Merge branch 'ui-v2' of github.com:IGS/gEAR into ui-v2

IGS · Dec 5, 2023 · 04688d9 · 04688d9
2 parents e56f7aa + 8e1136d
commit 04688d9
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diff --git a/docs/setup.new_server.notes.md b/docs/setup.new_server.notes.md
@@ -4,14 +4,18 @@
 
 Instances of a gEAR Portal are most often run within a cloud instance, where you can choose your own operating system and resources.  On Google Cloud for a starter instance I chose an e2-standard-2 (2 vCPUs and 48GB RAM) with 300GB of solid state disk space.  You'll definitely want to increase the CPU as you gain more simultaneous users and RAM depending on your dataset sizes.  Once you create and start the instance:
 
-    $ sudo apt update
-    $ sudo apt upgrade
+```bash
+    sudo apt update
+    sudo apt upgrade
+```
 
 Reboot if there are kernel updates (or just to be safe if you don't know.)
 
-    $ cd && mkdir git
-    $ sudo apt install git
-    $ git clone https://github.com/jorvis/gEAR.git
+```bash
+    cd && mkdir git
+    sudo apt install git
+    git clone https://github.com/jorvis/gEAR.git
+```
 
 ### Updating Ubuntu version to 22.04 LTS
 
@@ -33,7 +37,7 @@ At this point, we could remove the Python2 packages using `sudo apt autoremove`.
 
 ### MYSQL
 
-    $ sudo apt install mysql-server
+    sudo apt install mysql-server
 
 Follow instructions in our setup.mysql.md document
 
@@ -57,17 +61,17 @@ Follow instructions in setup.python.md document
 
 ### APACHE
 
-    $ sudo apt install apache2 apache2-dev
+    sudo apt install apache2 apache2-dev
 
 Follow instructions in setup.apache.md document
 
 ### gEAR portal
 
 ```bash
-$ cd ~/git
-$ git clone https://github.com/jorvis/gEAR.git
-$ cd /var
-$ sudo rm -rf www && sudo ln -s ~/git/gEAR/www
+cd ~/git
+git clone https://github.com/jorvis/gEAR.git
+cd /var
+sudo rm -rf www && sudo ln -s ~/git/gEAR/www
 ```
 
 ### Data transfer
@@ -83,6 +87,13 @@ $HOME/git/gEAR/www/analyses
 Permissions need to be writeable for your apache user.
 
 ```bash
-$ cd /var/www
-$ chmod 777 datasets analyses/* uploads/files/
+cd /var/www
+chmod 777 datasets analyses/* uploads/files/
 ```
+
+### (For devel servers) Github Actions self-hosted runner
+
+The idea here is that when commiting code, we can use Github Actions to pull the code down on to the server to do things like automated testing.
+
+(to be continued in https://github.com/IGS/gEAR/issues/632)
+
diff --git a/tests/README.md b/tests/README.md
@@ -18,7 +18,9 @@ None yet listed
 
 * Deleting an account
 
-## UI testing
+## UI (acceptance) testing
+
+NOTE: This will be outdated as soon as the new tests are written in `<root>/www/js/test`
 
 We use Selenium for this and these steps can take a while. Automated UI testing isn't necessarily quick, and there are a lot of pages/features to check.
 

diff --git a/www/cgi/search_gene_carts.cgi b/www/cgi/search_gene_carts.cgi
@@ -86,58 +86,58 @@ def main():
             wheres.append("AND (gc.is_public = 1 OR gc.user_id = %s)")
             qry_params.extend([user.id])
 
-        if search_terms:
-            selects.append(' MATCH(gc.label, gc.ldesc) AGAINST("%s" IN BOOLEAN MODE) as rscore')
-            wheres.append(' AND MATCH(gc.label, gc.ldesc) AGAINST("%s" IN BOOLEAN MODE)')
-
-            # this is the only instance where a placeholder can be in the SELECT statement, so it will
-            #  be the first qry param
-            qry_params.insert(0, ' '.join(search_terms))
-            qry_params.append(' '.join(search_terms))
-
-        if organism_ids:
-            ## only numeric characters and the comma are allowed here
-            organism_ids = re.sub("[^,0-9]", "", organism_ids)
-            wheres.append("AND gc.organism_id in ({0})".format(organism_ids))
-
-        if date_added:
-            date_added = re.sub("[^a-z]", "", date_added)
-            wheres.append("AND gc.date_added BETWEEN date_sub(now(), INTERVAL 1 {0}) AND now()".format(date_added))
-
-        if sort_by == 'relevance':
-            # relevance can only be ordered if a search term was used
-            if search_terms:
-                orders_by.append(" rscore DESC")
-            else:
-                orders_by.append(" gc.date_added DESC")
-        elif sort_by == 'title':
-            orders_by.append(" gc.label")
-        elif sort_by == 'owner':
-            orders_by.append(" g.user_name")
-        else:
-            orders_by.append(" gc.date_added DESC")
+    if search_terms:
+        selects.append(' MATCH(gc.label, gc.ldesc) AGAINST("%s" IN BOOLEAN MODE) as rscore')
+        wheres.append(' AND MATCH(gc.label, gc.ldesc) AGAINST("%s" IN BOOLEAN MODE)')
 
-        # build query
-        qry = """
-        SELECT {0}
-        FROM {1}
-        WHERE {2}
-        ORDER BY {3}
-        """.format(
-            ", ".join(selects),
-            ", ".join(froms),
-            " ".join(wheres),
-            " ".join(orders_by)
-        )
+        # this is the only instance where a placeholder can be in the SELECT statement, so it will
+        #  be the first qry param
+        qry_params.insert(0, ' '.join(search_terms))
+        qry_params.append(' '.join(search_terms))
+
+    if organism_ids:
+        ## only numeric characters and the comma are allowed here
+        organism_ids = re.sub("[^,0-9]", "", organism_ids)
+        wheres.append("AND gc.organism_id in ({0})".format(organism_ids))
 
-        # if a limit is defined, add it to the query
-        if int(limit):
-            qry += " LIMIT {0}".format(limit)
+    if date_added:
+        date_added = re.sub("[^a-z]", "", date_added)
+        wheres.append("AND gc.date_added BETWEEN date_sub(now(), INTERVAL 1 {0}) AND now()".format(date_added))
 
-        # if a page is defined, add it to the query
-        if int(page):
-            offset = int(page) - 1
-            qry += " OFFSET {0}".format(offset * int(limit))
+    if sort_by == 'relevance':
+        # relevance can only be ordered if a search term was used
+        if search_terms:
+            orders_by.append(" rscore DESC")
+        else:
+            orders_by.append(" gc.date_added DESC")
+    elif sort_by == 'title':
+        orders_by.append(" gc.label")
+    elif sort_by == 'owner':
+        orders_by.append(" g.user_name")
+    else:
+        orders_by.append(" gc.date_added DESC")
+
+    # build query
+    qry = """
+    SELECT {0}
+    FROM {1}
+    WHERE {2}
+    ORDER BY {3}
+    """.format(
+        ", ".join(selects),
+        ", ".join(froms),
+        " ".join(wheres),
+        " ".join(orders_by)
+    )
+
+    # if a limit is defined, add it to the query
+    if int(limit):
+        qry += " LIMIT {0}".format(limit)
+
+    # if a page is defined, add it to the query
+    if int(page):
+        offset = int(page) - 1
+        qry += " OFFSET {0}".format(offset * int(limit))
 
     if DEBUG_MODE:
         ofh = open('/tmp/debug', 'wt')
@@ -153,7 +153,7 @@ def main():
         gc.user_name = row[1]
         gc.gene_count = len(gc.genes)
         gc.organism = "{0} {1}".format(row[8], row[9])
-        gc.is_owner = True if gc.user_id == user.id else False
+        gc.is_owner = True if user and gc.user_id == user.id else False
         gene_carts.append(gc)
 
     # Get count of total results

diff --git a/www/dataset_curator.html b/www/dataset_curator.html
@@ -391,6 +391,9 @@ <h4 class="title is-5 is-clickable js-collapsable-trigger">
     </section>
   </div>
 
+    <!--#include virtual="/include/curator_common.html" -->
+
+
   <!-- fancy select elements -->
   <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/nice-select2.min.js"></script>