Lab 4 – 1 Running Head: LAB 4 – READ User Manual
Lab 4 – READ User Manual 1
Running Head: LAB 4 – READ User Manual
CS 411
Lab 4: READ User Manual
Version 2
May 9 th
,2013
Jim Calderon,Troy Connor, Philip McDonald, Jacob Philmon, Andrew Sprague, Marcus Zehr
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Publication Viewing/Filtering Page: (Jim Calderon, Jacob Phillmon) ............................ 8
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1
Introduction (Phillip McDonald)
Welcome to READ -- the Repository for Electronic Aggregation of Documents. Sounds complicated, but don't worry -- it's here to make your life easier! The CS411 Black Team has created this prototype specifically for use by you, the Computer Science faculty of Old Dominion
University. We hope that this system allows you to stay up-to-date on the professional activities of your peers, and will allow the CS department website to display with pride the work and accomplishments of its faculty.
So what **is** READ?
READ is a place for you to store the complete publication and grant award history of your academic career. READ will help assist in the tedious task of cataloging this information, and make it available in a central location on the ODU CS website (http://www.cs.odu.edu/). The system is an easy way for a faculty member, student, or any visitor to the ODU website to readily find information about faculty members' recent publishing history, or maybe even their first NSF grant!
READ offers several services for the ODU faculty. The first function is to provide a centralized area for ODU CS faculty members to maintain and share their history of publication and receipt of research grants on the ODU CS website. As a website, the system will be available from any
Internet-connected web browser. Search and update functionality will make finding and adding publication and research grant information user-friendly. You'll also be able to create a short professional profile. READ will help keep the information up-to-date by providing an automated
Internet resource scraper to find and add new publications and grants to the system. Finally, it will allow card catalog-style searching of the publication/research grant information, by dates, author names, keywords, and other parameters.
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2
Getting Started (Jacob Phillmon)
First, you must go to 411black.cs.odu.edu to reach the READ system homepage. As a viewer of the system it is possible to view any recent publications and grants that have been added to the system from this page. If you wish to browse through publications stored within the system, you can click on the publications tab located at the top of the screen. From the
Publications Page, you can choose to either browse through the publications stored in the system, or choose from various filtering options. If you wish to browse through the grants stored in the system, you can click on the Grants tab located at the top of the page. From the Grants page you can choose to browse through grants stored within the system, or choose from numerous filtering options. Each publication and grant displayed within the system lists the names of all the authors that have a profile on the READ system which are associated with the document. If you click on their name, you will be brought to their profile page. While on their profile page you can view their profile information along with any publications and grants that person is associated with.
If you are an author with an account setup on the system, simply use the login form located on the side of each page to login to the system. Your username is your Computer Science login username and the password is your Computer science login password. Once you have logged in, you can choose to go to your profile by clicking the profile button located where the login form used to display on the side of the page. From your own login page you may choose to edit your profile information as well as add new grants and publications to the system manually by clicking the specified link located under your profile information. You can also edit any publications and grants that you are associated with by clicking the edit button located below each grant or publication.
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When adding new publications to the system you can choose from two options: manual submission or Bibtex submission. Using manual submission you may select from three different types of publications: conferences, journals, and tech reports. After filling in the applicable fields associated with the publication, you may choose to select a thumbnail image that will be displayed along with the publication; if no image is chosen, the system’s default thumbnail image will be used. Before submitting the publication to be added to the system you may choose to select other authors in the system that can edit this publication. If you wish to upload a Bibtex document which will automatically add the publication to the system for you, simply scroll down to the bottom of the screen and select the Bibtex file you wish to use and hit the submit button
(NOTE: the Bibtex file must be named in the following manner: (first name here)-(Last name here).bib . If the file is not named in this way the Bibtex file will not be read and the publication will not be added to the system.).
When editing your publications you have the option to edit any of the fields that currently exist. All the fields will be prefilled with their original values. You may also choose to remove or add editing capabilities to other authors in the system. The thumbnail image may also be altered from this page.
When adding new grants to the system you must fill in the fields manually; no bibtex file submission has been implemented. Fields that must be filled in have been marked with an asterisk. You may only add grants to the system where you are the principal investigator, as the page automatically sets you as the principal investigator. To add co-principal investigators, simply select their name using the checkbox menu at the bottom of the screen.
The edit grant page works similarly like the add grant page, except all the fields are initially filled in with the grant’s original information. If the grant does not belong to you, you
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Running Head: LAB 4 – READ User Manual may select the checkbox on this page and hit the submit button, and the grant will no longer be associated with you. As a system administrator you can choose to remove anyone from the grant or remove the grant entirely from the system from this page.
If you are a system administrator, you can reach the administration page by clicking the administration button after logging into the system. From the administration page you can select to add new faculty members to the system, add publications or grants to the system, view/edit current user’s administrative status, or change the system’s default pagination values. You can also go to anyone’s profile page by clicking on their name which is listed at the bottom of the page along with their administrative status. As and administrator you have the ability to edit anyone’s publications, grants, or profile information from their profile page.
3
Using the Product/Prototype
3.1
Homepage: (Jacob Phillmon)
The READ Homepage allows you to view publications and grants that have been recently added to the system. By default the page will list all recent publications, but by clicking the
“Grants” link below the recent publications message, it is possible to view recently added grants.
The number of publications and grants shown are controlled by the default number set by an administrative user on the administration page. Figure 1 illustrates the homepage display.
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Intentionally Left Blank
Figure 1: Homepage Display
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3.2
Login: (Jacob Phillmon)
The login form will be displayed on each page of the READ system. The login form has
2 fields: User Name and Password. The Username and password to be filled in are the user’s
ODU CS Username and Password. After a successful login has been made, the box will display your CS username, along with a link to your profile page. If the user is an administrative user, a link to the administration page will also be displayed. Figure 2 represents the Login form.
Figure 2: Login Form
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3.3
Publication Viewing/Filtering Page: (Jim Calderon, Jacob Phillmon)
Upon loading, the publications page will present the user with a drop down box with the following options: Browse, Author Last Name, Title, Year Published, and Keywords. Each time the user enters a letter or number into the search bar, it is sent to a PHP page where a new query is generated. This allows for the results to be narrowed on each key-down. All options sort the results by latest year published except for Author Last Name. The fields that will be displayed, if available, are: title, author, journal name, volume, pages, link, related authors, date published, and year published.
Browse displays all publications that are stored in the database, ordered from latest year published. Author last name displays a list of authors that match the search term, along with three of their latest publications for reference on their field of research. Title displays the publications whose title contains a match for the search term. Years published displays the publications whose Year Published field matches the search term. Lastly Keywords will display publications whose Tags field contains a match for the search term. Figure 3 illustrates the functionality of the Publications Page.
Steps to use the Pubs Page
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1.
Navigate to the Publications page from the home screen
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2.
Click on the drop down box to choose from the options offered to view the publications.
3.
After selecting an option (other than Browse), a text box will appear where a search variable/term is entered to display the publications by.
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4.
Publications containing the search term will appear on the screen along with available information.
Figure 3: Publications Page
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3.4
Grant Viewing/Filtering Page: (Andrew Moss)
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When the page loads, the user is presented with a drop-down menu that allows her to choose the method by which she wishes to filter the grants to be shown. This is followed by the display of information from all grants in the READ database that match the selected filtering criteria. For each grant, the following information is given: Funding Agency, Award Number,
Amount, Title, Principal Investigator, Co-Principal Investigators, Start Date, End Date, and a link to information about the grant on the Funding Agency’s web site. Each displayed Principal
Investigator and Co-Principal Investigator is a link to that individual’s public profile page.
The default filtering method is “Browse”. This will display every grant in the database. If the user chooses to filter by “Title” she is presented with a text input box and instructions to enter a search term. With each keystroke, a new query will be launched that will display all grants with titles containing the text the user has entered. The next selectable option is “Funding
Agency”. This option provides the same functionality as the “Title” filter except that it searches for grants where the Funding Agency contains the text entered by the user. Similarly, the
“Investigators” filter applies the same principal to the Principal Investigator and Co-Principal
Investigators fields. The penultimate option, “Status”, removes the input text box and replaces it with an additional drop-down menu from which the user can choose to show grants that are
“Active”, “Expired”, or “All” grants regardless of their status. The default option is to present
“Active” grants: those which have an end date beyond the date at which the page is accessed.
“Expired” grants have an end date prior to the date at which the page is accessed. “All Fields” is the final filtering method. If this option is chosen, three text input boxes and a drop-down menu are presented. This allows the user to combine one or more of the previously mentioned filters
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(other than “Browse”) to further restrict/customize the grants to be displayed. Figure 4 illustrates the Grants Page.
Figure 4: Grants Page
3.5
Profile Page: (Jacob Phillmon)
From the profile page viewers of the system can view an author’s profile information along with all the grants and publications that author is associated with. If an author is logged in and currently viewing their own profile page, it is possible to go to the following pages by clicking on the designated links located under their profile information: Edit Profile, Add
Publication, and Add grant. An author viewing their own profile page may also choose to edit
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Running Head: LAB 4 – READ User Manual their own publications and grants by clicking the “Edit This Publication” or “Edit This Grant” link located below each document. All of these features can be accessed by administrative users.
Figure 5 illustrates the Profile Page.
Figure 5: Profile Page
3.6
Profile Edit Page (Jacob Phillmon)
The Profile Edit Page can be accessed if you are logged in and currently viewing your own
Profile Page, or are logged in as an administrative user. From this page you can edit your basic information such as your job title and a personal description about yourself. You can also choose to change your profile image from here. Figure 6 illustrates the Edit Profile Page.
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Using the Edit Profile Page:
1.
Login to the system using the login form on the left side of the page.
2.
Click the view/edit profile link located on the left side of the page
3.
Click on the Edit Profile link located under your profile information
4.
Edit the applicable fields
5.
Click submit.
Figure 6: Profile Edit Page
3.7
Publication Add Page(Marcus Zerh, Jacob Phillmon
In order to add publications to the system, users must access the page though the profile page. Once on this page the user may enter publication information into the text fields and also select other authors for the document. Users will select from a pull down menu the type of publication they are adding to the database and will choose between a conference, journal, or technical report. The user will then input into text fields the title of the publication as well as any authors who helped to write this document. Next, the author of the publication will insert the date which the publication being added to the database was published in the format specified on
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Running Head: LAB 4 – READ User Manual the page which is four digits signifying the year, 2 digits for the month, and 2 digits for the day separated by a backslash. A DOI text box is also available for use by the user if they so desire to add this information..
The abstract text area is reserved for a brief description of the publication and along with this there is also another text area field reserved for any keywords the user wishes to tie to this publication. Link is reserved for the URL to where the actual publication is stored online. The user may also opt to add a thumbnail image to display along with the publication but if they do not a default image will be assigned.
The user must select a publication type to proceed further and depending on the type of publication selected the next fields change to publication specific input. For conferences these fields include: Conference name and pages. If journal is selected as the publication type the fields listed are: Journal name, volume, issue, and pages. Lastly if a technical report is selected the fields displayed are: Tech report number and pages.
Towards the bottom of the page is a scrollable list of authors in the system to associate as secondary authors for the publication who are on the READ system. To select more than one multiple author the use must hold CTRL and click on each name and the authors are listed in alphabetical order by last name. Once all of the information is entered above the user can click the submit button to add this data into the READ database. Alternatively the user can also opt to add a Bibtex file instead of manually inserting the above information.
Adding a publication to the system:
1.
Log in to the system using the login form on the side of the page.
2.
Click the view/edit profile button
3.
Click the add publication link located under your profile information
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4.
Fill in the applicable fields
5.
Add other users who also helped author the publication.
6.
Submit the form.
3.8
Publication Edit Page
The publication edit page has identical input areas as the publication add page, except the section where multiple authors may be added. Here, all of the information for the specific publication being edited will populate into the appropriate fields and the user will also have the opportunity to add or remove authors to the publication. After the user has made their changes and click submit, the updated publication information will be inserted into the database.
At the bottom of the page is a checkbox for the option of removing the publication from the database. When this box is checked and the submit button is clicked, the publication will be deleted from READ.
3.9
Grants Add page (Andrew Sprague, Jacob Phillmon)
In order to Add grants to the system users must access the page though the profile page.
Once on the page you may enter grant information into the text fields and select other people who have worked with you on the grant. Only integers will be accepted for the fields: Award
Number, Award Amount, Start Year, End Year. Title is the name of the grant. Funding Agency and Division are information about the group that is administering the grant. The Award number field is for the identification that the group awarding the grant gives it. For the Award Amount the user will have to round to the nearest dollar.
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Start Date, End Date, Start Year, and End Year fields are all self-explanatory. The Start and end date must be filled out in a particular format. The format that they must be in is by yyyy-mm-dd where yyyy represents a year, mm represents the month, and dd represents the day.
Abstract is for a brief description of a grant. Link is to enter a url for the agency’s grant page. Finally the keywords section is for users to enter tags to associate with your grant.
At the bottom of the page is a list of authors in the system to associate as CO Principal investigators with your grant. After checking their names off the system will associate that particular author with your grant. For your convenience the list is in Alphabetical order.
When you click the Add Grant button your grant will be submitted into the READ system. It will be viewable to others and will be editable via the edit page. Afterwards you may submit more grants. Figure 7 illustrates the Grant Add Page.
Adding a Grant to the system:
7.
Log in to the system using the login form on the side of the page.
8.
Click the view/edit profile button
9.
Click the add grant link located under your profile information
10.
Fill in the applicable fields
11.
Add other users who are co-principal investigators using the checkboxes.
12.
Submit the form.
Intentionally Left Blank
Figure 7: Add Grant Page
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3.10
Grants Edit Page (Andrew Sprague)
The Grants Edit page has all of the text areas as the Grants Add page, except the
Keywords section. The current information is displayed in the fields to be edited. After you change the fields and click submit the grants information, the information will be updated.
At the bottom there is a checkbox for if the grant is not yours. When checked and the submit box is clicked it will remove you from the grant. If you were the last person associated with the grant then the whole grant will be removed from the system.
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3.11
Administration Page: (Jacob Phillmon)
From the Administration Page an administrator can choose to update the default pagination values for items displayed on the READ system. To do this, select the default item number you wish to alter, update the value, and hit the submit button. Below the pagination values is a list of all the users that are currently in the system. By clicking on a users name in this list it is possible to reach that persons profile page. By clicking on the select box below each user’s name it is possible to alter that person’s privilege level: either author status or administrative status. At the top of the page there are links that lead the Add Publication Page,
Add Grant Page, and Add Faculty Page. Figure 8 illustrates the Administration Page.
Alter Systems Pagination Values:
1.
Login as an administrative user
2.
Click the administration link located on the left side of the page
3.
Alter the current pagination values for the specific pagination you wish to change
4.
Submit the values.
Add a publication to the system as an administrator:
1.
Login to the system as an administrator
2.
Click the administration link located on the left side of the page
3.
Click the add publication link located under the pages description
4.
If you wish to add a publication manually, select the publication type you wish to use. Otherwise, skip to step 8 if you wish to submit a bibtex file.
5.
Fill in the appropriate fields (NOTE: The title, Authors, published date, and publication type must be filled in)
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6.
Select the authors that have ownership of the system(note, at least one person must be selected as you have the right to add anyone as an owner including yourself.).
7.
Use the submit button located under the people you wish to add as owners and omit steps 8 and 9.
8.
Select a bibtex file to submit
9.
Click the submit button located under the bibtex file
Adding a Grant as an administrator:
1.
Log into the system as an administrator
2.
Click the administration link located on the left side of the page
3.
Select the Add Grant link located below the page’s description
4.
Fill in all the applicable fields
5.
Select the principal investigator
6.
Select the co-principal investigators
7.
Submit the grant
Adding a new faculty member to the system:
1.
Log in as an administrator
2.
Click the administration link located on the left side of the page.
3.
Click the Add Faculty link located below the page’s description
4.
Select the User’s administrative level
5.
Add in the User’s Microsoft Academic Search Scraper String
6.
Click the Submit button
Editing an Author’s Profile:
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1.
Log in as an administrator
2.
Click the administration button located on the left side of the page.
3.
Scroll down the page and click on the author’s name
4.
Click the edit profile link located on their page
5.
Alter the applicable fields
6.
Click Submit.
Altering a User’s administrative level:
1.
Log in as an administrator
2.
Click the administration button located on the left side of the screen
3.
Scroll down the and find the author’s name
4.
Use the selector next to their name to adjust their administrative level
5.
Click the submit button next to their name.
Figure 8: Administration Page
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3.12
Add Faculty Page
From here an administrator can add CS faculty to the READ database. All faculty members must have a Old Dominion University Computer Science email address.
1) The administrator will start by logging in at the home screen.
2) The administrator will then click the link for the administration page in the left taskbar.
3) After clicking the link the administrator will see the administration page. The links below will allow the administrator to add publications, add grants, and add faculty. The administrator will click the link to add faculty.
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4) The administrator will fill out the following form to add a faculty member. The form fields that must be filled out are labeled with an asterisk.
5) The fields that the administrator will use are sampled in the text box. The Scraper String will be in the following format below. The administrator can find the link on http://academic.research.microsoft.com
. The administrator will look for the faculty member’s page and use that link for the Scraper String.
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6) The administrator will complete the form and be redirected to the home page on success. If there is an error in the form the administrator will get an error. The error will tell the administrator what fields were not completed. The administrator can then return to the form and complete it with the errors missing.
7) The add faculty will create a scraper script for the faculty member. The administrator can then use this script to fetch publications for the added user. The script can be executed for the terminal window.
8) Once the faculty member is added they will be provided with a profile page and have publications listed.
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4
Error Messages
4.1
Login
If you try to visit any page that requires you to be logged in, you will be blocked from viewing anything on that page and an error message telling you to log in will appear. If you try to visit administrative pages a similar message stating “You are not an administrative user.” will appear. If for any reason you enter invalid credentials into the login form that appears on the left side of the screen, a new page will be loaded asking you to renter your information again in a similar form.
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4.2
Publication Add/Edit
If the user is not logged into the system the publication add page will print an error stating that you must log in. If required fields are not filled out once the submit button is clicked then when the page reloads itself a list of error message will populate on the screen and prompt the user to go back and fill them in. These required fields include: Title, author, date published, and publication type.
Also, for publication type selected, all of the specific fields are also required and will prompt error messages. Figure 6 and 7 will show the error messages which are generated when required fields are left black on the publication add and edit pages. If you are not logged into the system as a user who has the ability to edit the publication you will be displayed an error page stating that you don’t have the right to edit the page. If you are not logged into the system at all, then the system will tell you to log in as a user.
4.3
Grant add/edit Page
If you are not logged into the system the grants add page will give you an error telling you to log in. If you didn’t fill out the title, start date, end date, or funding agency the grant will not be added to the system and the fields you forgot will be listed. Unlike when you are not logged in, if you left fields blank you will still be have a chance to submit a grant. If you are not logged into the system as someone who has the ability to edit the grants you will be displayed an error page telling you that you don’t have the right to edit the page. If you are not logged into the system at all, then the system will tell you to log in as a user.
4.4
Faculty Add Page
When you enter the form data to add a faculty member, you will have fields that you have to fill out. The following errors can occur if the fields are not filled out.
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1) First name error:
2) Last Name error:
3) CS email error:
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4) Scraper String error
The User level mandatory field forces the administrator to choose what the faculty member is. No error will be thrown because this drop down value is always selected at default Author.
The cancel button on the form will delete all the data filled out to start all over again.
When submitted and all areas of the form are correct, you will be redirected to the homepage.
5
Glossary
Administrator/Administrative User : a user with increased privileges for editing database content
Author : a person who publishes in an academic journal or other academic
BibTeX : A file format for reference information in XML format. It will be used to automatically fill in key information when uploading or editing publications and grants.
Computer Science (CS) : An academic discipline based on advancing computing theory and algorithm development, that sometimes includes theory about software engineering
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Running Head: LAB 4 – READ User Manual methods.
Client application : In a client/server architecture, the module that takes input and creates queries to be processed by a server, and receives the results from the server.
Client/Server Architecture : A software engineering paradigm that separates functionality into a
“client” application and a “server” application that interact.
CSS : A programming language used to specify presentation of HTML pages
Data Mining : The act of going through a source of input to find specific information.
Database Schema : A description of the structure of database
Funding Agency : The source of funds for research grants. These organizations usually have a limited amount of money to (pass out) principle investigator’s that submit an accepted application for research funds.
GIT : A software system for controlling and organizing software versioning.
GoogleScholar ( http://scholar.google.com
): Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.
Google Scholar helps you find relevant work across the world of scholarly research. scholar.google.com
Graphical User Interface (GUI) : A computer interface composed of icons, text fields, menus, etc. that can be interacted with via a mouse and keyboard, through which a user interacts with a software application. Used to differentiate from a “command-line interface”, in which a user interacts with a software application solely through a text terminal. internet scraper : internet scraper / web scraper - (wikipedia) web scraping focuses more on the
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JQuery Sparklines : A development library for the visualization of data.
ODU : Old Dominion University.
MicrosoftAcademic ( http://academic.research.microsoft.com/ ): Microsoft Academic Search is a free service developed by Microsoft Research to help scholars, scientists, students, and practitioners quickly and easily find academic content, researchers, institutions, and activities. Microsoft Academic Search indexes not only millions of academic publications, it also displays the key relationships between and among subjects, content, and authors, highlighting the critical links that help define scientific research. Microsoft
Academic Search makes it easy for you to direct your search experience in interesting and heretofore hidden directions with its suite of unique features and visualizations.
MySQL : A database querying language.
Parse : A technical term usually used to describe the processing of a statement written in a programming language. May be used generally to describe the processing of any statement for specific meaning.
Perl : A widely-used programming language on the server-side of web applications.
PHP : A widely-used programming language on the server-side of web applications.
Principle Investigator (PI) : The primary researcher that a research grant is bestowed upon, responsible for documenting the work and publishing research results.
Publication or Academic Publication : A document created by a faculty member to share research. They are usually published in an academic journals, technical reports, and
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Query : An algorithm sent to the database to either change the database or get back results
READ : Repository for Electronic Aggregation of Documents
RSS : A system for subscribing to and distributing news.
Scraper : An automated application designed to scan a source of input such as a document or a website for pertinent information.
Server application : In a client/server architecture, the module that takes queries or requests from a client module, process them, and returns the result to the client.
Software Compatibility : A description of whether different softwares, or versions of software, can communicate/interact.
SQL : A widely-used programming language used to query databases.
SQL injection : Performing unauthorized queries on a database for malicious purposes.
User Authentication : The process of verifying the access credentials of a user of an automated system, usually accomplished by requesting a username and password combination.
Viewer : In the scope of our project an outside person who wishes to query the information contained in the READ database.
Version Control : A method for organizing and recording different versions of documents that have been created over time.
Virtual Private Server (VPS) : A software version of a hardware server. Used to create independent servers (....) on a single piece of hardware.
Webserver : A group of applications run on a computer or VPS in to serve webpages and provide server-side computation for browser-based client applications. A web server is a constantly “on” resource whose sole or main job is to respond to HTTP requests from
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XML : Extensible markup language.
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