Skip to content

Commit

Permalink
added docstrings
Browse files Browse the repository at this point in the history
  • Loading branch information
@adkinsrs
adkinsrs committed Nov 22, 2023
1 parent 089f650 commit 13697e0
Show file tree
Hide file tree
Showing 7 changed files with 708 additions and 43 deletions.
1 change: 0 additions & 1 deletion www/compare_datasets.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,6 @@ <h5 class="title is-5">
<script src="https://unpkg.com/axios/dist/axios.min.js"></script>

<script src="js/vendor/js.cookie.js"></script>
<script src="https://d3js.org/d3.v5.min.js"></script>
<script src="https://cdn.plot.ly/plotly-2.26.0.min.js" charset="utf-8"></script>

<!-- Helps ensure the user gets the latest code, needed while we're pushing out so many updates -->
Expand Down
1 change: 0 additions & 1 deletion www/dataset_curator.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -405,7 +405,6 @@ <h4 class="title is-5 is-clickable js-collapsable-trigger">

<script src="js/vendor/js.cookie.js"></script>
<script src="js/vendor/snap.svg-min.js"></script>
<script src="https://d3js.org/d3.v5.min.js"></script>
<script src="https://cdn.plot.ly/plotly-2.26.0.min.js" charset="utf-8"></script>

<!-- Helps ensure the user gets the latest code, needed while we're pushing out so many updates -->
Expand Down
145 changes: 145 additions & 0 deletions www/js/common.v2.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -413,36 +413,86 @@ Any axios methods that impolement these calls, must provide their own success/er
? Some "classes" JS files like "genecart" are already abstracted away... should we keep their methods or move them here?
*/

/**
* Mixin containing various API calls for interacting with datasets, displays, and analyses.
* @mixin
*/
const apiCallsMixin = {
sessionId: null,
colorblindMode: null,

/**
* Deletes a display.
* @param {string} displayId - The ID of the display to be deleted.
* @returns {Promise<null>} - A promise that resolves to null.
*/
async deleteDisplay(displayId) {
const payload = {session_id: this.sessionId, id: displayId};
await axios.post("/cgi/delete_dataset_display.cgi", convertToFormData(payload));
return null;
},
/**
* Fetches aggregations for a given dataset and analysis.
* @param {string} datasetId - The ID of the dataset.
* @param {string} analysisId - The ID of the analysis.
* @param {object} filters - The filters to apply to the aggregations.
* @returns {Promise<object>} - The aggregated data.
*/
async fetchAggregations(datasetId, analysisId, filters) {
const payload = {session_id: this.sessionId, dataset_id: datasetId, analysis_id: analysisId, filters};
const {data} = await axios.post(`/api/h5ad/${datasetId}/aggregations`, payload);
return data;
},
/**
* Fetches analyses for a given dataset.
* @param {string} datasetId - The ID of the dataset.
* @returns {Promise<any>} - A promise that resolves to the fetched data.
*/
async fetchAnalyses(datasetId) {
const {data} = await axios.get(`./api/h5ad/${datasetId}/analyses`)
return data;
},
/**
* Fetches the available plot types for a given dataset and analysis.
* @param {string} datasetId - The ID of the dataset.
* @param {string} analysisId - The ID of the analysis.
* @param {boolean} [isMultigene=false] - Indicates whether the plot types are for a multigene analysis.
* @returns {Promise<any>} - A promise that resolves to the available plot types data.
*/
async fetchAvailablePlotTypes(datasetId, analysisId, isMultigene=false){
const flavor = isMultigene ? "mg_availableDisplayTypes" : "availableDisplayTypes";
const payload = {session_id: this.sessionId, dataset_id: datasetId, analysis_id: analysisId};
const {data} = await axios.post(`/api/h5ad/${datasetId}/${flavor}`, payload);
return data;
},
/**
* Fetches dashboard data from the server.
* @param {string} datasetId - The ID of the dataset.
* @param {string} analysis - The type of analysis.
* @param {string} plotType - The type of plot.
* @param {object} plotConfig - The configuration for the plot.
* @returns {Promise<object>} - The fetched data.
*/
async fetchDashData(datasetId, analysis, plotType, plotConfig) {
// NOTE: gene_symbol should already be already passed to plotConfig
const payload = { ...plotConfig, plot_type: plotType, analysis, colorblind_mode: this.colorblindMode };
const {data} = await axios.post(`/api/plot/${datasetId}/mg_dash`, payload);
return data;
},
/**
* Fetches dataset comparison data.
*
* @param {string} datasetId - The ID of the dataset.
* @param {object} filters - The filters to apply to the dataset.
* @param {string} compareKey - The key to compare the dataset.
* @param {string} conditionX - The X condition for comparison.
* @param {string} conditionY - The Y condition for comparison.
* @param {number} foldChangeCutoff - The fold change cutoff value.
* @param {number} stDevNumCutoff - The standard deviation number cutoff value.
* @param {number} logBase - The base for logarithmic transformation.
* @param {string} statisticalTestAction - The statistical test action to perform.
* @returns {Promise<any>} The dataset comparison data.
*/
async fetchDatasetComparison(datasetId, filters, compareKey, conditionX, conditionY, foldChangeCutoff, stDevNumCutoff, logBase, statisticalTestAction) {
const payload = {
dataset_id: datasetId,
Expand All @@ -458,80 +508,168 @@ const apiCallsMixin = {
const {data} = await axios.post("cgi/get_dataset_comparison.cgi", convertToFormData(payload));
return data;
},
/**
* Fetches datasets asynchronously.
* @returns {Promise<any>} The fetched data.
*/
async fetchDatasets() {
const payload = {session_id: this.sessionId};
const {data} = await axios.post("cgi/get_h5ad_dataset_list.cgi", convertToFormData(payload));
return data;
},
/**
* Fetches the display image for a dataset.
* @param {string} datasetId - The ID of the dataset.
* @param {string} displayId - The ID of the display.
* @returns {Promise<any>} - A promise that resolves to the fetched data.
*/
async fetchDatasetDisplayImage(datasetId, displayId) {
// POST due to payload variables being sensitive
const payload = {dataset_id: datasetId, display_id: displayId};
const {data} = await axios.post("/cgi/get_dataset_display_image.cgi", convertToFormData(payload));
return data;
},
/**
* Fetches dataset displays.
* @param {string} datasetId - The ID of the dataset.
* @returns {Promise<any>} - A promise that resolves to the fetched data.
*/
async fetchDatasetDisplays(datasetId) {
const payload = {session_id: this.sessionId, dataset_id: datasetId};
const {data} = await axios.post("/cgi/get_dataset_displays.cgi", convertToFormData(payload));
return data;
},
/**
* Fetches the default display for a dataset.
* @param {string} datasetId - The ID of the dataset.
* @param {boolean} [isMultigene=false] - Indicates if the dataset is multigene.
* @returns {Promise<any>} - A promise that resolves to the fetched data.
*/
async fetchDefaultDisplay(datasetId, isMultigene=false) {
const payload = {session_id: this.sessionId, dataset_id: datasetId, is_multigene: isMultigene};
const {data} = await axios.post("/cgi/get_default_display.cgi", convertToFormData(payload));
return data;
},
/**
* Fetches the members of a gene cart.
* @param {string} geneCartId - The ID of the gene cart.
* @returns {Promise<any>} - A promise that resolves to the data of the gene cart members.
*/
async fetchGeneCartMembers(geneCartId) {
const payload = { session_id: this.sessionId, gene_cart_id: geneCartId };
const {data} = await axios.post(`/cgi/get_gene_cart_members.cgi`, convertToFormData(payload));
return data;
},
/**
* Fetches gene carts based on the specified cart type.
* @param {string} cartType - The type of gene cart to fetch.
* @returns {Promise<any>} - A promise that resolves to the fetched gene carts data.
*/
async fetchGeneCarts(cartType) {
const payload = {session_id: this.sessionId, cart_type: cartType};
const {data} = await axios.post(`/cgi/get_user_gene_carts.cgi`, convertToFormData(payload));
return data;
},
/**
* Fetches gene symbols for a given dataset and analysis.
* @param {string} datasetId - The ID of the dataset.
* @param {string} analysisId - The ID of the analysis (optional).
* @returns {Promise<Array<string>>} - A promise that resolves to an array of gene symbols.
*/
async fetchGeneSymbols(datasetId, analysisId) {
let url = `./api/h5ad/${datasetId}/genes`;
if (analysisId) url += `?analysis_id=${analysisId}`;
const {data} = await axios.get(url);
return data;
},
/**
* Fetches H5ad info from the server.
* @param {string} datasetId - The ID of the dataset.
* @param {string} [analysisId] - The ID of the analysis (optional).
* @returns {Promise<any>} - A promise that resolves to the fetched data.
*/
async fetchH5adInfo(datasetId, analysisId) {
let url = `/api/h5ad/${datasetId}`
if (analysisId) url += `?analysis_id=${analysisId}`;
const {data} = await axios.get(url);
return data;
},
/**
* Fetches Plotly data for a given dataset, analysis, plot type, and plot configuration.
* @param {string} datasetId - The ID of the dataset.
* @param {string} analysis - The analysis type.
* @param {string} plotType - The type of plot.
* @param {object} plotConfig - The configuration object for the plot.
* @returns {Promise<object>} - The fetched Plotly data.
*/
async fetchPlotlyData(datasetId, analysis, plotType, plotConfig) {
// NOTE: gene_symbol should already be already passed to plotConfig
const payload = { ...plotConfig, plot_type: plotType, analysis, colorblind_mode: this.colorblindMode };
const {data} = await axios.post(`/api/plot/${datasetId}`, payload);
return data;
},
/**
* Fetches SVG data for a given dataset ID and gene symbol.
* @param {string} datasetId - The ID of the dataset.
* @param {string} geneSymbol - The symbol of the gene.
* @returns {Promise<any>} - A promise that resolves to the fetched SVG data.
*/
async fetchSvgData(datasetId, geneSymbol) {
const {data} = await axios.get(`/api/plot/${datasetId}/svg?gene=${geneSymbol}`);
return data;
},
/**
* Fetches the TSNE image for a given dataset, analysis, plot type, and plot configuration.
* @param {string} datasetId - The ID of the dataset.
* @param {string} analysis - The analysis type.
* @param {string} plotType - The type of plot.
* @param {Object} plotConfig - The configuration for the plot.
* @returns {Promise<any>} - A promise that resolves with the fetched TSNE image data.
*/
async fetchTsneImage(datasetId, analysis, plotType, plotConfig) {
// NOTE: gene_symbol should already be already passed to plotConfig
const payload = { ...plotConfig, plot_type: plotType, analysis, colorblind_mode: this.colorblindMode };
const {data} = await axios.post(`/api/plot/${datasetId}/tsne`, payload);
return data;
},
/**
* Fetches user history entries.
* @param {Array} entries - The entries to fetch.
* @returns {Promise} - A promise that resolves with the fetched data.
*/
async fetchUserHistoryEntries(entries) {
const payload = { session_id: this.sessionId, entries };
const {data} = await axios.post("/cgi/get_user_history_entries.cgi", convertToFormData(payload));
return data;
},
/**
* Retrieves session information.
* @returns {Promise<Object>} The session information.
*/
async getSessionInfo() {
const payload = {session_id: this.sessionId};
const {data} = await axios.post("/cgi/get_session_info.v2.cgi", convertToFormData(payload));
return data;
},
/**
* Logs in the user.
* @param {FormData} formData - The form data containing the login credentials.
* @returns {Promise<any>} - A promise that resolves to the login response data.
*/
async login(formData) {
const payload = new URLSearchParams(formData);
const {data} = await axios.post("/cgi/login.v2.cgi", payload);
return data;
},
/**
* Saves the dataset display with the specified parameters.
* @param {string} datasetId - The ID of the dataset.
* @param {string} displayId - The ID of the display.
* @param {string} label - The label for the display.
* @param {string} plotType - The type of plot for the display.
* @param {object} plotConfig - The configuration object for the plot.
* @returns {Promise<any>} - A promise that resolves to the saved data.
*/
async saveDatasetDisplay(datasetId, displayId, label, plotType, plotConfig) {
const payload = {
id: displayId,
Expand All @@ -548,6 +686,13 @@ const apiCallsMixin = {
const {data} = await axios.post("/cgi/save_dataset_display.cgi", convertToFormData(payload));
return data;
},
/**
* Saves the default display for a dataset.
* @param {string} datasetId - The ID of the dataset.
* @param {string} displayId - The ID of the display.
* @param {boolean} [isMultigene=false] - Indicates if the display is for multiple genes.
* @returns {Promise<any>} - A promise that resolves to the saved data.
*/
async saveDefaultDisplay(datasetId, displayId, isMultigene=false) {
const payload = {display_id: displayId, session_id: this.sessionId, dataset_id: datasetId, is_multigene: isMultigene};
const {data} = await axios.post("/cgi/save_default_display.cgi", convertToFormData(payload));
Expand Down
Loading

0 comments on commit 13697e0

Please sign in to comment.