Bhamilton18 Week 9 - Revision history

Bhamilton18: added to acknowledgments

2017-10-30T19:08:39Z

added to acknowledgments

Bhamilton18: Added API Results and clarification on tests

2017-10-30T19:02:22Z

Added API Results and clarification on tests

Bhamilton18: Added tondi hints and solution title

2017-10-30T03:05:53Z

Added tondi hints and solution title

Bhamilton18: added Web Service API Exploration section

2017-10-30T03:01:21Z

added Web Service API Exploration section

Bhamilton18: Final tests:16,17,18

2017-10-30T02:59:58Z

Final tests:16,17,18

Bhamilton18: Added tests 10,11,12, 13, 14 ,15

2017-10-30T02:56:20Z

Added tests 10,11,12, 13, 14 ,15

Bhamilton18: Added screenshots and tests 4,5,6,7,8,9

2017-10-30T02:48:53Z

Added screenshots and tests 4,5,6,7,8,9

Bhamilton18: fixed picture formatting and numbering

2017-10-30T02:09:01Z

fixed picture formatting and numbering

Bhamilton18: added screenshot

2017-10-30T02:03:45Z

added screenshot

Bhamilton18: added test 4

2017-10-30T01:59:35Z

added test 4

@@ Line 101: / Line 101: @@
 ==Acknowledgments==
-#I worked with my partner [[User: Emmatyrnauer | Emma Tyrnauer]] on this assignment.
+#I worked with my partner [[User: Emmatyrnauer | Emma Tyrnauer]] on this assignment. We texteed and met in portion to collaborate on how our tests passed or failed and which documents to choose for that potion of the assignment.
 #Utilized this, ([[Media:GRNsight_Testing-Gray_Threshold_and_Zoom.pdf|Gray Threshold + Zoom]]) document, in order to complete our detailed GRNsight beta testing.
 #We used three separate documents: Excel workbook (.xlsx), SIF (.sif) and GraphML (.graphml) files. These files were obtained from [https://github.com/dondi/GRNsight/tree/beta/test-files/demo-files from this web page]. The three different files that were chosen from the website were as follows:

@@ Line 61: / Line 61: @@
 #*'''Expected:''' GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom out (get smaller).
 #*'''Occurred:''' '''''FAILED TEST''''' This is due to the earlier problem of no Grey Threshold option.
 ===Web Service API Exploration===
@@ Line 79: / Line 81: @@
 ** NCBI stores ''organism''s by their full name, in our case ''Saccharomyces cerevisiae'' (note the space)
-====API Solution====
+====API NCBI Results====
 ==Acknowledgments==

← Older revision		Revision as of 03:05, 30 October 2017
Line 63:		Line 63:

	===Web Service API Exploration===		===Web Service API Exploration===
		+	==== NCBI Dondi Hints====
		+	* Relevant documentation:
		+	** https://www.ncbi.nlm.nih.gov/gene
		+	** https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
		+	** https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database
		+	** https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Document_Summaries
		+	** https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Full_Records
		+	* Technical information:
		+	** Your URLs will include ampersands ('''&'''), which will need special handling with '''curl''': in these cases, enclose the URL in apostrophes (e.g., '''curl -L '<nowiki>http://www.uniport.org?query=this&type=that</nowiki>'''')
		+	** Your URLs will also include brackets ('''<nowiki>[ ]</nowiki>'''), which will need special handling with '''curl''': in these cases, make sure to add the '''-g''' switch (i.e., '''curl -g '''…)
		+	** Your URLs may include spaces; typically, we replace those with ''+'' (plus) symbols
		+	* Miscellaneous information:
		+	** NCBI consists of multiple databases; we care about the ''gene'' database
		+	** NCBI abbreviates the gene name/symbol field as ''sym''
		+	** NCBI stores ''organism''s by their full name, in our case ''Saccharomyces cerevisiae'' (note the space)
		+
		+	====API Solution====

	==Acknowledgments==		==Acknowledgments==

@@ Line 61: / Line 61: @@
 #*'''Expected:''' GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom out (get smaller).
 #*'''Occurred:''' '''''FAILED TEST''''' This is due to the earlier problem of no Grey Threshold option.
 ==Acknowledgments==

@@ Line 52: / Line 52: @@
 #*'''Expected:''' GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should zoom out (get smaller).
 #*'''Occurred:''' '''''PASSED TEST'''''
-#Test 16
+#Test 16 for '''21-genes_31-edges_Schade-data_input.xlsx'''
-#Test 17
+#*'''Expected:''' GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray.The graph should zoom out (get smaller).
-#Test 18
+#*'''Occurred:''' '''''FAILED TEST''''' This is due to the earlier problem of no Grey Threshold option.
 ==Acknowledgments==
 #I worked with my partner [[User: Emmatyrnauer | Emma Tyrnauer]] on this assignment.

@@ Line 34: / Line 34: @@
 #*'''Expected:''' GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should zoom in (get larger).
 #*'''Occurred:''' '''''PASSED TEST'''''
-#Test 10
+#Test 10 for '''21-genes_31-edges_Schade-data_input.xlsx'''
-#Test 11
+#*'''Expected:'''GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom in (get larger).
-#Test 12
+#*'''Occurred:''' '''''FAILED TEST''''' This is due to the earlier problem of no Grey Threshold option.
-#Test 13
+#Test 11 for '''21-genes_31-edges_Schade-data_estimation_output.sif'''
-#Test 14
+#*'''Expected:''' GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should zoom in (get larger).
-#Test 15
+#*'''Occurred:''' '''''PASSED TEST'''''
 #Test 16
 #Test 17

@@ Line 1: / Line 1: @@
 ==Notebook==
 ===Hands-On with GRNsight===
-#We worked on the Gray Threshold + Zoom portion of the GRNsight Beta version.
+We worked on the Gray Threshold + Zoom portion of the GRNsight Beta version.
-#Tests found: [[Media:GRNsight_Testing-Gray_Threshold_and_Zoom.pdf|Gray Threshold + Zoom]]
 #Test 1 for file: '''21-genes_31-edges_Schade-data_input.xlsx'''
 #*'''Expected:''' GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
-#*'''Occurred:'''  '''''FAILED TEST''''' The file was unable to load, and an error message was displayed. The error message stated: "Your graph failed to load. Unable to read input. The file may be corrupt."
+#*'''Occurred:'''  '''''PASSED TEST'''''
 #Test 2 for '''21-genes_31-edges_Schade-data_estimation_output.sif'''
 #*'''Expected:''' GRNsight should lay out a network graph from the SIF file if there are no errors in the file.
-#*'''Occurred:'''  '''''FAILED TEST''''' The file was imported, but then the screen/gene window did not display any errors or fixtures.
+#*'''Occurred:'''  '''''PASSED TEST'''''
 #Test 3 for '''21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml'''
 #*'''Expected:''' GRNsight should lay out a network graph from the GraphML file if there are no errors in the file.
-#*'''Occurred:''' '''''FAILED TEST''''' The file was imported, but then the screen/gene window did not display any errors or fixtures.
+#*'''Occurred:''' '''''PASSED TEST'''''
-#**The file was downloaded by going to the github demo files website and "clicking" on the link to  21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml. I then clicked raw file and chose to download this file to my computer and then uploaded it to the beta site.
+#Test 4 for '''21-genes_31-edges_Schade-data_input.xlsx'''
 #*'''Expected:''' GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray.
-#*'''Occurred:''' '''''FAILED TEST''''' The Demo version for the xlsx file did not have a grey threshold option therefore the test could not be completed. Screenshot below.
+#*'''Occurred:''' '''''FAILED TEST''''' This version for the xlsx file did not have a grey threshold option therefore the test could not be completed. Screenshot below.
 #**[[File:Nogrey.png|500px|thumb|center|No Grey Threshold Option]]
-#Test 5 for
+#Test 5 for '''21-genes_31-edges_Schade-data_estimation_output.sif'''
-#Test 6
+#*'''Expected:''' GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray.
-#Test 7
+#*'''Occurred:''' '''''PASSED TEST'''''
-#Test 8
+#Test 6 for '''21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml'''
-#Test 9
+#*'''Expected:''' GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray.
 #Test 10
 #Test 11