Add documentation page

src/components/Navbar.vue

@@ -6,6 +6,7 @@ const items = ref([
   { href: { name: "search" }, text: "Search" },
   { href: { name: "composition" }, text: "Species composition" },
   { href: { name: "statistics" }, text: "Repository statistics" },
+  { href: { name: "docs" }, text: "Documentation" },
   { href: { name: "about" }, text: "About" },
 ]);
 </script>

src/router/index.ts

@@ -55,6 +55,11 @@ const router = createRouter({
       name: "statistics",
       component: () => import("../views/statistics/StatisticsView.vue"),
     },
+    {
+      path: "/docs",
+      name: "docs",
+      component: () => import("../views/documentation/DocumentationMain.vue"),
+    },
   ],
 });
 

src/views/documentation/DocumentationMain.vue

@@ -0,0 +1,109 @@
+<template>
+  <div class="container">
+    <h1>BakRep documentation</h1>
+
+    <article>
+      <h2>Searching for datasets</h2>
+
+      <p>
+        You can search for datasets of your interest on the search page. First
+        you will define your search query via the query builder on top of the
+        page. Then you click on "Search" to find all datasets that match your
+        query.
+      </p>
+
+      <h3>Build a search query</h3>
+      <p>
+        The query builder consists of three parts: The query type selector, the
+        query-element selector and the query-element configuration area.
+      </p>
+      <p>
+        Each group of criteria has a type. Either all criteria must match
+        (logical and) or at least one criterion must match (logical or). Select
+        the type on the top of each criteria group. You can change the type at
+        any time.
+      </p>
+      <p>
+        BakRep provides a set of criteria for searching the repository. To add
+        them select your criterion of interest in the query-element selector and
+        add click on add field. A new entry will be added to the configuration
+        area. At the moment BakRep has four different criteria types:
+        number-fields, text-fields, nested fields and groups.
+      </p>
+      <p>
+        With groups you can nest up to three levels of grouped criteria. Each
+        group has its type and a list of criteria. Example: You want find all
+        datasets for a species with less than 10 contigs and all datasets for
+        another species with 10-20 contigs. This can be mapped to "At least one
+        must match"-type on the toplevel group, with two groups having "All must
+        match"-type and the properly configured species and contigs criteria.
+      </p>
+      <p>
+        Number-fields require a comparison operator and a reference number.
+        BakRep supports the equals (==), not equals (!=), less (&lt;), less or
+        equal (&lt;=), greater (>), greater or equal(>=) and between ([])
+        operations. The between operation requires two reference numbers: The
+        lower- and upper-limits.
+      </p>
+      <p>
+        Similar to Number-fields, String-fields require a comparison operator
+        and a text. BakRep supports exact text match (eq), exclude exact text
+        match (neq), exact word match(~) and exclude exact word match (!~). For
+        some criteria suggestions from the database will be presented when you
+        type.
+      </p>
+      <p>
+        The only nested field are the annotated features. They have a work
+        similar to the groups, but provide criteria that are only available for
+        the nested field.
+      </p>
+      <p>
+        When you compiled your query click on search and after a few moments the
+        results should appear below the query builder. You can refine your query
+        at any moment and click on search again to obtain the new results.
+      </p>
+
+      <h3>Use the results table</h3>
+      <p>
+        The search results are presented in the result table. On top it shows
+        the total number of datasets that match your query. By default it only
+        shows the first 20 elements. Below the table you can switch to other
+        pages of your results. You can visit a detailed page for each dataset
+        via the link in the id column.
+      </p>
+      <p>
+        The table header has symbols with arrows next to header labels. These
+        indicate the sorting. An up and a down-arrow indicate that the column is
+        not used for sorting. An up arrow indicates ascending sort direction
+        whereas a down arrow indicates descending sort direction. To switch
+        between the sorting modes for a column click on the array symbol.
+      </p>
+      <p>
+        It is also possible to sort by multiple columns. The last modified
+        column will become the first sort criterion and the previously changed
+        sort columns become the secondary, tertiary etc. sort criteria. Example:
+        To sort descending by species and for each species ascending by contig
+        count, change the contigs column to ascending first and the species
+        column to descending.
+      </p>
+      <h3>Export the table as a tsv file</h3>
+      <p>
+        You can download the results table as a tsv file that will include the
+        visible columns and additional columns available in the repository. The
+        download will take a moment. An indicator will show the progress. Do not
+        close or switch the page until the download is completed and the file is
+        saved.
+      </p>
+      <p>
+        The resulting tsv file can be used to download the complete datasets to
+        your computer with the BakRep-Download Tool. See:
+        <a
+          href="https://github.com/ag-computational-bio/bakrep-cli"
+          target="_blank"
+        >
+          https://github.com/ag-computational-bio/bakrep-cli
+        </a>
+      </p>
+    </article>
+  </div>
+</template>