added deployment notes

keithhurley · Mar 11, 2024 · f456978 · f456978
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diff --git a/FinCatchAnalysis_1_Methods.qmd b/FinCatchAnalysis_1_Methods.qmd
@@ -8,4 +8,4 @@
 ## fca_fishSampleMetadata
 
 -   returns metadata for fish samples included in analysis
--   returns fc_fishSampleMetadata object
+-   returns fc_fishSampleMetadata object
diff --git a/FinCatchAnalysis_2_HelperFunctions.qmd b/FinCatchAnalysis_2_HelperFunctions.qmd
@@ -41,7 +41,7 @@ some_data %>%
 
 ### fca_getAnalysisFunctions
 
-This function returns a list and description of the analysis functions available in the FinCatchAnalysis package. 
+This function returns a list and description of the analysis functions available in the FinCatchAnalysis package.
 
 Example:
 
@@ -55,7 +55,7 @@ fca_getAnalysisFunctions()
 
 This function creates a label for each survey to be used in outputs such as reports and plots. The arguments are a vector of surveyUid values and a reference to the analysis data object. The label returned is structured like:
 
->Title1 (WB=5110 | Method=21 |  Year=2022 | Season=Spring)
+> Title1 (WB=5110 \| Method=21 \| Year=2022 \| Season=Spring)
 
 Example:
 
@@ -68,7 +68,7 @@ some_data %>%
 
 This function creates a label for each fish sample to be used in outputs such as reports and plots. The arguments are a vector of surveyUid values and a dataframe of fish samples in the analysis taken from the data object. The label returned is structured like:
 
->WB=2832 | Method=45 | 2022-03-11 | Station=627
+> WB=2832 \| Method=45 \| 2022-03-11 \| Station=627
 
 Example:
 
@@ -79,10 +79,9 @@ some_data %>%
 
 ### fc_labeler_wqSample
 
-
 This function creates a label for each fish sample to be used in outputs such as reports and plots. The arguments are a vector of surveyUid values and a dataframe of fish samples in the analysis taken from the data object. The label returned is structured like:
 
->WB=2832 | 2022-03-11 | Station=627
+> WB=2832 \| 2022-03-11 \| Station=627
 
 Example:
 

diff --git a/FinCatchAnalysis_3_CreateAnalysis.qmd b/FinCatchAnalysis_3_CreateAnalysis.qmd
@@ -36,31 +36,31 @@ Make sure to test each analysis function for:
 
 7.  Set grouping variables.
 
-  -   To group analysis calculations during analysis, use the dplyr verbs
+-   To group analysis calculations during analysis, use the dplyr verbs
 
 ``` r
         group_by(across(all_of(myGroups))
 ```
 
-  -   add addition fields as necessary "group_by(across(all_of(myGroups), anotherFieldHere)"
+-   add addition fields as necessary "group_by(across(all_of(myGroups), anotherFieldHere)"
 
 8.  Write analysis code
 
-  -   Always include Standard Error and Sample size (if appropriate), this allow users to calculate difference confidence intervals post hoc
+-   Always include Standard Error and Sample size (if appropriate), this allow users to calculate difference confidence intervals post hoc
 
-  -   When including confidence intervals, include 95% and 80%
+-   When including confidence intervals, include 95% and 80%
 
-  -   Make sure to account for missing data in any input
+-   Make sure to account for missing data in any input
 
 9.  Label values like survey, sample, species, waterbody, etc.
 
-  -   Labelers exist for samples and surveys (make sure surveyUid's are set to -1 if not grouping by survey
+-   Labelers exist for samples and surveys (make sure surveyUid's are set to -1 if not grouping by survey
 
-  -   Helper functions are available for coded values
+-   Helper functions are available for coded values
 
-10.  If analysis is calculated (as opposed to raw data summations), screen out species NOT in the processing list.  This is necessisary because species NOT in the list do not carry the assumption that all specimans for that species were processed.
+10. If analysis is calculated (as opposed to raw data summations), screen out species NOT in the processing list. This is necessisary because species NOT in the list do not carry the assumption that all specimans for that species were processed.
 
-11.  Attach all results to an analysis object (either base or custom). Example:
+11. Attach all results to an analysis object (either base or custom). Example:
 
 ``` r
     #create return object at beginning of function 
@@ -87,7 +87,7 @@ Make sure to test each analysis function for:
 
 ```
 
-12. Add the function to the list of analysis functions available in the package (found in inst folder).  This list is used to populate the FinCatchRA UI and to feed the fc_getAvailableAnalysis function.
+12. Add the function to the list of analysis functions available in the package (found in inst folder). This list is used to populate the FinCatchRA UI and to feed the fc_getAvailableAnalysis function.
 
 ### Create Custom Analysis R6 Object
 

diff --git a/FinCatchDE_0_Deployment.qmd b/FinCatchDE_0_Deployment.qmd
@@ -0,0 +1,77 @@
+# FinCatchDE Deployment
+
+## **Before Deployment**
+
+Change:
+
+1.       ConnectionString in AppSettings.json
+
+2.       redirectUri at line 45 in previousFishSamples
+
+3\.       redirectUri at line 164 in previousWaterSamples
+
+4.       auth0 settings in clsAuthFunctions, fetchController.cs, and index.tsx
+
+## **Deployment Steps**
+
+The application needs to be self-contained (See REF-3 and REF-4); you might want to investigate publishing the application through Visual Studio's IIS publishing, but this is the way that has worked best for our development.
+
+1.       Open the Projects in Visual Studio
+
+2.       Ensure the application runs locally through Visual Studio
+
+3.       Right click the solution and select Publish\...
+
+4.       Select the Web Server (IIS) Target
+
+5.       Select Web Deploy Package
+
+6.       Put the package location in the same folder as the project
+
+7.       Any name will do for the Site Name, we did Fish-Test, and click finish
+
+8.       Select Show All Settings
+
+9.       Change Deployment mode to Self-contained
+
+10.    Change the target runtime to the required runtime (for us that was win-x64)
+
+11.    Select Save
+
+12.    Click the Publish button
+
+13.    Wait for the Publish to be successful
+
+14.    Open the Console/Git Bash/PowerShell
+
+15.    Navigate to fisheries-field-sampling\\FisheriesFieldSampling\\FisheriesFieldSampling\\client-app\\ 
+
+16.    Run npm run build
+
+17.    Open File Explorer
+
+18.    Navigate to fisheries-field-sampling\\FisheriesFieldSampling\\FisheriesFieldSampling\\client-app\\
+
+19.    Copy the build folder within the project
+
+20.    Navigate to the newly created zip file from the Publish button
+
+21.    Extract into a folder named publish
+
+22.    Navigate to publish\\Content\\D_C\\GitHub\\fish-test\\fisheries-field-sampling\\FisheriesFieldSampling\\FisheriesFieldSampling\\obj\\Release\\netcoreapp3.1\\win-x64\\PubTmp\\Out\\client-app folder
+
+23.    Replace the build folder with the copied build folder
+
+24.    Copy everything within the publish\\Content\\D_C\\GitHub\\fish-test\\fisheries-field-sampling\\FisheriesFieldSampling\\FisheriesFieldSampling\\obj\\Release\\netcoreapp3.1\\win-x64\\PubTmp\\Out\\ folder
+
+25.    Open Remote Desktop
+
+26.    Connect to the fincatchag.fishstaff.info computer
+
+27.    Open the file explorer on the Remote Desktop
+
+28.    Replace the contents of C:\\Websites\\FinCatchDE with the copied files/folders
+
+29.    Open the IIS Manager
+
+30.    Restart the FinCatchDE website
diff --git a/_quarto.yml b/_quarto.yml
@@ -15,6 +15,9 @@ book:
         - FinCatch_SamplingRestrictions.qmd
         - FinCatch_DataDesign.qmd
         - FinCatch_Architecture.qmd
+    - part: FinCatchDE
+      chapters: 
+        - FinCatchDE_0_Deployment.qmd
     - part: Analysis R Package
       chapters:
         - FinCatchAnalysis_0.qmd

diff --git a/docs/FInCatchAnalysis_WarningsErrors.html b/docs/FInCatchAnalysis_WarningsErrors.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>FinCatch Documentation - 7&nbsp; Warnings and Errors</title>
+<title>FinCatch Documentation - 8&nbsp; Warnings and Errors</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -73,7 +73,7 @@
       <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./FinCatchAnalysis_0.html">Analysis R Package</a></li><li class="breadcrumb-item"><a href="./FInCatchAnalysis_WarningsErrors.html"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Warnings and Errors</span></a></li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./FinCatchAnalysis_0.html">Analysis R Package</a></li><li class="breadcrumb-item"><a href="./FInCatchAnalysis_WarningsErrors.html"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Warnings and Errors</span></a></li></ol></nav>
       <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
       </a>
       <button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
@@ -142,64 +142,81 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
- <span class="menu-text">Analysis R Package</span></a>
+ <span class="menu-text">FinCatchDE</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="./FinCatchDE_0_Deployment.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">FinCatchDE Deployment</span></span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Analysis R Package</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="./FinCatchAnalysis_0.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Overview</span></span></a>
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Overview</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./FinCatchAnalysis_DataObject.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Data Object</span></span></a>
+ <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Data Object</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./FInCatchAnalysis_WarningsErrors.html" class="sidebar-item-text sidebar-link active">
- <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Warnings and Errors</span></span></a>
+ <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Warnings and Errors</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./FinCatchAnalysis_0_ExampleScript.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Example Script</span></span></a>
+ <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Example Script</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./FinCatchAnalysis_0_BaseObject.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Base Object</span></span></a>
+ <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Base Object</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./FinCatchAnalysis_1_Objects.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Objects</span></span></a>
+ <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Objects</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./FinCatchAnalysis_1_Methods.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Methods</span></span></a>
+ <span class="menu-text"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Methods</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./FinCatchAnalysis_2_HelperFunctions.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Helpers</span></span></a>
+ <span class="menu-text"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Helpers</span></span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./FinCatchAnalysis_3_CreateAnalysis.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Create Analysis</span></span></a>
+ <span class="menu-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Create Analysis</span></span></a>
   </div>
 </li>
       </ul>
@@ -225,7 +242,7 @@
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Warnings and Errors</span></h1>
+<h1 class="title"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Warnings and Errors</span></h1>
 </div>
 
 
@@ -480,12 +497,12 @@ <h1 class="title"><span class="chapter-number">7</span>&nbsp; <span class="chapt
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
       <a href="./FinCatchAnalysis_DataObject.html" class="pagination-link">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Data Object</span></span>
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Data Object</span></span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
       <a href="./FinCatchAnalysis_0_ExampleScript.html" class="pagination-link">
-        <span class="nav-page-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Example Script</span></span> <i class="bi bi-arrow-right-short"></i>
+        <span class="nav-page-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Example Script</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>