Merge pull request #376 from bioinfo-chru-strasbourg/improve_perf

fix strict param, add interactive mode #362, add docs #4
bioinfo-chru-strasbourg · Jan 23, 2025 · 2112a4f · 2112a4f
2 parents b5476d3 + 49c5a2f
commit 2112a4f
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Showing 21 changed files with 18,327 additions and 18,386 deletions.
diff --git a/README.pdf b/README.pdf
diff --git a/RELEASE_NOTES.pdf b/RELEASE_NOTES.pdf
diff --git a/docs/docs.pdf b/docs/docs.pdf
diff --git a/docs/help.configuration.calculation.pdf b/docs/help.configuration.calculation.pdf
diff --git a/docs/help.configuration.pdf b/docs/help.configuration.pdf
diff --git a/docs/help.configuration.prioritization.pdf b/docs/help.configuration.prioritization.pdf
diff --git a/docs/help.html b/docs/help.html
@@ -532,6 +532,14 @@ <h2 data-number="2.3" id="query"><span
 Either None (native), &#39;markdown&#39;, &#39;tabulate&#39; or disabled.</code></pre>
 </blockquote>
 <p></small></p>
+<p><small></p>
+<blockquote>
+<pre><code>    --interactive_mode=&lt;interactive mode&gt; [&#39;table&#39;, &#39;view&#39;] (default: table)
+
+Iteractive mode for variants view.
+Either &#39;table&#39; for loading data and speed up queries, or &#39;view&#39; for dynamic queries (slower).</code></pre>
+</blockquote>
+<p></small></p>
 <h2 data-number="2.4" id="export"><span
 class="header-section-number">2.4</span> Export</h2>
 <p><small></p>

diff --git a/docs/help.md b/docs/help.md
@@ -283,6 +283,15 @@ Usage examples:
 
 </small>
 
+<small>
+
+>     --interactive_mode=<interactive mode> ['table', 'view'] (default: table)
+>
+>     Iteractive mode for variants view.
+>     Either 'table' for loading data and speed up queries, or 'view' for dynamic queries (slower).
+
+</small>
+
 ## Export
 
 <small>

diff --git a/docs/help.parameters.databases.pdf b/docs/help.parameters.databases.pdf
diff --git a/docs/help.parameters.pdf b/docs/help.parameters.pdf
diff --git a/docs/help.pdf b/docs/help.pdf
diff --git a/docs/pdoc/howard/objects/variants.html b/docs/pdoc/howard/objects/variants.html
diff --git a/docs/pdoc/howard/tools/interactive.html b/docs/pdoc/howard/tools/interactive.html
diff --git a/docs/pdoc/howard/tools/tools.html b/docs/pdoc/howard/tools/tools.html
diff --git a/docs/pdoc/search.js b/docs/pdoc/search.js
diff --git a/docs/tips.pdf b/docs/tips.pdf
diff --git a/docs/user_guide.pdf b/docs/user_guide.pdf
diff --git a/howard/objects/variants.py b/howard/objects/variants.py
diff --git a/howard/tools/interactive.py b/howard/tools/interactive.py
@@ -37,7 +37,10 @@ def launch_interactive_terminal(
     conn = variants.get_connexion()
 
     # Query limit
-    query_limit = 1000
+    if "query_limit" in args and args.query_limit is not None:
+        query_limit = args.query_limit
+    else:
+        query_limit = 1000
 
     try:
         # Execute query to test connexion
@@ -58,9 +61,19 @@ def launch_interactive_terminal(
         log.debug("View 'header' can not be loaded")
 
     # Variants table param
+    if "interactive_mode" in args and args.interactive_mode is not None:
+        interactive_mode = args.interactive_mode
+    else:
+        interactive_mode = "table"
+    log.debug(f"Interactive mode set to '{interactive_mode}'")
+
     view_name = "variants_view"
-    view_type = "table"
-    view_mode = "full"
+    if interactive_mode == "view":
+        view_type = "view"
+        view_mode = "explore"
+    elif interactive_mode == "table":
+        view_type = "table"
+        view_mode = "full"
 
     # Create variants table
     log.debug(f"Loading table '{view_name}' as '{view_type}' (mode '{view_mode}')")
@@ -77,8 +90,10 @@ def launch_interactive_terminal(
             detect_type_list=True,
             drop_view=True,
         )
-    except:
+    except Exception as e:
         log.warning(f"View '{view_name}' can not be created")
+        log.warning(f"Error: {e}")
+        log.warning("Please check variants annotations formats")
 
     # Print welcome message
     log.info("Interactive DuckDB SQL terminal")
@@ -506,7 +521,7 @@ def print_prompt(line: int = 0) -> str:
                 rows_plus = result.fetchmany(1)
 
                 if rows_plus or (query_limited_check and len(rows) == query_limit):
-                    msg_query_limit = f"Only {query_limit} lines shown (use 'limit' command to change)"
+                    msg_query_limit = f"Only {query_limit} first lines shown (use 'limit' command to change)"
                 else:
                     msg_query_limit = None
                 # Get column names

diff --git a/howard/tools/tools.py b/howard/tools/tools.py
@@ -1788,6 +1788,22 @@ def __call__(self, string):
         "action": "store_true",
         "default": False,
     },
+    "interactive_mode": {
+        "metavar": "interactive mode",
+        "help": """Iteractive mode for variants view.\n"""
+        """Either 'table' for loading data and speed up queries"""
+        """, or 'view' for dynamic queries (slower).\n""",
+        "default": "table",
+        "type": str,
+        "choices": ["table", "view"],
+        "gooey": {"widget": "Dropdown", "options": {}},
+        "extra": {
+            "examples": {
+                "Table mode": '"interactive_mode": "table"',
+                "View mode": '"interactive_mode": "view"',
+            }
+        },
+    },
     # Verbosity
     "quiet": {"help": argparse.SUPPRESS, "action": "store_true", "default": False},
     "verbose": {"help": argparse.SUPPRESS, "action": "store_true", "default": False},
@@ -1832,7 +1848,11 @@ def __call__(self, string):
                 "explode_infos_prefix": False,
                 "explode_infos_fields": False,
             },
-            "Query": {"query_limit": False, "query_print_mode": False},
+            "Query": {
+                "query_limit": False,
+                "query_print_mode": False,
+                "interactive_mode": False,
+            },
             "Export": {"include_header": False, "parquet_partitions": False},
         },
     },

diff --git a/plugins/README.pdf b/plugins/README.pdf