Adding a page showing test server usage per package

OHDSI · Mar 25, 2024 · 139da54 · 139da54
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diff --git a/Rmd/_site.yml b/Rmd/_site.yml
@@ -54,6 +54,8 @@ navbar:
           href: releaseProcess.html 
         - text: "Package Statuses"
           href: packageStatuses.html 
+        - text: "Test server usage"
+          href: testServerUsage.html 
         - text: "Development Roadmap"
           href: "developmentRoadmap.html"
         - text: "HADES Package Requirements"

diff --git a/Rmd/style.css b/Rmd/style.css
@@ -52,3 +52,50 @@
 	text-align: center;
 	margin-bottom: 0px;
 }
+
+#slanttable {
+  display: flex;
+  flex-direction: column;
+  justify-content: space-around;
+  max-width: 50vw;
+  margin-top: 50px;
+}
+#slanttable table{
+  border-collapse: collapse;
+  --table-border-width: 1px;
+}
+#slanttable th {
+  white-space: nowrap;
+  position: relative;
+}
+#slanttable th > div {
+  /* place div at bottom left of the th parent */
+  position: absolute;
+  bottom: 0;
+  left: 0;
+  /* Make sure short setting names still meet the corner of the parent otherwise you'll get a gap */
+  text-align: left;
+  /* Move the top left corner of the span bottom-border to line up with the top left corner of the td border-right border so that the border corners are matched */
+  /* Rotate -45 degrees about matched border corners */
+  transform: 
+    translate(calc(100% - var(--table-border-width) / 2), var(--table-border-width))
+    rotate(315deg);
+  transform-origin: 0% calc(100% - var(--table-border-width));
+  width: 100%;
+}
+#slanttable th > div > span {
+  /* make sure the bottom of the span is matched up with the bottom of the parent div */
+  position: absolute;
+  bottom: 0;
+  left: 0;
+  border-bottom: var(--table-border-width) solid gray;
+}
+#slanttable td {
+    border-right: var(--table-border-width) solid gray;
+    /* make sure this is at least as wide as sqrt(2) * height of your tallest letter or the headers will overlap each other */
+    min-width: 30px;
+    text-align: right;
+    padding-top: 2px;
+    padding-left: 5px;
+    padding-right: 5px;
+}
diff --git a/Rmd/testServerUsage.Rmd b/Rmd/testServerUsage.Rmd
@@ -0,0 +1,44 @@
+---
+title: "Test server usage"
+output: 
+    html_document:
+        toc: FALSE
+---
+
+The table below lists, for each package, which database testing servers it uses as part of its unit tests.
+
+- T means the package uses the database server for testing
+- X means the package does **not** use the database server for testing
+- An empty cell means the package does not directly talk to the database
+
+```{r, results='asis', echo=FALSE}
+data <- readRDS("../extras/DatabaseTestServerUsage.rds")
+data <- data[order(data$package), ]
+dbmss <- colnames(data)
+dbmss <- dbmss[dbmss != "package"]
+
+lines <- c(
+  "<div id=slanttable>",
+  "<table>",
+  "  <thead>",
+  "    <tr>",
+  "      <th>Package</th>",
+  sprintf("      <th><div><span>%s</span></div></th>", dbmss),
+  "    </tr>",
+  "  </thead>",
+  "  <tbody>",
+   sapply(seq_len(nrow(data)), function(i) c("    <tr>",
+                                            sprintf("      <td>%s</td>", data$package[i]),
+                                            sprintf("      <td%s>%s</td>", 
+                                                    ifelse(is.na(data[i, dbmss]), "", ifelse(data[i, dbmss], " style=\"background:#cdf5bf;\"", " style=\"background:#f5c3bf;\"")),
+                                                    ifelse(is.na(data[i, dbmss]), "&nbsp;", ifelse(data[i, dbmss], "T", "X"))
+                                                    ),
+                                            "    </tr>")),
+  "  </tbody>",
+  "</table>",
+  "</div>"
+)
+writeLines(lines)
+```
+
+This table was constructed simply by looking for the environmental variable names of the test server credentials in each package's test code, and may therefore not reflect actual testing. Whether a package connects to a database at all was determined by evaluating whether it imports DatabaseConnector.
diff --git a/docs/codeStyle.html b/docs/codeStyle.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/community.html b/docs/community.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/connecting.html b/docs/connecting.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/contribute.html b/docs/contribute.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/developerGuidelines.html b/docs/developerGuidelines.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/developmentRoadmap.html b/docs/developmentRoadmap.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/index.html b/docs/index.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/installingHades.html b/docs/installingHades.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/packageRequirements.html b/docs/packageRequirements.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/packageStatuses.html b/docs/packageStatuses.html
@@ -340,6 +340,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/packages.html b/docs/packages.html
@@ -416,6 +416,9 @@
     <li>
       <a href="packageStatuses.html">Package Statuses</a>
     </li>
+    <li>
+      <a href="testServerUsage.html">Test server usage</a>
+    </li>
     <li>
       <a href="developmentRoadmap.html">Development Roadmap</a>
     </li>

diff --git a/docs/pare_reports/Achilles.html b/docs/pare_reports/Achilles.html
diff --git a/docs/pare_reports/Andromeda.html b/docs/pare_reports/Andromeda.html
diff --git a/docs/pare_reports/BigKnn.html b/docs/pare_reports/BigKnn.html
diff --git a/docs/pare_reports/BrokenAdaptiveRidge.html b/docs/pare_reports/BrokenAdaptiveRidge.html
diff --git a/docs/pare_reports/Capr.html b/docs/pare_reports/Capr.html
diff --git a/docs/pare_reports/Characterization.html b/docs/pare_reports/Characterization.html
diff --git a/docs/pare_reports/CirceR.html b/docs/pare_reports/CirceR.html
diff --git a/docs/pare_reports/CohortDiagnostics.html b/docs/pare_reports/CohortDiagnostics.html
diff --git a/docs/pare_reports/CohortExplorer.html b/docs/pare_reports/CohortExplorer.html
diff --git a/docs/pare_reports/CohortGenerator.html b/docs/pare_reports/CohortGenerator.html
diff --git a/docs/pare_reports/CohortMethod.html b/docs/pare_reports/CohortMethod.html
diff --git a/docs/pare_reports/Cyclops.html b/docs/pare_reports/Cyclops.html
diff --git a/docs/pare_reports/DataQualityDashboard.html b/docs/pare_reports/DataQualityDashboard.html
diff --git a/docs/pare_reports/DatabaseConnector.html b/docs/pare_reports/DatabaseConnector.html
diff --git a/docs/pare_reports/EmpiricalCalibration.html b/docs/pare_reports/EmpiricalCalibration.html
diff --git a/docs/pare_reports/Eunomia.html b/docs/pare_reports/Eunomia.html
diff --git a/docs/pare_reports/EvidenceSynthesis.html b/docs/pare_reports/EvidenceSynthesis.html
diff --git a/docs/pare_reports/FeatureExtraction.html b/docs/pare_reports/FeatureExtraction.html
diff --git a/docs/pare_reports/Hydra.html b/docs/pare_reports/Hydra.html
diff --git a/docs/pare_reports/IterativeHardThresholding.html b/docs/pare_reports/IterativeHardThresholding.html
diff --git a/docs/pare_reports/MethodEvaluation.html b/docs/pare_reports/MethodEvaluation.html
diff --git a/docs/pare_reports/OhdsiSharing.html b/docs/pare_reports/OhdsiSharing.html
diff --git a/docs/pare_reports/OhdsiShinyModules.html b/docs/pare_reports/OhdsiShinyModules.html
diff --git a/docs/pare_reports/ParallelLogger.html b/docs/pare_reports/ParallelLogger.html
diff --git a/docs/pare_reports/PatientLevelPrediction.html b/docs/pare_reports/PatientLevelPrediction.html
diff --git a/docs/pare_reports/PheValuator.html b/docs/pare_reports/PheValuator.html
diff --git a/docs/pare_reports/PhenotypeLibrary.html b/docs/pare_reports/PhenotypeLibrary.html
diff --git a/docs/pare_reports/ROhdsiWebApi.html b/docs/pare_reports/ROhdsiWebApi.html
diff --git a/docs/pare_reports/ResultModelManager.html b/docs/pare_reports/ResultModelManager.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -416,6 +416,9 @@ @@
         <li>
           <a href="packageStatuses.html">Package Statuses</a>
         </li>
+        <li>
+          <a href="testServerUsage.html">Test server usage</a>
+        </li>
         <li>
           <a href="developmentRoadmap.html">Development Roadmap</a>
         </li>
@@ Expand Down @@