Merge pull request #212 from pepkit/dev

v0.12.5
pepkit · Dec 13, 2019 · 0b4f93b · 0b4f93b
2 parents 0af5ab5 + 3d2a3fa
commit 0b4f93b
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Showing 14 changed files with 414 additions and 283 deletions.
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -2,6 +2,11 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. 
 
+## [0.12.5] -- 2019-12-13
+### Changed
+- reduce verbosity of missing options; [Issue 174](https://github.com/pepkit/looper/issues/174)
+- switch to [Bootstrap Table](https://bootstrap-table.com/) in the summary index page table and sample status tables
+
 ## [0.12.4] -- 2019-07-18
 ### Added
 - Ability to declare `required_executables` in a `PipelineInterface`, to trigger a naive "runnability" check for a sample submission

diff --git a/looper/__init__.py b/looper/__init__.py
@@ -16,6 +16,7 @@
 from ._version import __version__
 from .parser_types import *
 
+from ubiquerg import VersionInHelpParser
 from divvy import DEFAULT_COMPUTE_RESOURCES_NAME, NEW_COMPUTE_KEY as COMPUTE_KEY
 # Not used here, but make this the main import interface between peppy and
 # looper, so that other modules within this package need not worry about
@@ -37,13 +38,6 @@
                        logging.INFO, logging.DEBUG]
 
 
-class _VersionInHelpParser(argparse.ArgumentParser):
-    def format_help(self):
-        """ Add version information to help text. """
-        return "version: {}\n".format(__version__) + \
-               super(_VersionInHelpParser, self).format_help()
-
-
 class _StoreBoolActionType(argparse.Action):
     """
     Enables the storage of a boolean const and custom type definition needed for systematic html interface generation.
@@ -55,7 +49,7 @@ def __init__(self, option_strings, dest, type, default, required=False, help=Non
             option_strings=option_strings,
             dest=dest,
             nargs=0,
-            const=not(default),
+            const=not default,
             default=default,
             type=type,
             required=required,
@@ -74,18 +68,10 @@ def build_parser():
 
     # Main looper program help text messages
     banner = "%(prog)s - Loop through samples and submit pipelines."
-    additional_description = "For subcommand-specific options, type: " \
-                             "'%(prog)s <subcommand> -h'"
+    additional_description = "For subcommand-specific options, type: '%(prog)s <subcommand> -h'"
     additional_description += "\nhttps://github.com/pepkit/looper"
 
-    parser = _VersionInHelpParser(
-            description=banner,
-            epilog=additional_description)
-
-    parser.add_argument(
-            "-V", "--version",
-            action="version",
-            version="%(prog)s {v}".format(v=__version__))
+    parser = VersionInHelpParser(description=banner, epilog=additional_description, version=__version__)
 
     # Logging control
     parser.add_argument(

diff --git a/looper/_version.py b/looper/_version.py
@@ -1 +1 @@
-__version__ = "0.12.4"
+__version__ = "0.12.5"
diff --git a/looper/html_reports.py b/looper/html_reports.py
@@ -211,7 +211,7 @@ def create_object_html(self, single_object, navbar, footer):
 
             # Set the PATH to the image/file. Catch any errors.
             # Check if the object is an HTML document
-            if not str(row['filename']).lower().endswith(IMAGE_EXTS):
+            if not str(row['anchor_image']).lower().endswith(IMAGE_EXTS):
                 image_path = page_path
             else:
                 try:
@@ -231,10 +231,12 @@ def create_object_html(self, single_object, navbar, footer):
             if os.path.isfile(image_path) and os.path.isfile(page_path):
                 image_relpath = os.path.relpath(image_path, self.reports_dir)
                 # If the object has a valid image, use it!
+                _LOGGER.debug("Checking image path: {}".format(image_path))
                 if str(image_path).lower().endswith(IMAGE_EXTS):
                     figures.append([page_relpath, str(row['sample_name']), image_relpath])
                 # Or if that "image" is not an image, treat it as a link
                 elif not str(image_path).lower().endswith(IMAGE_EXTS):
+                    _LOGGER.debug("Got link")
                     links.append([str(row['sample_name']), image_relpath])
             else:
                 warnings.append(str(row['filename']))

diff --git a/looper/jinja_templates/footer_index.html b/looper/jinja_templates/footer_index.html
@@ -1,82 +1,6 @@
-
-<!-- jQuery first, then Popper.js, then Bootstrap JS -->
 <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js" integrity="sha384-ZMP7rVo3mIykV+2+9J3UJ46jBk0WLaUAdn689aCwoqbBJiSnjAK/l8WvCWPIPm49" crossorigin="anonymous"></script>
-
-<!-- D3.js -->
-<script src="https://d3js.org/d3.v5.min.js"></script>
-<!-- Plotly -->
 <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
-
-<!-- DataTables JQuery extension -->
-<script src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>
-<script src="https://cdn.datatables.net/fixedcolumns/3.2.6/js/dataTables.fixedColumns.min.js"></script>
-<script src="https://cdn.datatables.net/responsive/2.2.3/js/dataTables.responsive.min.js"></script>
-
 <script type="text/javascript">
-
-    $.fn.dataTable.render.ellipsis = function ( cutoff, wordbreak, escapeHtml ) {
-        var esc = function ( t ) {
-            return t
-                .replace( /&/g, '&amp;' )
-                .replace( /</g, '&lt;' )
-                .replace( />/g, '&gt;' )
-                .replace( /"/g, '&quot;' );
-        };
-        function numberWithCommas(x) {
-            var parts = x.toString().split(".");
-            parts[0] = parts[0].replace(/\B(?=(\d{3})+(?!\d))/g, ",");
-            return parts.join(".");
-
-        }
-        return function ( d, type, row ) {
-            // Order, search and type get the original data
-            if ( type !== 'display' ) {
-                return d;
-            }
-            if ( typeof d !== 'number' && typeof d !== 'string' ) {
-                return d;
-            }
-            d = d.toString(); // cast numbers
-            if(!isNaN(d)){
-                return numberWithCommas(d);
-            }
-            if ( d.length < cutoff ) {
-                return d;
-            }
-            var shortened = d.substr(0, cutoff-1);
-            // Find the last white space character in the string
-            if ( wordbreak ) {
-                shortened = shortened.replace(/\s([^\s]*)$/, '');
-            }
-            // Protect against uncontrolled HTML input
-            if ( escapeHtml ) {
-                shortened = esc( shortened );
-            }
-            return shortened;
-        };
-    };
-
-    $(document).ready(function() {
-        $('#data-table').DataTable({
-            scrollX: true,
-            fixedColumns: {
-              leftColumns: 1
-            },
-            columnDefs: [
-              {
-                targets: 0,
-                render: $.fn.dataTable.render.ellipsis(1000, true, false)
-              },
-              {
-                targets: '_all',
-                render: $.fn.dataTable.render.ellipsis(17, true, true)
-              }
-            ],
-        });
-    } );
-
-    //var table = document.getElementById("data-table");
     var plotDict = {}; // variable containing column values (col_name:string -> col_values:list)
     var statsTable = {{ stats_json }}; // Jinja template variable
     // make a list of the first column values, which are the names of the samples
@@ -125,7 +49,7 @@
     }
     function displayPlottableColumns(){
         for(var col in plotDict){
-            $("#plot-cols").append("<li class='list-group-item'><a href='#' title='Click to visualize this column' onclick='graphCol(\"" + col + 
+            $("#plot-cols").append("<li class='list-group-item'><a href='#' title='Click to visualize this column' onclick='graphCol(\"" + col +
                 "\");return false;'>" + col+ "</a></li>");
         }
     }

diff --git a/looper/jinja_templates/head.html b/looper/jinja_templates/head.html
@@ -1,29 +1,11 @@
 <!-- Required meta tags -->
 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-
-<!-- Bootstrap CSS
-/*!
-* Bootswatch v4.1.1
-* Homepage: https://bootswatch.com
-* Copyright 2012-2018 Thomas Park
-* Licensed under MIT
-* Based on Bootstrap
-*//*!
-* Bootstrap v4.1.1 (https://getbootstrap.com/)
-* Copyright 2011-2018 The Bootstrap Authors
-* Copyright 2011-2018 Twitter, Inc.
-* Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
--->
-<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/jquery.dataTables.min.css">
+<link rel="stylesheet" type="text/css" href="https://netdna.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css">
 <link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous">
-<script src="http://code.jquery.com/jquery-latest.min.js" type="text/javascript"></script>
+<script src="https://code.jquery.com/jquery-3.3.1.js" type="text/javascript"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.6/umd/popper.min.js" integrity="sha384-wHAiFfRlMFy6i5SRaxvfOCifBUQy1xHdJ/yoi7FRNXMRBu5WHdZYu1hA6ZOblgut" crossorigin="anonymous"></script>
 <script src="https://netdna.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js"></script>
-<link rel="stylesheet" type="text/css" href="https://netdna.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css">
-<!-- DataTables JQuery extension -->
-<script src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>
-<script src="https://cdn.datatables.net/fixedcolumns/3.2.6/js/dataTables.fixedColumns.min.js"></script>
-<script src="https://cdn.datatables.net/responsive/2.2.3/js/dataTables.responsive.min.js"></script>
 <style type="text/css">
     p#footer {
         margin-left: 10px;
@@ -52,8 +34,13 @@
     .container {
         overflow: auto;
         padding-bottom: 40px;
+        padding-left: 25px;
         margin-top: 20px;
         min-height: 100%;
+        margin-left: 0px;
+        margin-right: 0px;
+        max-width: none;
+        min-width: none;
         /* must be same height as the footer */
     }
 
@@ -147,5 +134,4 @@
     div#navbar_links {
       display: flex;
     }
-
 </style>