Help for Project Summary Page - materials-commons/materialscommons.org GitHub Wiki

Project page

In the projects index page, when you click on a project title, you will be taken to the Project page. This page shows a list of experiments for the project, and a side-bar menu to navigate through the detail of the project. The initial state of this page might look something like this (shown here using the demo project):

On this page the top is the same as before: the toggles for Projects and Published data, a search interface, the help button, the Report Issue Button, and the user-action pull down menu (which we already encountered in the description of the top level Projects Page).

The left side panel shows the project parts and actions: the Project title (which is a button that will return you to this page), the Project Description, the list of people sharing the project, the Notes/To-dos panel, the Project-Datasets panel, the Experiments list opener (with the number of experiments), the Samples panel, the Files panel, the Settings panel, the Sync button, the Globus Commands, and the Shortcuts list. See the section Left Side Navigation Bar, below.

The right side shows a list of Experiments with the experiment actions. For a brief introduction, see the section Experiments list and actions, below. For a detailed description, see the Experiment Page help page, also listed in the "Experiment Page and Panels" section in the Table of Contents side bar, top right of the page.

A brief review the functions of the top-most banner. In the upper left corner of the page, the Materials Commons buttons are used to navigate to the top level pages of the site. Clicking on the 'Projects' link will return you to the top level of the Project management area of the site Projects Index Page. Clicking on the 'Published Data' link will take you to the top level Public Data Page.

Next to the these top level navigation links is the "Search Project..." text entry. To search just type some part of any name in the project (for example, part of a sample name). When you hit return the search index will retrieve those object (Files, Samples, Experiments) that match the search string. To reset the search, click on the project title at the top of the left-side navigation bar, or refresh the page in the browser.

On the right side of this banner is the User Action pull down menu (which we encountered in the help on the Projects Index Page), and a link to report issues. When you click on the link to report issues, your default mail application should open with a message addressed to [email protected]. Use this to report any problems that you are having. When you report a problem, please try to be as detail as possible about what you were doing at the time, what went wrong, and what you expected to happen instead. Obviously, if your message says something like "it doesn't work", we can't be of much help.

The '?' icon links you to these help pages.

Experiments list and actions

In the right side of the projects page is the panel containing the list of experiments for the project. At the top of that experiments-list panel is set of radio buttons that show Experiments in the list by activity state: 'active', 'completed', and 'on hold'. The activity state of an experiment is set in the experiment detail panel described elsewhere. In addition there are three buttons for actions on experiments: START NEW EXPERIMENT, MERGE EXPERIMENTS, DELETE EXPERIMENTS, and NEW EXPERIMENT USING ETL. The buttons for a new experiment and to merge experiments are described in the Experiment Page. The button regarding ETL is described in the help page on Creating experiments from ELT.

Left-Side Navigation Bar

The navigation bar, on the left, starts with the name of the project, which is also a "home" button; clicking on it will bring you back to the starting page, that is the list of experiments, shown above.

In addition, this navigation bar contains the following items:

Project Description

Select this item to chance the project description: type a new description and click Save; or click Cancel

Collaborators

Select user with whom you wish to share this project. Any user selected becomes a co-author on the project. That person will be able to edit any part of the project and carry out any action on the project that is permitted to the owner of the project (except "delete the project"; only the owner of the project is able to delete the project).

Notes and To-do items

Use these interfaces to add notes and do-to items to the project. For the to-do items, click "ADD TO-DO" and type the text for the item; delete the item, mark it Done, or check it off the list. For notes, click "ADD NOTE" and type the title and content of the note in the right side edit panel. Click "DONE" to save the note. For the text of the note, styling with GitHub markdown is supported; click the "Styling with..." link to see markdown docs.

Datasets

A data set is a collections of project experiments, samples, and file, intended for publication. You can create datasets at the Project or Experiment level. Once published, a dataset becomes world readable and appears in the Materials Commons "Published Data" list. A dataset can be un-published and deleted. A published dataset can not be deleted. An unpublished dataset that is not deleted can be republished.

Use this interface to see your list of Project datasets, and select then for editing. Published dataset can not be edited. To edit a dataset un-publish it first. To add an new dataset, click "ADD DATASET". When you add a new dataset the Initialize Database panel will appear:

Set the name of the dataset, then select the experiments you want covered by the dataset (EXPERIMENTS tab). and then select the samples from those experiments that you want covered by the dataset (SAMPLES tab). This initial selection will determine what experiments are used for the source of samples, processes, and files, for the dataset. And when set of samples are initially offered as a the ones involved in the selected processes. These selections can be changed later in the dataset edit panels.

When you initially add a dataset, it will be displayed in the dataset list, as shown above. In our example, the Demo Dataset was added and it appears in the list of datasets. Click on the dataset name to open the initial dataset edit panel:

At the top of the panel a button to "SAVE CHANGES" to the details of the dataset, a button to "CANCEL" the edit, and a button to "PUBLISH" the dataset.

In this edit-details panel you can set the details of the datasets metadata: name (rename), description, institution, funding, license, tags/keywords (comma seperated), authors, and releted papers.

You can also add a DOI to the dataset. Once you have added a DOI to a dataset, it can not be deleted. It can be unpublished, and this will remove it from the published dataset list, but the DOI requires that the we keep the dataset record, so it can not be deleted. If someone follows the link from the DOI to an unpublished dataset, they will see a message to the effect that the dataset is unpublished, most likely because it is being edited by the owner, and to check back later.

Once you have set the desired values be sure to click "SAVE CHANGES" at the top of the panel.

The tabs: Details, Samples, Files, will take you to the those panels in the edit panel.

The Edit Samples panel lets you select, and add or remove samples from the dataset. Be sure to "SAVE CHANGES" before leaving the panel, or "DISCARD" the changes made to reset.

The Edit Files panel lets you add files or remove files from dataset.

Experiments

The Experiments button in the left-side menu shows the number of experiments. If you click on it you will see a popup-menu of the list of experiments. Click off the menu to close it, click on the menu to select an experiment. We will cover the details of the Experiment editing options in a separate set of help pages. See Experiment Page in the Experiment Page and Panels part of the Help pages.

Samples

In the Samples panel you can view all the samples in the project. Shown are the sample name, its experiment, the data the sample was noted, the number of files associated with the sample, and the number of processes that the sample is effected by (e.g. Created, Transformed, Measured).

Clicking on the name of the sample will show the sample process graph: the processes effecting the sample an the order in which they occur in the relevant experiment's process workflow.

All Files

The All Files panel shows the projects directory structure and the files within that structure. Initially shown are the top level directory (with the same name as the project) and it's contents: file and directory list on the left and files list with details on the right. Clicking on a directory on the left side will open it in the files and directories display and show it's files in the right-side (file-list) panel.

The the top of the right side (file-list) panel shows a set of directory and file action buttons (left to right): upload file(s), add directory, rename current directory, download selected file(s), delete selected file(s), move files and/or directories into this directory.

The file list can be filtered by name and/or type to limit the list of files shown. For example, to make search and selection easier.

Settings and Sync

The settings panel is used to change the name of the project and the Sync button is used to synchronize the contents of the project with changes that may have happened elsewhere, as (for example) with a Globus upload.

Globus Commands

The Globus Commands are buttons that can be used to pair Material Commons with the globus interface to upload files to the project or download from the project. The Status button show the status of upload and download when there are background tasks that are necessary to complete long-running requests (greater the 2 min). The details of these commands/actions are described in the section on Globus Commands.

Shortcuts

Shortcuts are links to selected directories in the projects directory structure. By default there are links to three pre-defined directories: Literature, Presentations, and Project Documents.

These settings can be modified using the "Add/Modify Shortcuts" button, which will bring up the panel:

If there are additional top-level directories that will be listed as unselected and can be selected. The default top level directories can be deselected. Those changes will be reflected in the list of shortcuts.