ + form: 'featurize', + fields: [''], + validate +}, mapStateToProps)(FeaturizeForm); diff --git a/static/js/components/UploadFeaturesForm.jsx b/static/js/components/UploadFeaturesForm.jsx new file mode 100644 index 0000000..557e71b --- /dev/null +++ b/static/js/components/UploadFeaturesForm.jsx @@ -0,0 +1,13 @@ +import React from 'react'; + + +const UploadFeaturesForm = props => { + return ( +
+ Upload Features Form content +
+ ); +}; + + +export default UploadFeaturesForm; From 5bf2f0e051b531244e246a5b58eda80aab8b2300 Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Tue, 13 Feb 2018 16:58:33 -0800 Subject: [PATCH 02/10] Add associated dataset to all new featuresets --- cesium_app/handlers/feature.py | 1 + cesium_app/models.py | 5 +++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/cesium_app/handlers/feature.py b/cesium_app/handlers/feature.py index 8d84511..e0dcff2 100644 --- a/cesium_app/handlers/feature.py +++ b/cesium_app/handlers/feature.py @@ -99,6 +99,7 @@ async def post(self): fset = Featureset(name=featureset_name, file_uri=fset_path, project=dataset.project, + dataset=dataset, features_list=features_to_use, custom_features_script=None) DBSession().add(fset) diff --git a/cesium_app/models.py b/cesium_app/models.py index f538d17..adf357a 100644 --- a/cesium_app/models.py +++ b/cesium_app/models.py @@ -26,6 +26,7 @@ class Dataset(Base): project_id = sa.Column(sa.ForeignKey('projects.id', ondelete='CASCADE'), nullable=False, index=True) project = relationship('Project', back_populates='datasets') + featureset = relationship('Featureset', back_populates='dataset') files = relationship('DatasetFile', backref='dataset', cascade='all') def display_info(self): @@ -66,6 +67,8 @@ class Featureset(Base): project_id = sa.Column(sa.ForeignKey('projects.id', ondelete='CASCADE'), nullable=False, index=True) project = relationship('Project', back_populates='featuresets') + dataset_id = sa.Column(sa.ForeignKey('datasets.id')) + dataset = relationship('Dataset') name = sa.Column(sa.String(), nullable=False) features_list = sa.Column(sa.ARRAY(sa.VARCHAR()), nullable=False, index=True) custom_features_script = sa.Column(sa.String()) @@ -73,8 +76,6 @@ class Featureset(Base): task_id = sa.Column(sa.String()) finished = sa.Column(sa.DateTime) - project = relationship('Project') - class Model(Base): project_id = sa.Column(sa.ForeignKey('projects.id', ondelete='CASCADE'), From 89456dce69a71ac46d168b426899f562a5b87204 Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Thu, 15 Feb 2018 11:33:56 -0800 Subject: [PATCH 03/10] Add upload features functionality --- cesium_app/app_server.py | 2 + cesium_app/handlers/__init__.py | 1 + cesium_app/handlers/feature.py | 1 + static/js/actions.js | 49 +++++++++++++ static/js/components/Features.jsx | 6 +- static/js/components/FeaturesetsTable.jsx | 10 +++ static/js/components/FeaturizeForm.jsx | 3 +- static/js/components/UploadFeaturesForm.jsx | 76 ++++++++++++++++++++- 8 files changed, 143 insertions(+), 5 deletions(-) diff --git a/cesium_app/app_server.py b/cesium_app/app_server.py index 8b4b5c4..3f2a269 100644 --- a/cesium_app/app_server.py +++ b/cesium_app/app_server.py @@ -15,6 +15,7 @@ ProjectHandler, DatasetHandler, FeatureHandler, + PrecomputedFeaturesHandler, ModelHandler, PredictionHandler, FeatureListHandler, @@ -58,6 +59,7 @@ def make_app(cfg, baselayer_handlers, baselayer_settings): (r'/dataset(/.*)?', DatasetHandler), (r'/features(/[0-9]+)?', FeatureHandler), (r'/features/([0-9]+)/(download)', FeatureHandler), + (r'/precomputed_features(/.*)?', PrecomputedFeaturesHandler), (r'/models(/[0-9]+)?', ModelHandler), (r'/models/([0-9]+)/(download)', ModelHandler), (r'/predictions(/[0-9]+)?', PredictionHandler), diff --git a/cesium_app/handlers/__init__.py b/cesium_app/handlers/__init__.py index cdb6373..44b01ee 100644 --- a/cesium_app/handlers/__init__.py +++ b/cesium_app/handlers/__init__.py @@ -10,3 +10,4 @@ from .plot_features import PlotFeaturesHandler from .prediction import PredictionHandler, PredictRawDataHandler from .sklearn_models import SklearnModelsHandler +from .feature import PrecomputedFeaturesHandler diff --git a/cesium_app/handlers/feature.py b/cesium_app/handlers/feature.py index e0dcff2..dede335 100644 --- a/cesium_app/handlers/feature.py +++ b/cesium_app/handlers/feature.py @@ -13,6 +13,7 @@ from os.path import join as pjoin import uuid import datetime +from io import StringIO import pandas as pd diff --git a/static/js/actions.js b/static/js/actions.js index a1af2d8..0faa9ef 100644 --- a/static/js/actions.js +++ b/static/js/actions.js @@ -438,6 +438,55 @@ export function computeFeatures(form) { } +export function uploadFeatureset(form, currentProject) { + + function fileReaderPromise(form, fileName, binary = false){ + return new Promise(resolve => { + var filereader = new FileReader(); + if (binary) { + filereader.readAsDataURL(form[fileName][0]); + } else { + filereader.readAsText(form[fileName][0]); + } + filereader.onloadend = () => resolve({ body: filereader.result, + name: form[fileName][0].name }); + }); + } + + form['projectID'] = currentProject.id; + + return dispatch => + promiseAction( + dispatch, + UPLOAD_DATASET, + + fileReaderPromise(form, 'dataFile') + .then(data => { + form['dataFile'] = data; + return fetch('/precomputed_features', { + credentials: 'same-origin', + method: 'POST', + body: JSON.stringify(form), + headers: new Headers({ + 'Content-Type': 'application/json' + }) + }) + }) + .then(response => response.json()) + .then((json) => { + if (json.status == 'success') { + dispatch(showNotification('Successfully uploaded new feature set')); + dispatch(hideExpander('uploadFeatsFormExpander')); + dispatch(resetForm('uploadFeatures')); + } else { + return Promise.reject({ _error: json.message }); + } + return json; + }) + ); +} + + export function deleteDataset(id) { return dispatch => promiseAction( diff --git a/static/js/components/Features.jsx b/static/js/components/Features.jsx index 51d5d44..fbe677d 100644 --- a/static/js/components/Features.jsx +++ b/static/js/components/Features.jsx @@ -56,9 +56,11 @@ FeaturesTab.defaultProps = { selectedProject: {} }; -const ftMapDispatchToProps = dispatch => ( +const ftMapDispatchToProps = (dispatch, ownProps) => ( { - computeFeatures: form => dispatch(Action.computeFeatures(form)) + computeFeatures: form => dispatch(Action.computeFeatures(form)), + uploadFeatures: form => dispatch( + Action.uploadFeatureset(form, ownProps.selectedProject)) } ); diff --git a/static/js/components/FeaturesetsTable.jsx b/static/js/components/FeaturesetsTable.jsx index bcdfed6..f9bd3f5 100644 --- a/static/js/components/FeaturesetsTable.jsx +++ b/static/js/components/FeaturesetsTable.jsx @@ -2,6 +2,10 @@ import React from 'react'; import { connect } from 'react-redux'; import { reformatDatetime } from '../utils'; +import Plot from './Plot'; +import FoldableRow from './FoldableRow'; +import Delete from './Delete'; +import * as Action from '../actions'; const FeaturesetsTable = props => ( @@ -60,4 +64,10 @@ const ftMapStateToProps = (state, ownProps) => ( } ); +const deleteMapDispatchToProps = dispatch => ( + { delete: id => dispatch(Action.deleteFeatureset(id)) } +); + +const DeleteFeatureset = connect(null, deleteMapDispatchToProps)(Delete); + export default connect(ftMapStateToProps)(FeaturesetsTable); diff --git a/static/js/components/FeaturizeForm.jsx b/static/js/components/FeaturizeForm.jsx index 45a6001..dc2e288 100644 --- a/static/js/components/FeaturizeForm.jsx +++ b/static/js/components/FeaturizeForm.jsx @@ -7,6 +7,7 @@ import { FormComponent, Form, TextInput, TextareaInput, SubmitButton, CheckBoxInput, SelectInput } from './Form'; import Expand from './Expand'; import { contains } from '../utils'; +import * as Action from '../actions'; const Tab = ReactTabs.Tab; @@ -29,7 +30,7 @@ const FeaturizeForm = (props) => {
diff --git a/static/js/components/UploadFeaturesForm.jsx b/static/js/components/UploadFeaturesForm.jsx index 557e71b..7233864 100644 --- a/static/js/components/UploadFeaturesForm.jsx +++ b/static/js/components/UploadFeaturesForm.jsx @@ -1,13 +1,85 @@ import React from 'react'; +import { reduxForm } from 'redux-form'; + +import { FormComponent, Form, TextInput, TextareaInput, SubmitButton, + CheckBoxInput, SelectInput, FileInput } from './Form'; +import * as Validate from '../validate'; +import CesiumTooltip from './Tooltip'; const UploadFeaturesForm = props => { + const { fields, fields: { datasetID, featuresetName, dataFile }, + handleSubmit, submitting, resetForm, error, featuresList, + featureDescriptions } = props; + const datasets = props.datasets.map(ds => ( + { id: ds.id, + label: ds.name } + )); + return (
- Upload Features Form content + + + + + + +
); }; +UploadFeaturesForm.propTypes = { + fields: React.PropTypes.object.isRequired, + datasets: React.PropTypes.arrayOf(React.PropTypes.object).isRequired, + error: React.PropTypes.string, + handleSubmit: React.PropTypes.func.isRequired, + submitting: React.PropTypes.bool.isRequired, + resetForm: React.PropTypes.func.isRequired, + selectedProject: React.PropTypes.object +}; + + +const mapStateToProps = (state, ownProps) => { + + const initialValues = { }; + + const filteredDatasets = state.datasets.filter(dataset => + (dataset.project_id === ownProps.selectedProject.id)); + + return { + datasets: filteredDatasets, + fields: ['datasetID', 'featuresetName', 'dataFile'], + initialValues: { ...initialValues, + datasetID: "No associated dataset" } + }; +}; + +const validate = Validate.createValidator({ + featuresetName: [Validate.required], + dataFile: [Validate.oneFile] +}); -export default UploadFeaturesForm; +export default reduxForm( + { + form: 'uploadFeatures', + fields: [''], + validate + }, mapStateToProps)(UploadFeaturesForm); From 2f88ec049e68e272891bcffb385a968fc142ba51 Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Thu, 15 Feb 2018 15:21:23 -0800 Subject: [PATCH 04/10] Correctly handle multi-channel data and labels --- cesium_app/handlers/feature.py | 42 ++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/cesium_app/handlers/feature.py b/cesium_app/handlers/feature.py index dede335..af16ede 100644 --- a/cesium_app/handlers/feature.py +++ b/cesium_app/handlers/feature.py @@ -140,3 +140,45 @@ def delete(self, featureset_id): def put(self, featureset_id): f = Featureset.get_if_owned_by(featureset_id, self.current_user) self.error("Functionality for this endpoint is not yet implemented.") + + +class PrecomputedFeaturesHandler(BaseHandler): + @auth_or_token + def post(self): + data = self.get_json() + if data['datasetID'] not in [None, 'None']: + dataset = Dataset.query.filter(Dataset.id == data['datasetID']).one() + else: + dataset = None + current_project = Project.get_if_owned_by(data['projectID'], + self.current_user) + feature_data = StringIO(data['dataFile']['body']) + fset = pd.read_csv(feature_data, index_col=0, header=[0, 1]) + if 'labels' in fset: + labels = fset.pop('labels').values.ravel() + if labels.dtype == 'O': + labels = [str(label) for label in labels] + else: + labels = [None] + fset_path = pjoin( + self.cfg['paths:features_folder'], + '{}_{}.npz'.format(uuid.uuid4(), data['dataFile']['name'])) + + featurize.save_featureset(fset, fset_path, labels=labels) + + # Meta-features will have channel values of an empty string or a string + # beginning with 'Unnamed:' + features_list = [el[0] for el in fset.columns.tolist() if + (el[1] != '' and not el[1].startswith('Unnamed:'))] + + featureset = Featureset(name=data['featuresetName'], + file_uri=fset_path, + project=current_project, + dataset=dataset, + features_list=features_list, + finished=datetime.datetime.now(), + custom_features_script=None) + DBSession().add(featureset) + DBSession().commit() + + self.success(featureset, 'cesium/FETCH_FEATURESETS') From ad0d64ef5919bb5cf27804d47ea5d90e942c26a7 Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Wed, 21 Feb 2018 14:12:19 -0800 Subject: [PATCH 05/10] Add tests for uploading pre-computed features --- .../data/downloaded_cesium_featureset.csv | 9 ++ cesium_app/tests/frontend/test_features.py | 25 +++- ...eline_sequentially_precomputed_features.py | 125 ++++++++++++++++++ 3 files changed, 158 insertions(+), 1 deletion(-) create mode 100644 cesium_app/tests/data/downloaded_cesium_featureset.csv create mode 100644 cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py diff --git a/cesium_app/tests/data/downloaded_cesium_featureset.csv b/cesium_app/tests/data/downloaded_cesium_featureset.csv new file mode 100644 index 0000000..4303db0 --- /dev/null +++ b/cesium_app/tests/data/downloaded_cesium_featureset.csv @@ -0,0 +1,9 @@ +feature,amplitude,flux_percentile_ratio_mid20,flux_percentile_ratio_mid35,flux_percentile_ratio_mid50,flux_percentile_ratio_mid65,flux_percentile_ratio_mid80,max_slope,maximum,median,median_absolute_deviation,minimum,percent_amplitude,percent_beyond_1_std,percent_close_to_median,percent_difference_flux_percentile,period_fast,qso_log_chi2_qsonu,qso_log_chi2nuNULL_chi2nu,skew,std,stetson_j,stetson_k,weighted_average,meta1,meta2,meta3,labels +channel,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,,,, +217801,3.4145,0.026237634586002364,0.058162853124671635,0.10309627831781239,0.17599090611586052,0.41575052067669566,24.652777777737825,14.626,12.42,0.9030000000000005,7.797,69.66429004252072,0.27001862197392923,0.3649906890130354,23.06668928889701,375.6510827444723,4.230919840093198,2.671853833598369,-0.9236797091091277,1.4663914712199768,11.369853415776587,0.9189839436611995,12.040512767456608,0.18073430690900003,0.548427238218,0.18795623725299998,Mira 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b/cesium_app/tests/frontend/test_features.py index 7e65073..2cf4c98 100644 --- a/cesium_app/tests/frontend/test_features.py +++ b/cesium_app/tests/frontend/test_features.py @@ -177,8 +177,31 @@ def test_delete_featureset(driver, project, dataset, featureset): driver.find_element_by_partial_link_text('Delete').click() driver.wait_for_xpath("//div[contains(text(),'Feature set deleted')]") try: - el = driver.wait_for_xpath("//td[contains(text(),'{test_featureset_name}')]") + el = driver.wait_for_xpath(f"//td[contains(text(),'{test_featureset_name}')]") except TimeoutException: pass else: raise Exception("Featureset still present in table after delete.") + + +def test_upload_precomputed_features(driver, project, dataset): + driver.get('/') + driver.refresh() + proj_select = Select(driver.find_element_by_css_selector('[name=project]')) + proj_select.select_by_value(str(project.id)) + + driver.find_element_by_id('react-tabs-4').click() + driver.find_element_by_partial_link_text('Upload Pre-Computed Features')\ + .click() + ds_select = Select(driver.find_element_by_css_selector('[name=datasetID]')) + ds_select.select_by_value(str(dataset.id)) + + fs_name = driver.find_element_by_css_selector('[name=featuresetName]') + fs_name.send_keys(test_featureset_name) + + file_field = driver.find_element_by_css_selector('[name=dataFile]') + file_field.send_keys(pjoin(os.path.dirname(os.path.dirname(__file__)), + 'data', 'downloaded_cesium_featureset.csv')) + driver.find_element_by_class_name('btn-primary').click() + + driver.wait_for_xpath(f"//td[contains(text(),'{test_featureset_name}')]") diff --git a/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py b/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py new file mode 100644 index 0000000..1a420f7 --- /dev/null +++ b/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py @@ -0,0 +1,125 @@ +import pytest +from selenium import webdriver +from selenium.webdriver.support.ui import Select +import uuid +import os +from os.path import join as pjoin +import time + + +def test_pipeline_sequentially(driver): + driver.get("/") + + # Add new project + driver.wait_for_xpath( + '//*[contains(text(), "Or click here to add a new one")]').click() + + project_name = driver.find_element_by_css_selector('[name=projectName]') + test_proj_name = str(uuid.uuid4()) + project_name.send_keys(test_proj_name) + project_desc = driver.find_element_by_css_selector( + '[name=projectDescription]') + project_desc.send_keys("Test Description") + + driver.find_element_by_class_name('btn-primary').click() + + status_td = driver.wait_for_xpath( + "//div[contains(text(),'Added new project')]") + driver.refresh() + + # Ensure new project is selected + proj_select = Select(driver.find_element_by_css_selector('[name=project]')) + proj_select.select_by_visible_text(test_proj_name) + + # Add new dataset + test_dataset_name = str(uuid.uuid4()) + driver.find_element_by_id('react-tabs-2').click() + driver.find_element_by_partial_link_text('Upload new dataset').click() + + dataset_name = driver.find_element_by_css_selector('[name=datasetName]') + dataset_name.send_keys(test_dataset_name) + + header_file = driver.find_element_by_css_selector('[name=headerFile]') + header_file.send_keys(pjoin( + os.path.dirname(os.path.dirname(__file__)), 'data', + 'larger_asas_training_subset_classes_with_metadata.dat')) + + tar_file = driver.find_element_by_css_selector('[name=tarFile]') + tar_file.send_keys(pjoin(os.path.dirname(os.path.dirname(__file__)), 'data', + 'larger_asas_training_subset.tar.gz')) + + driver.find_element_by_class_name('btn-primary').click() + + status_td = driver.wait_for_xpath( + "//div[contains(text(),'Successfully uploaded new dataset')]") + driver.refresh() + + # Ensure new project is selected + proj_select = Select(driver.find_element_by_css_selector('[name=project]')) + proj_select.select_by_visible_text(test_proj_name) + + # Generate new feature set + test_featureset_name = str(uuid.uuid4()) + driver.find_element_by_id('react-tabs-4').click() + driver.find_element_by_partial_link_text('Upload Pre-Computed Features')\ + .click() + + featureset_name = driver.find_element_by_css_selector( + '[name=featuresetName]') + featureset_name.send_keys(test_featureset_name) + + # Ensure dataset from previous step is selected + dataset_select = Select(driver.find_element_by_css_selector( + '[name=datasetID]')) + dataset_select.select_by_visible_text(test_dataset_name) + + file_field = driver.find_element_by_css_selector('[name=dataFile]') + file_field.send_keys(pjoin(os.path.dirname(os.path.dirname(__file__)), + 'data', 'downloaded_cesium_featureset.csv')) + + driver.find_element_by_class_name('btn-primary').click() + status_td = driver.wait_for_xpath( + "//div[contains(text(),'Successfully uploaded new feature set')]") + status_td = driver.wait_for_xpath("//td[contains(text(),'Completed')]", 30) + + # Build new model + driver.find_element_by_id('react-tabs-6').click() + driver.find_element_by_partial_link_text('Create New Model').click() + + model_select = Select(driver.find_element_by_css_selector( + '[name=modelType]')) + model_select.select_by_visible_text('RandomForestClassifier (fast)') + + model_name = driver.find_element_by_css_selector('[name=modelName]') + test_model_name = str(uuid.uuid4()) + model_name.send_keys(test_model_name) + + # Ensure featureset from previous step is selected + fset_select = Select(driver.find_element_by_css_selector( + '[name=featureset]')) + fset_select.select_by_visible_text(test_featureset_name) + + driver.find_element_by_class_name('btn-primary').click() + + driver.wait_for_xpath("//div[contains(text(),'Model training begun')]") + + driver.wait_for_xpath("//td[contains(.,'Completed')]", 30) + + # Predict using dataset and model from this test + driver.find_element_by_id('react-tabs-8').click() + driver.find_element_by_partial_link_text('Predict Targets').click() + + # Ensure model from previous step is selected + model_select = Select(driver.find_element_by_css_selector('[name=modelID]')) + model_select.select_by_visible_text(test_model_name) + + # Ensure dataset from previous step is selected + dataset_select = Select(driver.find_element_by_css_selector( + '[name=datasetID]')) + dataset_select.select_by_visible_text(test_dataset_name) + + driver.find_element_by_class_name('btn-primary').click() + + driver.wait_for_xpath("//div[contains(text(),'Model predictions begun')]") + + driver.wait_for_xpath("//td[contains(text(),'Completed')]", 10) From 541b5cd3119fda4f3984452b6eb9f8de9677b8b5 Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Thu, 12 Apr 2018 11:51:53 -0700 Subject: [PATCH 06/10] Bump wait times in precomputed features sequential pipeline test --- .../test_pipeline_sequentially_precomputed_features.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py b/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py index 1a420f7..bbf1e68 100644 --- a/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py +++ b/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py @@ -7,7 +7,7 @@ import time -def test_pipeline_sequentially(driver): +def test_pipeline_sequentially_precomputed_features(driver): driver.get("/") # Add new project @@ -103,7 +103,7 @@ def test_pipeline_sequentially(driver): driver.wait_for_xpath("//div[contains(text(),'Model training begun')]") - driver.wait_for_xpath("//td[contains(.,'Completed')]", 30) + driver.wait_for_xpath("//td[contains(.,'Completed')]", 60) # Predict using dataset and model from this test driver.find_element_by_id('react-tabs-8').click() @@ -122,4 +122,4 @@ def test_pipeline_sequentially(driver): driver.wait_for_xpath("//div[contains(text(),'Model predictions begun')]") - driver.wait_for_xpath("//td[contains(text(),'Completed')]", 10) + driver.wait_for_xpath("//td[contains(text(),'Completed')]", 20) From 2ded9d540d50073242df27c2d33f9d2fcb558f4b Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Wed, 2 May 2018 13:38:56 -0700 Subject: [PATCH 07/10] Lint-roll the JS sources --- static/js/actions.js | 14 +++--- static/js/components/Features.jsx | 4 +- static/js/components/FeaturesetsTable.jsx | 11 +++-- static/js/components/FeaturizeForm.jsx | 47 ++++++++++++--------- static/js/components/UploadFeaturesForm.jsx | 28 ++++++------ 5 files changed, 57 insertions(+), 47 deletions(-) diff --git a/static/js/actions.js b/static/js/actions.js index 0faa9ef..1c42a1c 100644 --- a/static/js/actions.js +++ b/static/js/actions.js @@ -439,20 +439,18 @@ export function computeFeatures(form) { export function uploadFeatureset(form, currentProject) { - - function fileReaderPromise(form, fileName, binary = false){ + function fileReaderPromise(formFields, fileName, binary = false) { return new Promise(resolve => { - var filereader = new FileReader(); + const filereader = new FileReader(); if (binary) { - filereader.readAsDataURL(form[fileName][0]); + filereader.readAsDataURL(formFields[fileName][0]); } else { - filereader.readAsText(form[fileName][0]); + filereader.readAsText(formFields[fileName][0]); } filereader.onloadend = () => resolve({ body: filereader.result, - name: form[fileName][0].name }); + name: formFields[fileName][0].name }); }); } - form['projectID'] = currentProject.id; return dispatch => @@ -470,7 +468,7 @@ export function uploadFeatureset(form, currentProject) { headers: new Headers({ 'Content-Type': 'application/json' }) - }) + }); }) .then(response => response.json()) .then((json) => { diff --git a/static/js/components/Features.jsx b/static/js/components/Features.jsx index fbe677d..1a649c4 100644 --- a/static/js/components/Features.jsx +++ b/static/js/components/Features.jsx @@ -50,6 +50,7 @@ let FeaturesTab = (props) => { FeaturesTab.propTypes = { featurePlotURL: PropTypes.string.isRequired, computeFeatures: PropTypes.func.isRequired, + uploadFeatures: PropTypes.func.isRequired, selectedProject: PropTypes.object }; FeaturesTab.defaultProps = { @@ -60,7 +61,8 @@ const ftMapDispatchToProps = (dispatch, ownProps) => ( { computeFeatures: form => dispatch(Action.computeFeatures(form)), uploadFeatures: form => dispatch( - Action.uploadFeatureset(form, ownProps.selectedProject)) + Action.uploadFeatureset(form, ownProps.selectedProject) + ) } ); diff --git a/static/js/components/FeaturesetsTable.jsx b/static/js/components/FeaturesetsTable.jsx index f9bd3f5..bd2e081 100644 --- a/static/js/components/FeaturesetsTable.jsx +++ b/static/js/components/FeaturesetsTable.jsx @@ -1,4 +1,5 @@ import React from 'react'; +import PropTypes from 'prop-types'; import { connect } from 'react-redux'; import { reformatDatetime } from '../utils'; @@ -44,15 +45,19 @@ const FeaturesetsTable = props => ( {foldedContent} - ); }) + ); + }) } ); FeaturesetsTable.propTypes = { - featuresets: React.PropTypes.arrayOf(React.PropTypes.object), - featurePlotURL: React.PropTypes.string + featuresets: PropTypes.arrayOf(PropTypes.object).isRequired, + featurePlotURL: PropTypes.string +}; +FeaturesetsTable.defaultProps = { + featurePlotURL: null }; diff --git a/static/js/components/FeaturizeForm.jsx b/static/js/components/FeaturizeForm.jsx index dc2e288..1e133c1 100644 --- a/static/js/components/FeaturizeForm.jsx +++ b/static/js/components/FeaturizeForm.jsx @@ -1,4 +1,5 @@ import React from 'react'; +import PropTypes from 'prop-types'; import { reduxForm } from 'redux-form'; import ReactTabs from 'react-tabs'; @@ -10,11 +11,7 @@ import { contains } from '../utils'; import * as Action from '../actions'; -const Tab = ReactTabs.Tab; -const Tabs = ReactTabs.Tabs; -const TabList = ReactTabs.TabList; -const TabPanel = ReactTabs.TabPanel; - +const { Tab, Tabs, TabList, TabPanel } = { ...ReactTabs }; const FeaturizeForm = (props) => { const { fields, fields: { datasetID, featuresetName, customFeatsCode }, @@ -69,9 +66,13 @@ const FeaturizeForm = (props) => { { + onClick={ + () => { props.dispatch(Action.groupToggleCheckedFeatures( - props.featuresByCategory[ctgy])); }} + props.featuresByCategory[ctgy] + )); + } + } > Check/Uncheck All @@ -103,7 +104,8 @@ const FeaturizeForm = (props) => { @@ -113,19 +115,21 @@ const FeaturizeForm = (props) => { ); }; FeaturizeForm.propTypes = { - fields: React.PropTypes.object.isRequired, - datasets: React.PropTypes.arrayOf(React.PropTypes.object).isRequired, - error: React.PropTypes.string, - handleSubmit: React.PropTypes.func.isRequired, - submitting: React.PropTypes.bool.isRequired, - resetForm: React.PropTypes.func.isRequired, - selectedProject: React.PropTypes.object, - featuresByCategory: React.PropTypes.object, - tagList: React.PropTypes.arrayOf(React.PropTypes.string).isRequired, - featuresList: React.PropTypes.array, - featureDescriptions: React.PropTypes.object + fields: PropTypes.object.isRequired, + datasets: PropTypes.arrayOf(PropTypes.object).isRequired, + error: PropTypes.string, + handleSubmit: PropTypes.func.isRequired, + submitting: PropTypes.bool.isRequired, + resetForm: PropTypes.func.isRequired, + selectedProject: PropTypes.object.isRequired, + featuresByCategory: PropTypes.object.isRequired, + tagList: PropTypes.arrayOf(PropTypes.string).isRequired, + featuresList: PropTypes.array.isRequired, + featureDescriptions: PropTypes.object.isRequired +}; +FeaturizeForm.defaultProps = { + error: "" }; - const mapStateToProps = (state, ownProps) => { const featuresList = state.features.featsWithCheckedTags; @@ -144,7 +148,8 @@ const mapStateToProps = (state, ownProps) => { featureDescriptions: state.features.descriptions, datasets: filteredDatasets, fields: featuresList.concat( - ['datasetID', 'featuresetName', 'customFeatsCode']), + ['datasetID', 'featuresetName', 'customFeatsCode'] + ), initialValues: { ...initialValues, datasetID: zerothDataset ? zerothDataset.id.toString() : "", customFeatsCode: "" } diff --git a/static/js/components/UploadFeaturesForm.jsx b/static/js/components/UploadFeaturesForm.jsx index 7233864..63e8ebd 100644 --- a/static/js/components/UploadFeaturesForm.jsx +++ b/static/js/components/UploadFeaturesForm.jsx @@ -1,4 +1,5 @@ import React from 'react'; +import PropTypes from 'prop-types'; import { reduxForm } from 'redux-form'; import { FormComponent, Form, TextInput, TextareaInput, SubmitButton, @@ -9,8 +10,7 @@ import CesiumTooltip from './Tooltip'; const UploadFeaturesForm = props => { const { fields, fields: { datasetID, featuresetName, dataFile }, - handleSubmit, submitting, resetForm, error, featuresList, - featureDescriptions } = props; + handleSubmit, submitting, resetForm, error } = props; const datasets = props.datasets.map(ds => ( { id: ds.id, label: ds.name } @@ -47,23 +47,22 @@ const UploadFeaturesForm = props => { }; UploadFeaturesForm.propTypes = { - fields: React.PropTypes.object.isRequired, - datasets: React.PropTypes.arrayOf(React.PropTypes.object).isRequired, - error: React.PropTypes.string, - handleSubmit: React.PropTypes.func.isRequired, - submitting: React.PropTypes.bool.isRequired, - resetForm: React.PropTypes.func.isRequired, - selectedProject: React.PropTypes.object + fields: PropTypes.object.isRequired, + datasets: PropTypes.arrayOf(PropTypes.object).isRequired, + error: PropTypes.string, + handleSubmit: PropTypes.func.isRequired, + submitting: PropTypes.bool.isRequired, + resetForm: PropTypes.func.isRequired, + selectedProject: PropTypes.object.isRequired +}; +UploadFeaturesForm.defaultProps = { + error: "" }; - const mapStateToProps = (state, ownProps) => { - const initialValues = { }; - const filteredDatasets = state.datasets.filter(dataset => (dataset.project_id === ownProps.selectedProject.id)); - return { datasets: filteredDatasets, fields: ['datasetID', 'featuresetName', 'dataFile'], @@ -82,4 +81,5 @@ export default reduxForm( form: 'uploadFeatures', fields: [''], validate - }, mapStateToProps)(UploadFeaturesForm); + }, mapStateToProps +)(UploadFeaturesForm); From 22b09c95bd2c96b53af4ffa0e985906e032ecbf7 Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Mon, 7 May 2018 11:47:05 -0700 Subject: [PATCH 08/10] Delete existing project if exists in sequential pipeline test --- cesium_app/tests/frontend/test_pipeline_sequentially.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/cesium_app/tests/frontend/test_pipeline_sequentially.py b/cesium_app/tests/frontend/test_pipeline_sequentially.py index d060a5e..4a786e8 100644 --- a/cesium_app/tests/frontend/test_pipeline_sequentially.py +++ b/cesium_app/tests/frontend/test_pipeline_sequentially.py @@ -1,6 +1,7 @@ import pytest from selenium import webdriver from selenium.webdriver.support.ui import Select +from selenium.common.exceptions import NoSuchElementException, TimeoutException import uuid import os from os.path import join as pjoin @@ -10,6 +11,11 @@ def test_pipeline_sequentially(driver): driver.get("/") + # Delete existing project if present + try: + driver.wait_for_xpath('//*[contains(text(), "Delete Project")]').click() + except (NoSuchElementException, TimeoutException): + pass # Add new project driver.wait_for_xpath('//*[contains(text(), "Or click here to add a new one")]').click() From bc5c4aea18c4b77c4d7477f3f5281ade23164f8b Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Mon, 7 May 2018 14:26:41 -0700 Subject: [PATCH 09/10] Update sequential pipeline test --- .../frontend/test_pipeline_sequentially_precomputed_features.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py b/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py index bbf1e68..d1c44d7 100644 --- a/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py +++ b/cesium_app/tests/frontend/test_pipeline_sequentially_precomputed_features.py @@ -103,7 +103,7 @@ def test_pipeline_sequentially_precomputed_features(driver): driver.wait_for_xpath("//div[contains(text(),'Model training begun')]") - driver.wait_for_xpath("//td[contains(.,'Completed')]", 60) + driver.wait_for_xpath("//td[contains(text(),'Completed')]", 60) # Predict using dataset and model from this test driver.find_element_by_id('react-tabs-8').click() From 5a8dc3426fc453b2d0d8a869aa6a1929f5e7335c Mon Sep 17 00:00:00 2001 From: Ari Crellin-Quick Date: Tue, 8 May 2018 11:17:52 -0700 Subject: [PATCH 10/10] Bump cesium requirement to 0.9.5 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 2e2ec8b..475a9fe 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -cesium>=0.9.4 +cesium>=0.9.5 joblib>=0.11 bokeh==0.12.5 pytest-randomly