Mckay/c2pro reports test

.github/workflows/integration_tests.yml

@@ -64,6 +64,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           repository: edilytics/CRISPResso2_tests
+          ref: 'mckay/c2pro-tests'
           # ref: '<BRANCH-NAME>' # update to specific branch
 
       - name: Run Basic

CRISPResso2/CRISPRessoReports/.gitattributes

@@ -0,0 +1,2 @@
+*.html text eol=lf
+*.md text eol=lf

CRISPResso2/CRISPRessoReports/CRISPRessoReport.py

@@ -10,27 +10,30 @@
 from CRISPResso2 import CRISPRessoShared
 
 if CRISPRessoShared.is_C2Pro_installed():
+    from CRISPRessoPro import __version__ as CRISPRessoProVersion
     import CRISPRessoPro
     C2PRO_INSTALLED = True
 else:
     C2PRO_INSTALLED = False
 
 
 def get_jinja_loader(root, logger):
-    UndefinedLogger = make_logging_undefined(logger=logger)
+    """
+    Get the Jinja2 environment for rendering templates.
+    """
+    undefined_logger = make_logging_undefined(logger=logger)
     if C2PRO_INSTALLED:
         return Environment(
             loader=ChoiceLoader([
                 FileSystemLoader(os.path.join(root, 'CRISPRessoReports', 'templates')),
                 FileSystemLoader(os.path.join(os.path.dirname(CRISPRessoPro.__file__), 'templates')),
             ]),
-            undefined=UndefinedLogger,
-        )
-    else:
-        return Environment(
-            loader=FileSystemLoader(os.path.join(root, 'CRISPRessoReports', 'templates')),
-            undefined=UndefinedLogger,
+            undefined=undefined_logger,
         )
+    return Environment(
+        loader=FileSystemLoader(os.path.join(root, 'CRISPRessoReports', 'templates')),
+        undefined=undefined_logger,
+    )
 
 
 def render_template(template_name, jinja2_env, **data):
@@ -67,20 +70,20 @@ def custom_partial_render(partial_template_name, **partial_data):
     )
 
 
-def make_report_from_folder(crispresso_report_file, crispresso_folder, _ROOT):
+def make_report_from_folder(crispresso_report_file, crispresso_folder, _root):
     """
     Makes an html report for a crispresso run
 
     Parameters:
     crispresso_report_file (string): name of the html file to create
     crispresso_folder (string): path to the crispresso output
-    _ROOT (string): path to crispresso executables (for templates)
+    _root (string): path to crispresso executables (for templates)
 
     Returns:
     Nothin
     """
     run_data = CRISPRessoShared.load_crispresso_info(crispresso_folder)
-    make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT)
+    make_report(run_data, crispresso_report_file, crispresso_folder, _root)
 
 
 def add_fig_if_exists(fig, fig_name, fig_root, fig_title, fig_caption, fig_data,
@@ -106,15 +109,15 @@ def add_fig_if_exists(fig, fig_name, fig_root, fig_title, fig_caption, fig_data,
             if os.path.exists(os.path.join(crispresso_folder, data_file)):
                 amplicon_figures['datas'][fig_name].append((data_caption, data_file))
         if os.path.exists(htmlfullpath):
-            with open(htmlfullpath, encoding="utf-8") as html:
+            with open(htmlfullpath, encoding='utf-8') as html:
                 html_string = "<div align='center'>"
                 html_string += html.read()
                 html_string += "</div>"
             amplicon_figures['htmls'][fig_name] = html_string
         elif os.path.exists(jsonfullpath) and C2PRO_INSTALLED:
             root_name = fig_root.replace('.', '_').replace('-', '_')
             d3_nuc_quilt_names.append(f"nuc_quilt_{root_name}")
-            with open(jsonfullpath) as fig_json_fh:
+            with open(jsonfullpath, encoding='utf-8') as fig_json_fh:
                 amplicon_figures['htmls'][fig_name] = f"""
                 <div class="d-flex justify-content-between" style="max-height: 80vh; overflow-y: auto;" id="{f"nuc_quilt_{root_name}"}"></div>
                 <script type="text/javascript">const {f"nuc_quilt_{root_name}"} = {fig_json_fh.read().strip()}</script>
@@ -177,10 +180,10 @@ def assemble_figs(run_data, crispresso_folder):
     return data
 
 
-def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, logger):
-    # dicts for each amplicon fig_names[amp_name] = [list of fig names]
-    #                        fig_locs[amp_name][fig_name] = figure location
-    #    print('crispresso_report file: ' + crispresso_report_file + ' crispresso_folder : ' + crispresso_folder + ' root: ' + _ROOT)
+def make_report(run_data, crispresso_report_file, crispresso_folder, _root, logger):
+    """
+    Writes an HMTL report for a CRISPResso run
+    """
     data = assemble_figs(run_data, crispresso_folder)
 
     report_display_name = ""
@@ -203,19 +206,22 @@ def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, logg
         'nuc_quilt_names': data['nuc_quilt_names'],
     }
 
-    j2_env = get_jinja_loader(_ROOT, logger)
+    j2_env = get_jinja_loader(_root, logger)
 
     #    dest_dir = os.path.dirname(crispresso_report_file)
-    #    shutil.copy2(os.path.join(_ROOT,'templates','CRISPResso_justcup.png'),dest_dir)
-    #    shutil.copy2(os.path.join(_ROOT,'templates','favicon.ico'),dest_dir)
+    #    shutil.copy2(os.path.join(_root,'templates','CRISPResso_justcup.png'),dest_dir)
+    #    shutil.copy2(os.path.join(_root,'templates','favicon.ico'),dest_dir)
 
     with open(crispresso_report_file, 'w', encoding="utf-8") as outfile:
         outfile.write(render_template(
             'report.html', j2_env, report_data=report_data, C2PRO_INSTALLED=C2PRO_INSTALLED,
         ))
 
 
-def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, batch_folder, _ROOT, logger):
+def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, batch_folder, _root, logger):
+    """
+    Makes a report for a CRIPSRessoBatch run
+    """
     batch_names = crispresso2_info['results']['completed_batch_arr']
     failed_runs = crispresso2_info['results']['failed_batch_arr']
     failed_runs_desc = crispresso2_info['results']['failed_batch_arr_desc']
@@ -305,7 +311,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info,
     summary_plot_htmls = {}
     for plot_name in window_nuc_pct_quilts + nuc_pct_quilts:
         if os.path.exists(os.path.join(batch_folder, f'{plot_name}.json')):
-            with open(os.path.join(batch_folder, f'{plot_name}.json')) as window_nuc_pct_json_fh:
+            with open(os.path.join(batch_folder, f'{plot_name}.json'), encoding='utf-8') as window_nuc_pct_json_fh:
                 summary_plot_htmls[plot_name] = f"""
             <div class="d-flex justify-content-between" style="max-height: 80vh; overflow-y: auto;" id="{plot_name}"></div>
             <script type="text/javascript">const {plot_name} = {window_nuc_pct_json_fh.read().strip()}</script>
@@ -346,7 +352,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info,
         sub_html_files,
         crispressoBatch_report_file,
         batch_folder,
-        _ROOT,
+        _root,
         output_title,
         'batch',
         logger,
@@ -366,41 +372,50 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info,
     )
 
 
-def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT, logger):
+def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, folder, _root, logger):
+    """
+    Makes a report for a CRISPRessoPooled run
+    """
     names_arr = crispresso2_info['results']['good_region_names']
     output_title = 'CRISPResso Pooled Output'
     if crispresso2_info['running_info']['args'].name != '':
         output_title += f"<br/>{crispresso2_info['running_info']['args'].name}"
-    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'pooled', logger)
+    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _root, 'pooled', logger)
 
 
-def make_compare_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT, logger):
+def make_compare_report_from_folder(crispresso_report_file, crispresso2_info, folder, _root, logger):
+    """
+    Makes a report for a CRISPRessoCompare run
+    """
     names_arr = []
     output_title = 'CRISPResso Compare Output'
     if crispresso2_info['running_info']['args'].name != '':
         output_title += "<br/>{crispresso2_info['running_info']['args'].name}"
-    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'compare', logger)
+    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _root, 'compare', logger)
 
 
-def make_meta_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT, logger):
+def make_meta_report_from_folder(crispresso_report_file, crispresso2_info, folder, _root, logger):
     names_arr = crispresso2_info['meta_names_arr']
     input_names = crispresso2_info['meta_input_names']
     output_title = 'CRISPresso Meta Output'
     if crispresso2_info['running_info']['args'].name != '':
         output_title += "<br/>{crispresso2_info['running_info']['args'].name}"
-    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'meta', logger,
+    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _root, 'meta', logger,
                                   display_names=input_names)
 
 
-def make_wgs_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT, logger):
+def make_wgs_report_from_folder(crispresso_report_file, crispresso2_info, folder, _root, logger):
+    """
+    Makes a report for a CRISPRessoWGS run
+    """
     names_arr = crispresso2_info['results']['good_region_names']
     output_title = 'CRISPResso WGS Output'
     if crispresso2_info['running_info']['args'].name != '':
         output_title += "<br/>{crispresso2_info['running_info']['args'].name}"
-    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'wgs', logger)
+    make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _root, 'wgs', logger)
 
 
-def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, crispresso_report_file, folder, _ROOT, crispresso_tool, logger,
+def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, crispresso_report_file, folder, _root, crispresso_tool, logger,
                                   display_names=None):
     """
     Prepares information to make a report of multiple CRISPResso runs - like CRISPRessoWGS or CRISPRessoPooled
@@ -411,7 +426,7 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris
     report_name (string): text to be shown at top of report
     crispresso_report_file (string): path to write report to
     folder (string): folder containing crispresso runs
-    _ROOT (string): location of crispresso assets (images, templates, etc)
+    _root (string): location of crispresso assets (images, templates, etc)
     logger (logging.Logger): logger to log messages to, mainly for undefined variables in Jinja2 templates
     display_names (dict): report_name->display_name; Titles to be shown for crispresso runs
         (if different from names_arr, e.g. if display_names have spaces or bad chars, they won't be the same as names_arr)
@@ -483,7 +498,7 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris
         sub_html_files,
         crispresso_report_file,
         folder,
-        _ROOT,
+        _root,
         report_name,
         crispresso_tool,
         logger,
@@ -503,7 +518,7 @@ def make_multi_report(
     sub_html_files,
     crispresso_multi_report_file,
     crispresso_folder,
-    _ROOT,
+    _root,
     report_name,
     crispresso_tool,
     logger,
@@ -525,7 +540,7 @@ def make_multi_report(
     crispresso_multi_report_file (string): path of file to write to
     report_name (string): description of report type to be shown at top of report
     crispresso_folder (string): absolute path to the crispresso output
-    _ROOT (string): absolute path to the crispresso executable
+    _root (string): absolute path to the crispresso executable
     summary_plots (dict): a dict with the following keys:
         names (list): list of plot names - keys for following dicts
         titles (dict): dict of plot_name->plot_title
@@ -547,7 +562,7 @@ def fill_default(dictionary, key, default_type=list):
         if key not in dictionary:
             dictionary[key] = default_type()
 
-    j2_env = get_jinja_loader(_ROOT, logger)
+    j2_env = get_jinja_loader(_root, logger)
 
     j2_env.filters['dirname'] = dirname
     if crispresso_tool == 'batch':
@@ -643,7 +658,7 @@ def make_aggregate_report(
     report_name,
     crispresso_report_file,
     crispresso_report_folder,
-    _ROOT,
+    _root,
     folder_arr,
     crispresso_html_reports,
     logger,
@@ -658,7 +673,7 @@ def make_aggregate_report(
     report_name (string): text to be shown at top of report
     crispresso_report_file (string): path to write report to
     crispresso_report_folder (string): path containing aggregated plots, etc.
-    _ROOT (string): location of crispresso assets (images, templates, etc)
+    _root (string): location of crispresso assets (images, templates, etc)
     folder_arr (arr of strings): paths to the aggregated crispresso folders
     crispresso_html_reports (dict): folder->html_path; Paths to the aggregated crispresso run html reports
     logger (logging.Logger): logger to log messages
@@ -778,7 +793,7 @@ def make_aggregate_report(
         sub_html_files,
         crispresso_report_file,
         crispresso_report_folder,
-        _ROOT,
+        _root,
         report_name,
         'aggregate',
         logger,

CRISPResso2/CRISPRessoReports/README.md

@@ -6,7 +6,7 @@ Take care when committing into these files as not to mix unrelated git histories
 
 ## How do I work with this repo?
 
-Step 1 only needs to be done once per cloned repo, the other steps will need to be dne more frequently.
+Step 1 only needs to be done once per cloned repo, the other steps will need to be done more frequently.
 
 1. Add the remote to this repo to the "parent" repo (i.e. `CRISPResso2` or `C2Web`). **You should only have to do this once.**
 
@@ -131,7 +131,7 @@ If a feature that you are working on requires changes to CRISPRessoReports, you
 1. Create a feature branch in the parent repo, based on the parent repo master.
 
 ``` shell
-git checkout -b <feature-branch>
+git checkout -b <feature-branch> origin/master
 ```
 
 2. Create a feature branch on `CRISPRessoReports`.

CRISPResso2/CRISPRessoReports/jinja_partials.py

@@ -30,6 +30,9 @@
 
 
 def render_partial(template_name, renderer=None, markup=True, **data):
+    """
+    Renders a partial template and returns the result. If `markup` is True, the result is wrapped in a `Markup` object.
+    """
     if renderer is None:
         if flask is None:
             raise PartialsException('No renderer specified')
@@ -43,4 +46,7 @@ def render_partial(template_name, renderer=None, markup=True, **data):
 
 
 def generate_render_partial(renderer, markup=True):
+    """
+    Returns a partial function that renders a template using the specified renderer.
+    """
     return partial(render_partial, renderer=renderer, markup=markup)