Ebachour Week 15 - Revision history

Aporras1: reformatted location of final paper

2017-12-16T00:10:42Z

reformatted location of final paper

Aporras1: final paper/group report

2017-12-15T23:58:47Z

final paper/group report

Ebachour: /* Reflection on the Process */ Finished reflection

2017-12-15T23:44:20Z

‎Reflection on the Process: Finished reflection

Ebachour: /* Assessment of Project */ Finished assessment of the project

2017-12-15T23:41:25Z

‎Assessment of Project: Finished assessment of the project

Ebachour: /* Statement of Work */ fixed

2017-12-15T23:33:11Z

‎Statement of Work: fixed

Ebachour: /* Statement of Work */ added my statement of work, everything above was also written in the paper.

2017-12-15T23:31:38Z

‎Statement of Work: added my statement of work, everything above was also written in the paper.

Ebachour: fixed template link

2017-12-15T23:27:58Z

fixed template link

Ebachour: /* Acknowledgements */ got rid of numbering

2017-12-15T21:30:11Z

‎Acknowledgements: got rid of numbering

Ebachour: Added references and acknowledgements

2017-12-15T21:29:26Z

Added references and acknowledgements

Ebachour: Fixed template

2017-12-15T21:28:28Z

Fixed template

@@ Line 3: / Line 3: @@
 [[Media:README.txt|JASPAR The Friendly Ghost Group Readme]] | December 15, 2017<br>
 [[Media:Api.txt|JASPAR The Friendly Ghost Group Code]] | December 15, 2017<br>
 ==Individual Assessment and Reflection / Electronic Journal==
@@ Line 39: / Line 40: @@
 **: Maybe I can type faster after all of the writing you guys made me do.
 =Acknowledgements=

@@ Line 38: / Line 38: @@
 ** With your hands (technical skills)?
 **: Maybe I can type faster after all of the writing you guys made me do.
 =Acknowledgements=

@@ Line 33: / Line 33: @@
 * What did you learn?
 ** With your head (biological or computer science principles)
 ** With your heart (personal qualities and teamwork qualities that make things work or not work)?
 ** With your hands (technical skills)?
-* What lesson will you take away from this project that you will still use a year from now?
+**: Maybe I can type faster after all of the writing you guys made me do.
 =Acknowledgements=

@@ Line 17: / Line 17: @@
 === Assessment of Project ===
 * Give an objective assessment of the success of your project workflow and teamwork.
-* What worked and what didn't work?
+*: Our team worked pretty well together to finish both the paper and the powerpoint together, but this was mainly due to good leadership from Quinn. He kept us up to date and he is the only reason this assignment was even remotely tolerable.
-* What would you do differently if you could do it all over again?
+* What worked and what didn't work?
 * Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
 *# Content: What is the quality of the work?
 *# Organization: Comment on the organization of the project and of your group's wiki pages.
 *# Completeness:  Did your team achieve all of the project objectives?  Why or why not?
 === Reflection on the Process ===

@@ Line 8: / Line 8: @@
 === Statement of Work ===
 There were a number of steps that the coders team members completed throughout this assignment. Before the coders moved their focus to the bulk of the GRNsight part of this project, they were asked to gain some background knowledge on the field of web development. They read “Chapter 6: How Are Apps Made?” in Paul Ford’s What is Code? which is an article from 2015 that covers most of the bases of the software development industry. They were asked to thoroughly read this chapter and then present to their class what it entailed. This chapter was specific to all of the tools that the coders used in development, highlighting some important tools at the time. After covering all of the background knowledge, the coders then began the introduction phase to the new project. Often when being assigned to a new project, software engineers are given an introduction to the code base so that they may understand how everything functions within the project before they begin their work. This project was no different, as the professor gave a quick introduction along with a manual which illustrated the relevant folders within the code bank that would be used for this feature. After JASPAR’s fellow team members forked GRNsight, the JASPAR team start by setting up a local version of GRNsight and making sure that everything was properly functioning. After this step, they began to acquaint themselves with GRNsight and understand their job in the implementation of this new feature. At this point, as as displayed in Figure C, the coders moved from the immersion phase (green) and into the intermediate phase (yellow).
 The intermediate phase was where most of the progress was made towards finishing their part of the feature. They started by creating the branch that would be solely for JASPAR team progress, as well as the new files that would contain their soon-to-be-written code. At this point the coders were all setup on the GRNsight side and were ready to move to learning about the JASPAR database and how it worked. The majority of this part was spent reading the JASPAR database documentation which clearly states how the database API calls work; specifically URL, return values, and headers. JASPAR was effective in laying out their different API calls and explaining what each call did. This made it much easier for the coders to decipher which of the calls was best for retrieving the information that they needed (JASPAR API).
-After studying JASPAR, and deciding which calls were to be use, the coders then moved on to implementing the first of the API calls. The first call used the inputted gene symbol to search the JASPAR database and retrieve a list of search results, from which they retrieved the matrix ID from the first result. The second call retrieves the object of gene information associated with that gene symbol. It used the matrix ID that was retrieved from the first call and returned the object with all of the information that JASPAR has for this gene, if any at all. At this point, as they were testing their code, they were getting something called an “Access-Control-Allow-Origin” error which is usually caused by an APIs lack of support for Cross-Origin Resource Sharing(CORS), but when they went and checked the websites overview page, they found the following:
+After studying JASPAR, and deciding which calls were to be use, the coders then moved on to implementing the first of the API calls. The first call used the inputted gene symbol to search the JASPAR database and retrieve a list of search results, from which they retrieved the matrix ID from the first result. The second call retrieves the object of gene information associated with that gene symbol. It used the matrix ID that was retrieved from the first call and returned the object with all of the information that JASPAR has for this gene, if any at all. At this point, as they were testing their code, they were getting something called an “Access-Control-Allow-Origin” error which is usually caused by an APIs lack of support for Cross-Origin Resource Sharing(CORS), but when they went and checked the websites overview page, they found that the API specifically stated that they supported CORS (API Overview). After reading this on the API Overview page of JASPAR, the coders began to believe that this error was due to miscoding of the getJasparInfo() function, but after studying the code and testing the API calls through the JASPAR interface, they realized that this issue was not due to the structure of their code, but in fact was due to JASPAR and the fact that they don’t support CORS. At this point, the JASPAR team met with the professor and decided that the best solution would be to implement a relay controller that would handle all traffic from JASPAR to GRNsight. Once the relay controller was done being integrated with the server-side of GRNsight, the API calls began working properly, which corresponded with the end of the intermediate phase of this project (Figure C).
 The next phase of the project was the finishing touches (red) phase, which was where the coders spent most of their time interacting with the other teams working on this feature, to make sure that all of the pieces were working together properly (Figure C). The first step was to make sure that the JASPAR information, that the biologists on the integration team were requiring for the final page, was properly being organized and returned so that the information was useful on the page. This required taking the object returned from the second API call and properly “filing” the relevant fields into their spots within the master object. At this point, all that was left to do was to pass the information onto the page design and integration team so that they knew what to expect when calling the JASPAR function, so that they could properly put it on the page, which then marked the end of the coders work on this GRNsight feature, as displayed in Figure C.

← Older revision		Revision as of 23:27, 15 December 2017
Line 41:		Line 41:
	* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15		* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

−	{{Template:~~Ebachoura~~}}	+	{{Template:Ebachour}}

@@ Line 33: / Line 33: @@
 =Acknowledgements=
-#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
+Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
 I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together.<br>
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''<br>

← Older revision		Revision as of 21:28, 15 December 2017
Line 35:		Line 35:
	#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables\|Deliverables Page]].		#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables\|Deliverables Page]].

−	[[Template:Ebachoura]]	+	{{Template:Ebachoura}}