Kwrigh35 Week 9 - Revision history

Kwrigh35: /* Viewport Size Testing Results */ changed color scheme of results table

2017-10-31T06:37:13Z

‎Viewport Size Testing Results: changed color scheme of results table

Kwrigh35: /* Viewport Size Testing Instructions */ removed extraneous quotation mark

2017-10-31T06:25:27Z

‎Viewport Size Testing Instructions: removed extraneous quotation mark

Kwrigh35: /* Viewport Size Testing Instructions */ formatting fix

2017-10-31T06:24:44Z

‎Viewport Size Testing Instructions: formatting fix

Kwrigh35: /* Electronic Notebook */ moved image for better page layout

2017-10-31T06:23:17Z

‎Electronic Notebook: moved image for better page layout

Kwrigh35: combined sections. added signature to acknowledgements.

2017-10-31T06:19:04Z

combined sections. added signature to acknowledgements.

Kwrigh35: /* API */ separated instructions regarding the first two commands from the third

2017-10-31T06:17:41Z

‎API: separated instructions regarding the first two commands from the third

Kwrigh35: /* API */ added commands and URL necessary for finding gene name in UniProt.

2017-10-31T06:09:16Z

‎API: added commands and URL necessary for finding gene name in UniProt.

Kwrigh35: /* Results */ added API section

2017-10-31T05:50:45Z

‎Results: added API section

Kwrigh35: /* Acknowledgements */ added acknowledgements

2017-10-30T23:19:53Z

‎Acknowledgements: added acknowledgements

Kwrigh35: /* References */ changed to MLA format

2017-10-30T22:49:18Z

‎References: changed to MLA format

@@ Line 13: / Line 13: @@
 ''Test numbers refer to tests found on [[media:GRNsight_Testing-Viewport_Size.pdf | this PDF]]'' [[File:GRNsight_Viewport_Fail.JPG|600px|thumb|right|'''Fig. 1''' Screenshot highlighting the scroll bar that appears when the "fit to window" functionality of the viewport fails.]]
-{| class="wikitable" style="Background: lavendar"
+{| class="wikitable"
 |-
-!style="background: mediumpurple;color:white"| Test Number !!style="background: mediumpurple;color:white"|  Results
+! Test Number !! Results
 |-
-|Test 1 ||PASS
+|Test 1 ||style="background: Honeydew"| PASS
 |-
-|Test 2 ||PASS
+|Test 2 ||style="background: Honeydew"| PASS
 |-
-|Test 3 ||PASS
+|Test 3 ||style="background: Honeydew"| PASS
 |-
-|Test 4 ||PASS
+|Test 4 ||style="background: Honeydew"| PASS
 |-
-|Test 5 ||PASS
+|Test 5 ||style="background: Honeydew"| PASS
 |-
-|Test 6 ||PASS
+|Test 6 ||style="background: Honeydew"| PASS
 |-
-|Test 7 ||PASS
+|Test 7 ||style="background: Honeydew"| PASS
 |-
-|Test 8 ||PASS
+|Test 8 ||style="background: Honeydew"| PASS
 |-
-|Test 9 ||PASS
+|Test 9 ||style="background: Honeydew"| PASS
 |-
-|Test 10 ||PASS
+|Test 10 ||style="background: Honeydew"| PASS
 |-
-|Test 11 ||PASS
+|Test 11 ||style="background: Honeydew"| PASS
 |-
-|Test 12 ||PASS
+|Test 12 ||style="background: Honeydew"| PASS
 |-
-|Test 13 ||FAIL
+|Test 13 ||style="background: MistyRose"| FAIL
 |-
-|Test 14 ||FAIL
+|Test 14 ||style="background: MistyRose"| FAIL
 |-
-|Test 15 ||FAIL
+|Test 15 ||style="background: MistyRose"| FAIL
 |}

@@ Line 6: / Line 6: @@
 **21-genes_31-edges_Schade-data_input.graphml,
 **21-genes_31-edges_Schade-data_input.sif
-**21-genes_31-edges_Schade-data_input.xlsx."
+**21-genes_31-edges_Schade-data_input.xlsx.
 *The files were downloaded from [https://github.com/dondi/GRNsight/tree/beta/test-files/demo-files this website].
 *We followed the testing instructions on [[media:GRNsight_Testing-Viewport_Size.pdf | this PDF]].

@@ Line 3: / Line 3: @@
 ===Viewport Size Testing Instructions===
 *We were tasked with testing the viewport on the [http://dondi.github.io/GRNsight/beta.html GRNsight Beta].
-*The files we used for testing were titled "21-genes_31-edges_Schade-data_input.graphml," "21-genes_31-edges_Schade-data_input.sif" and "21-genes_31-edges_Schade-data_input.xlsx."
+*The files we used for testing were titled
-**The files were downloaded from [https://github.com/dondi/GRNsight/tree/beta/test-files/demo-files this website].
+**21-genes_31-edges_Schade-data_input.graphml,
 *We followed the testing instructions on [[media:GRNsight_Testing-Viewport_Size.pdf | this PDF]].

@@ Line 8: / Line 8: @@
 ===Viewport Size Testing Results===
-''Test numbers refer to tests found on [[media:GRNsight_Testing-Viewport_Size.pdf | this PDF]]''
+''Test numbers refer to tests found on [[media:GRNsight_Testing-Viewport_Size.pdf | this PDF]]'' [[File:GRNsight_Viewport_Fail.JPG|600px|thumb|right|'''Fig. 1''' Screenshot highlighting the scroll bar that appears when the "fit to window" functionality of the viewport fails.]]
 {| class="wikitable" style="Background: lavendar"
@@ Line 46: / Line 46: @@
 ===Failed Test Explanation===
-[[File:GRNsight_Viewport_Fail.JPG|600px|thumb|right|Screenshot highlighting the scroll bar that appears when the "fit to window" functionality of the viewport fails.]]
+Tests 13, 14, and 15 were designed to test the "Fit to Window" functionality of the viewport.  We noticed that when the browser window was small (less than 1317 pixels wide) the viewport extended further than the scope of the browser.  '''Figure 1''' highlights the scroll bar that appears at the bottom of the browser window (which appears when the viewport extends beyond the width of the browser window.)
 ===API===

@@ Line 7: / Line 7: @@
 *We followed the testing instructions on [[media:GRNsight_Testing-Viewport_Size.pdf | this PDF]].
 ===Viewport Size Testing Results===
 ''Test numbers refer to tests found on [[media:GRNsight_Testing-Viewport_Size.pdf | this PDF]]''
@@ Line 68: / Line 67: @@
 *I'd like to thank my homework partner, [[User:Ebachour | Eddie Bachoura]], for meeting with me on Monday afternoon (10/30).  We worked on the assignment together and were able to finish in a couple of hours.
 *''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''
+[[User:Kwrigh35|Kwrigh35]] ([[User talk:Kwrigh35|talk]]) 23:19, 30 October 2017 (PDT)
 ==References==
 *LMU BioDB 2017. (2017). Week 9. Retrieved October 24, 2017, from [[Week 9]]
 *LMU BioDB 2017. (2017). GRNsight Client Side Testing Document: Viewport Size. Retrieved October 24, 2017, from [[media:GRNsight_Testing-Viewport_Size.pdf]]
 {{template:kwrigh35}}

@@ Line 51: / Line 51: @@
 ===API===
-The database my partner and I worked with was UniProt.  By executing the three commands given below, one can successfully find the gene ID number for any Saccharomyces Cerevisiae gene if the gene name is known.  Simply replace <code><gene name></code> with the name of the gene you are looking for (e.g. ASP1, ACT1, etc.)
+The database my partner and I worked with was UniProt.  By executing the first two commands given below, one can successfully find the gene ID number for any Saccharomyces Cerevisiae gene if the gene name is known.  Simply replace <code><gene name></code> with the name of the gene you are looking for (e.g. ASP1, ACT1, etc.)
 <pre>
@@ Line 62: / Line 62: @@
 We used this URL <code>http://www.uniprot.org/uniprot/?query=559292+$gene_name&sort=score</code> as part of the command.  The number ''559292'' refers to the Taxon ID that represents Saccharomyces Cerevisiae in UniProt.
 ==Acknowledgements==

← Older revision		Revision as of 06:09, 31 October 2017
Line 51:		Line 51:

	===API===		===API===
		+	The database my partner and I worked with was UniProt. By executing the three commands given below, one can successfully find the gene ID number for any Saccharomyces Cerevisiae gene if the gene name is known. Simply replace <code><gene name></code> with the name of the gene you are looking for (e.g. ASP1, ACT1, etc.)
		+
		+	<pre>
		+	gene_name=<gene name>
		+
		+	gene_id=$(curl -L "http://www.uniprot.org/uniprot/?query=559292+$gene_name&sort=score" \| grep -o -P '(?<=tbody><tr id=").*(?=\" class=" entry s)')
		+
		+	curl -L "http://uniprot.org/uniprot/$gene_id.xml"
		+	</pre>
		+
		+	We used this URL <code>http://www.uniprot.org/uniprot/?query=559292+$gene_name&sort=score</code> as part of the command. The number ''559292'' refers to the Taxon ID that represents Saccharomyces Cerevisiae in UniProt.

	==Acknowledgements==		==Acknowledgements==