Analysis refactor misc (#2161)

* Fixing race condition

* Removing unused code and fixing typo

* Hiding job step if success

* Showing loading gif and fixing typo

Author: josenavas

qiita_pet/handlers/analysis_handlers/base_handlers.py

@@ -21,7 +21,6 @@
 
 class CreateAnalysisHandler(BaseHandler):
     @authenticated
-    @execute_as_transaction
     def post(self):
         name = self.get_argument('name')
         desc = self.get_argument('description')

qiita_pet/handlers/api_proxy/__init__.py

@@ -30,9 +30,8 @@
     study_tags_request)
 from .artifact import (artifact_graph_get_req, artifact_types_get_req,
                        artifact_post_req, artifact_get_req,
-                       artifact_status_put_req,
-                       artifact_summary_get_request, artifact_get_prep_req,
-                       artifact_summary_post_request, artifact_patch_request)
+                       artifact_status_put_req, artifact_get_prep_req,
+                       artifact_patch_request)
 from .ontology import ontology_patch_handler
 from .processing import (
     list_commands_handler_get_req, process_artifact_handler_get_req,
@@ -62,7 +61,6 @@
            'study_tags_request', 'study_tags_patch_request',
            'study_get_tags_request',
            'prep_template_patch_req', 'ontology_patch_handler',
-           'artifact_summary_get_request', 'artifact_summary_post_request',
            'list_commands_handler_get_req', 'process_artifact_handler_get_req',
            'list_options_handler_get_req', 'workflow_handler_post_req',
            'workflow_handler_patch_req', 'workflow_run_post_req',

qiita_pet/handlers/api_proxy/artifact.py

@@ -5,7 +5,7 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-from os.path import join, basename
+from os.path import join
 from functools import partial
 from json import dumps
 
@@ -28,194 +28,6 @@
 PREP_TEMPLATE_KEY_FORMAT = 'prep_template_%s'
 
 
-def artifact_summary_get_request(user_id, artifact_id):
-    """Returns the information for the artifact summary page
-
-    Parameters
-    ----------
-    user_id : str
-        The user making the request
-    artifact_id : int or str
-        The artifact id
-
-    Returns
-    -------
-    dict of objects
-        A dictionary containing the artifact summary information
-        {'status': str,
-         'message': str,
-         'name': str,
-         'summary': str,
-         'job': list of [str, str, str]}
-    """
-    artifact_id = int(artifact_id)
-    artifact = Artifact(artifact_id)
-
-    access_error = check_access(artifact.study.id, user_id)
-    if access_error:
-        return access_error
-
-    user = User(user_id)
-    visibility = artifact.visibility
-    summary = artifact.html_summary_fp
-    job_info = None
-    errored_jobs = []
-    processing_jobs = []
-    for j in artifact.jobs():
-        if j.command.software.type == "artifact transformation":
-            status = j.status
-            if status == 'success':
-                continue
-            j_msg = j.log.msg if status == 'error' else None
-            processing_jobs.append(
-                [j.id, j.command.name, j.status, j.step, j_msg])
-
-    # Check if the HTML summary exists
-    if summary:
-        with open(summary[1]) as f:
-            summary = f.read()
-    else:
-        # Check if the summary is being generated
-        command = Command.get_html_generator(artifact.artifact_type)
-        all_jobs = set(artifact.jobs(cmd=command))
-        jobs = [j for j in all_jobs if j.status in ['queued', 'running']]
-        errored_jobs = [(j.id, j.log.msg)
-                        for j in all_jobs if j.status in ['error']]
-        if jobs:
-            # There is already a job generating the HTML. Also, there should be
-            # at most one job, because we are not allowing here to start more
-            # than one
-            job = jobs[0]
-            job_info = [job.id, job.status, job.step]
-
-    buttons = []
-    btn_base = (
-        '<button onclick="if (confirm(\'Are you sure you want to %s '
-        'artifact id: {0}?\')) {{ set_artifact_visibility(\'%s\', {0}) }}" '
-        'class="btn btn-primary btn-sm">%s</button>').format(artifact_id)
-
-    if qiita_config.require_approval:
-        if visibility == 'sandbox':
-            # The request approval button only appears if the artifact is
-            # sandboxed and the qiita_config specifies that the approval should
-            # be requested
-            buttons.append(
-                btn_base % ('request approval for', 'awaiting_approval',
-                            'Request approval'))
-
-        elif user.level == 'admin' and visibility == 'awaiting_approval':
-            # The approve artifact button only appears if the user is an admin
-            # the artifact is waiting to be approvaed and the qiita config
-            # requires artifact approval
-            buttons.append(btn_base % ('approve', 'private',
-                                       'Approve artifact'))
-
-    if visibility == 'private':
-        # The make public button only appears if the artifact is private
-        buttons.append(btn_base % ('make public', 'public', 'Make public'))
-
-    # The revert to sandbox button only appears if the artifact is not
-    # sandboxed nor public
-    if visibility not in {'sandbox', 'public'}:
-        buttons.append(btn_base % ('revert to sandbox', 'sandbox',
-                                   'Revert to sandbox'))
-
-    if user.level == 'admin':
-        if artifact.can_be_submitted_to_ebi:
-            if not artifact.is_submitted_to_ebi:
-                buttons.append(
-                    '<a class="btn btn-primary btn-sm" '
-                    'href="/ebi_submission/%d">'
-                    '<span class="glyphicon glyphicon-export"></span>'
-                    ' Submit to EBI</a>' % artifact_id)
-        if artifact.can_be_submitted_to_vamps:
-            if not artifact.is_submitted_to_vamps:
-                buttons.append(
-                    '<a class="btn btn-primary btn-sm" href="/vamps/%d">'
-                    '<span class="glyphicon glyphicon-export"></span>'
-                    ' Submit to VAMPS</a>' % artifact_id)
-
-    files = [(f_id, "%s (%s)" % (basename(fp), f_type.replace('_', ' ')))
-             for f_id, fp, f_type in artifact.filepaths
-             if f_type != 'directory']
-
-    # TODO: https://github.com/biocore/qiita/issues/1724 Remove this hardcoded
-    # values to actually get the information from the database once it stores
-    # the information
-    if artifact.artifact_type in ['SFF', 'FASTQ', 'FASTA', 'FASTA_Sanger',
-                                  'per_sample_FASTQ']:
-        # If the artifact is one of the "raw" types, only the owner of the
-        # study and users that has been shared with can see the files
-        if not artifact.study.has_access(user, no_public=True):
-            files = []
-
-    processing_parameters = (artifact.processing_parameters.values
-                             if artifact.processing_parameters is not None
-                             else {})
-
-    return {'status': 'success',
-            'message': '',
-            'name': artifact.name,
-            'summary': summary,
-            'job': job_info,
-            'errored_jobs': errored_jobs,
-            'processing_jobs': processing_jobs,
-            'visibility': visibility,
-            'buttons': ' '.join(buttons),
-            'files': files,
-            'editable': artifact.study.can_edit(user),
-            'study_id': artifact.study.id,
-            'prep_id': artifact.prep_templates[0].id,
-            'processing_parameters': processing_parameters}
-
-
-def artifact_summary_post_request(user_id, artifact_id):
-    """Launches the HTML summary generation and returns the job information
-
-    Parameters
-    ----------
-    user_id : str
-        The user making the request
-    artifact_id : int or str
-        The artifact id
-
-    Returns
-    -------
-    dict of objects
-        A dictionary containing the artifact summary information
-        {'status': str,
-         'message': str,
-         'job': list of [str, str, str]}
-    """
-    artifact_id = int(artifact_id)
-    artifact = Artifact(artifact_id)
-
-    access_error = check_access(artifact.study.id, user_id)
-    if access_error:
-        return access_error
-
-    # Check if the summary is being generated or has been already generated
-    command = Command.get_html_generator(artifact.artifact_type)
-    jobs = artifact.jobs(cmd=command)
-    jobs = [j for j in jobs if j.status in ['queued', 'running', 'success']]
-    if jobs:
-        # The HTML summary is either being generated or already generated.
-        # Return the information of that job so we only generate the HTML
-        # once
-        job = jobs[0]
-    else:
-        # Create a new job to generate the HTML summary and return the newly
-        # created job information
-        job = ProcessingJob.create(
-            User(user_id),
-            Parameters.load(command, values_dict={'input_data': artifact_id}))
-        job.submit()
-
-    return {'status': 'success',
-            'message': '',
-            'job': [job.id, job.status, job.step]}
-
-
 def artifact_get_req(user_id, artifact_id):
     """Returns all base information about an artifact