コード例 #1
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
 def _finalize_sip(obj, dummy_eng):
     d = Deposition(obj)
     sip = d.get_latest_sip(sealed=False)
     sip.package = make_record(
         sip.metadata, is_dump=is_dump
     ).legacy_export_as_marc()
     d.update()
コード例 #2
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
 def _prefill_draft(obj, eng):
     if not getattr(request, 'is_api_request', False):
         draft_cache = DepositionDraftCacheManager.get()
         if draft_cache.has_data():
             d = Deposition(obj)
             draft_cache.fill_draft(d, draft_id, clear=clear)
             d.update()
コード例 #3
0
ファイル: upload.py プロジェクト: IFCA/lifewatch_osf
 def _api_validate_files(obj, eng):
     if getattr(request, 'is_api_request', False):
         d = Deposition(obj)
         missing_files = False
         if len(d.files) < 1:
             for draft in d.drafts_list:
                 draft_type = draft.values.get('upload_type')
                 if draft_type != 'analysis':
                     missing_files = True
                     break
         if missing_files:
             d.set_render_context(dict(
                 response=dict(
                     message="Bad request",
                     status=400,
                     errors=[dict(
                         message="Minimum one file must be provided.",
                         code=error_codes['validation_error']
                     )],
                 ),
                 status=400,
             ))
             d.update()
             eng.halt("API: No files provided")
         else:
             # Mark all drafts as completed
             for draft in d.drafts.values():
                 draft.complete()
             d.update()
コード例 #4
0
ファイル: upload.py プロジェクト: IFCA/lifewatch_osf
    def _run_tasks(obj, dummy_eng):
        from invenio.legacy.bibsched.bibtask import task_low_level_submission

        d = Deposition(obj)
        sip = d.get_latest_sip(sealed=True)
        # XXX XXX XXX
        return

        recid = sip.metadata['recid']

        common_args = []
        sequenceid = getattr(d.workflow_object, 'task_sequence_id', None)
        if sequenceid:
            common_args += ['-I', str(sequenceid)]

        if update:
            tasklet_name = 'bst_openaire_update_upload'
        else:
            tasklet_name = 'bst_openaire_new_upload'

        task_id = task_low_level_submission(
            'bibtasklet', 'webdeposit', '-T', tasklet_name,
            '--argument', 'recid=%s' % recid, *common_args
        )
        sip.task_ids.append(task_id)

        d.update()
コード例 #5
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
    def create(obj, dummy_eng):
        # FIXME change share tmp directory
        from invenio.config import CFG_TMPSHAREDDIR
        from invenio.legacy.bibsched.bibtask \
            import task_low_level_submission, bibtask_allocate_sequenceid
        d = Deposition(obj)

        sip = d.get_latest_sip(sealed=False)
        sip.seal()

        tmp_file_fd, tmp_file_path = mkstemp(
            prefix="webdeposit-%s-%s" % (d.id, sip.uuid),
            suffix='.xml',
            dir=CFG_TMPSHAREDDIR,
        )

        os.write(tmp_file_fd, sip.package)
        os.close(tmp_file_fd)

        # Trick to have access to task_sequence_id in subsequent tasks.
        d.workflow_object.task_sequence_id = bibtask_allocate_sequenceid()

        task_id = task_low_level_submission(
            'bibupload', 'webdeposit',
            '-r' if 'recid' in sip.metadata else '-i', tmp_file_path,
            '-I', str(d.workflow_object.task_sequence_id)
        )

        sip.task_ids.append(task_id)

        d.update()
コード例 #6
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
    def _mint_pid(obj, dummy_eng):
        d = Deposition(obj)
        recjson = d.get_latest_sip(sealed=False).metadata

        if 'recid' not in recjson:
            raise Exception("'recid' not found in sip metadata.")

        pid_text = None
        pid = recjson.get(pid_field, None)
        if not pid:
            # No pid found in recjson, so create new pid with user supplied
            # function.
            pid_text = recjson[pid_field] = pid_creator(recjson)
        else:
            # Pid found - check if it should be minted
            if existing_pid_checker and existing_pid_checker(pid, recjson):
                pid_text = pid

        # Create an assign pid internally - actually registration will happen
        # asynchronously later.
        if pid_text:
            current_app.logger.info("Registering pid %s" % pid_text)
            pid_obj = PersistentIdentifier.create(pid_store_type, pid_text)
            if pid_obj is None:
                pid_obj = PersistentIdentifier.get(pid_store_type, pid_text)

            try:
                pid_obj.assign("rec", recjson['recid'])
            except Exception:
                register_exception(alert_admin=True)

        d.update()
コード例 #7
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
 def _bibdocfile_update(obj, eng):
     if process:
         d = Deposition(obj)
         sip = d.get_latest_sip(sealed=False)
         recid = sip.metadata.get('recid')
         if recid:
             brd = BibRecDocs(int(recid))
             process(d, brd)
             d.update()
コード例 #8
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
    def _process_sip(obj, dummy_eng):
        d = Deposition(obj)
        metadata = d.get_latest_sip(sealed=False).metadata

        if processor is not None:
            processor(d, metadata)
        elif processor is None and hasattr(d.type, 'process_sip_metadata'):
            d.type.process_sip_metadata(d, metadata)

        d.update()
コード例 #9
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
    def _create_recid(obj, dummy_eng):
        d = Deposition(obj)
        sip = d.get_latest_sip(sealed=False)
        if sip is None:
            raise Exception("No submission information package found.")

        if 'recid' not in sip.metadata:
            from invenio.legacy.bibupload.engine import create_new_record
            sip.metadata['recid'] = create_new_record()
        d.update()
コード例 #10
0
ファイル: upload.py プロジェクト: IFCA/lifewatch_osf
 def _process_file_descriptions(obj, eng):
     d = Deposition(obj)
     try:
         draft = d.get_draft("_files")
     except DraftDoesNotExists:
         return
     # draft_files = draft.values.get('file_description', [])
     for f in d.files:
         for df in draft.values.get('file_description', []):
             if f.uuid == df.get('file_id', None):
                 f.description = df.get('description', '')
     d.update()
コード例 #11
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
    def _merge_record(obj, eng):
        d = Deposition(obj)
        sip = d.get_latest_sip(sealed=False)

        # Get the current record, which contains all fields.
        current_record = get_record(
            sip.metadata.get('recid'), reset_cache=True
        )

        form_class = d.get_draft(draft_id).form_class

        # Create a simplified record from the current record, that only
        # contains fields concerning this deposition.
        current_simple_record = deposition_record(
            current_record,
            [form_class],
            pre_process_load=pre_process_load,
            post_process_load=post_process_load,
            process_export=partial(process_export, d),
        )
        # Create a simplified record from the changes the user have made.
        changed_simple_record = make_record(sip.metadata, is_dump=True)

        # Make an initial patch of current record (e.g. some default values set
        # by the form, might not exists in the current record)
        for k in current_simple_record:
            if k not in current_record:
                current_record[k] = current_simple_record[k]

        # Export clean dumps
        current_simple_json = current_simple_record.dumps(clean=True)
        changed_simple_json = changed_simple_record.dumps(clean=True)
        current_full_json = current_record.dumps(clean=True)

        # Merge changes from changed record into the current record.
        sip.metadata = merge_func(
            d,
            current_full_json,
            current_simple_json,
            changed_simple_json,
        )

        # Ensure we are based on latest version_id to prevent being rejected in
        # the bibupload queue.
        hst_record = HstRECORD.query.filter_by(
            id_bibrec=sip.metadata.get('recid')
        ).order_by(HstRECORD.job_date.desc()).first()

        sip.metadata['modification_date'] = hst_record.job_date.isoformat()

        d.update()
コード例 #12
0
ファイル: upload.py プロジェクト: IFCA/lifewatch_osf
def skip_files(obj, eng):
    if has_doi(obj, eng):
        return True
    d = Deposition(obj)
    try:
        draft = d.get_draft("_metadata")
        if draft.values.get('upload_type', '') == 'dataset':
            if int(draft.values.get('instrument', -1)) != -1:
                current_app.logger.debug(draft.values)
                return True
    except (DraftDoesNotExists, ValueError):
        # this should never happen
        pass
    return False
コード例 #13
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
    def _prepare_sip(obj, dummy_eng):
        d = Deposition(obj)

        sip = d.get_latest_sip(sealed=False)
        if sip is None:
            sip = d.create_sip()

        # FIXME: Move to somewhere more appropriate
        # create_sip by default stick files into the files attribute.
        if 'files' in sip.metadata:
            sip.metadata['fft'] = sip.metadata['files']
            del sip.metadata['files']

        sip.agents = [Agent(role='creator', from_request_context=True)]
        d.update()
コード例 #14
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
    def _render_form(obj, eng):
        d = Deposition(obj)
        draft = d.get_or_create_draft(draft_id)

        if getattr(request, 'is_api_request', False):
            form = draft.get_form(validate_draft=True)
            if form.errors:
                error_messages = []
                for field, msgs in form.errors:
                    for m in msgs:
                        error_messages.append(
                            field=field,
                            message=m,
                            code=error_codes['validation_error'],
                        )

                d.set_render_context(dict(
                    response=dict(
                        message="Bad request",
                        status=400,
                        errors=error_messages,
                    ),
                    status=400,
                ))
                eng.halt("API: Draft did not validate")
        else:
            if draft.is_completed():
                eng.jumpCallForward(1)
            else:
                form = draft.get_form(validate_draft=draft.validate)
                form.validate = True

                d.set_render_context(dict(
                    template_name_or_list=form.get_template(),
                    deposition=d,
                    deposition_type=(
                        None if d.type.is_default() else
                        d.type.get_identifier()
                    ),
                    uuid=d.id,
                    draft=draft,
                    form=form,
                    my_depositions=Deposition.get_depositions(
                        current_user, type=d.type
                    ),
                ))
                d.update()
                eng.halt('Wait for form submission.')
コード例 #15
0
ファイル: upload.py プロジェクト: IFCA/lifewatch_osf
def has_doi(obj, eng):
    if has_submission(obj, eng):
        d = Deposition(obj)
        return d.is_minted()
    return False
コード例 #16
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
def has_submission(obj, eng):
    """Check if deposition has submission."""
    d = Deposition(obj)
    return d.has_sip()
コード例 #17
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
 def _hold_for_approval(obj, dummy_eng):
     from invenio.modules.workflows.tasks.marcxml_tasks \
         import approve_record
     d = Deposition(obj)
     if d.type.hold_for_upload:
         approve_record(obj, dummy_eng)
コード例 #18
0
def do_upgrade():
    """ Implement your upgrades here  """
    from invenio.modules.workflows.models import BibWorkflowObject
    from invenio.modules.workflows.engine import ObjectVersion, WorkflowStatus
    from lw_daap.modules.invenio_deposit.models import Deposition

    for o in BibWorkflowObject.query.filter(
            BibWorkflowObject.id_user != 0).all():
        d = Deposition(o)
        if is_error(d):
            warn(o, 'ERROR', "run workflow")
            sip = d.get_latest_sip(sealed=False)
            for k in ['first_author', 'additional_authors']:
                if k in sip.metadata:
                    sip.metadata['_%s' % k] = sip.metadata[k]
                    del sip.metadata[k]
            d.run_workflow(headless=True)
        elif is_done(d):
            if (o.version != ObjectVersion.COMPLETED or
                    o.workflow.status != WorkflowStatus.COMPLETED):
                if (o.version == ObjectVersion.HALTED and
                        o.workflow.status == ObjectVersion.HALTED):
                    warn(
                        o, 'DONE', "wf status %s -> %s" %
                        (o.workflow.status, WorkflowStatus.COMPLETED))
                    warn(
                        o, 'DONE', "obj version %s -> %s" %
                        (o.version, ObjectVersion.COMPLETED))
                    o.workflow.status = WorkflowStatus.COMPLETED
                    o.version = ObjectVersion.COMPLETED
                elif (o.version == ObjectVersion.COMPLETED and
                      o.workflow.status == 5):
                    warn(
                        o, 'DONE', "wf status %s -> %s" %
                        (o.workflow.status, WorkflowStatus.COMPLETED))
                    o.workflow.status = WorkflowStatus.COMPLETED
                elif (o.version == ObjectVersion.HALTED and
                      o.workflow.status == WorkflowStatus.COMPLETED):
                    warn(
                        o, 'DONE', "obj version %s -> %s" %
                        (o.version, ObjectVersion.COMPLETED))
                    o.version = ObjectVersion.COMPLETED
                else:
                    warn(
                        o, 'DONE', "Unmatched version %s status %s" %
                        (o.version, o.workflow.status if o.workflow else None))
            else:
                info_msg(o, 'DONE')
        elif is_inprogress(d):
            if is_submitted(d):
                if (o.version == ObjectVersion.HALTED and
                        o.workflow.status == WorkflowStatus.HALTED):
                    info_msg(o, 'INPROGRESS/SUBMITTED')
                elif (o.version == ObjectVersion.INITIAL and
                      o.workflow.status == WorkflowStatus.NEW):
                    info_msg(o, 'INPROGRESS/SUBMITTED')
                elif (o.version == ObjectVersion.HALTED and
                      o.workflow.status == WorkflowStatus.COMPLETED):
                    warn(
                        o, 'INPROGRESS/SUBMITTED', "wf status %s -> %s" %
                        (o.workflow.status, WorkflowStatus.HALTED))
                    o.workflow.status = WorkflowStatus.HALTED
                else:
                    warn(
                        o, 'INPROGRESS/SUBMITTED',
                        "Unmatched version %s status %s" %
                        (o.version, o.workflow.status if o.workflow else None))
            elif is_unsubmitted(d):
                if o.workflow is None:
                    if o.version != ObjectVersion.INITIAL:
                        warn(
                            o, 'INPROGRESS/UNSUBMITTED',
                            "Unmatched version %s status %s" %
                            (o.version,
                             o.workflow.status if o.workflow else None))
                    else:
                        info_msg(o, 'INPROGRESS/UNSUBMITTED')
                elif (o.version == ObjectVersion.HALTED and
                      o.workflow.status == WorkflowStatus.HALTED):
                    info_msg(o, 'INPROGRESS/UNSUBMITTED')
                elif (o.version == ObjectVersion.HALTED and
                      o.workflow.status == WorkflowStatus.RUNNING):
                    warn(
                        o, 'INPROGRESS/UNSUBMITTED', "wf status %s -> %s" %
                        (o.workflow.status, WorkflowStatus.HALTED))
                    o.workflow.status = WorkflowStatus.HALTED
                elif (o.version == ObjectVersion.RUNNING and
                      o.workflow.status == WorkflowStatus.RUNNING):
                    warn(
                        o, 'INPROGRESS/UNSUBMITTED', "wf status %s -> %s" %
                        (o.workflow.status, WorkflowStatus.HALTED))
                    warn(
                        o, 'INPROGRESS/UNSUBMITTED', "obj version %s -> %s" %
                        (o.version, ObjectVersion.HALTED))
                    o.version = ObjectVersion.HALTED
                    o.workflow.status = WorkflowStatus.HALTED
                elif (o.version == ObjectVersion.HALTED and
                      o.workflow.status == WorkflowStatus.COMPLETED):
                    warn(
                        o, 'INPROGRESS/UNSUBMITTED', "wf status %s -> %s" %
                        (o.workflow.status, WorkflowStatus.HALTED))
                    o.workflow.status = WorkflowStatus.HALTED
                else:
                    warn(
                        o, 'INPROGRESS/UNSUBMITTED',
                        "Unmatched version %s status %s" %
                        (o.version, o.workflow.status if o.workflow else None))
            else:
                warn(o, 'INPROGRESS/?', "Unmatched version %s status %s" %
                     (o.version, o.workflow.status if o.workflow else None))
    global good, bad
    warnings.warn("Good: %s Bad: %s" % (good, bad))
    db.session.commit()
コード例 #19
0
ファイル: tasks.py プロジェクト: IFCA/lifewatch_osf
    def _load_record(obj, eng):
        d = Deposition(obj)
        sip = d.get_latest_sip(sealed=True)
        record = get_record(sip.metadata.get('recid'), reset_cache=True)

        if not is_sip_uploaded(sip, record=record):
            if getattr(request, 'is_api_request', False):
                d.set_render_context(dict(
                    response=dict(
                        message="Conflict",
                        status=409,
                        errors="Upload not yet fully integrated. Please wait"
                               " a few moments.",
                    ),
                    status=409,
                ))
            else:
                from flask import flash
                flash(
                    "Editing is only possible after your upload have been"
                    " fully integrated. Please wait a few moments, then try"
                    " to reload the page.",
                    category='warning'
                )
                d.set_render_context(dict(
                    template_name_or_list="deposit/completed.html",
                    deposition=d,
                    deposition_type=(
                        None if d.type.is_default() else
                        d.type.get_identifier()
                    ),
                    uuid=d.id,
                    sip=sip,
                    my_depositions=Deposition.get_depositions(
                        current_user, type=d.type
                    ),
                    format_record=format_record,
                ))
            d.update()
            eng.halt("Wait for record to be uploaded")

        # Check if record is already loaded, if so, skip.
        if d.drafts:
            eng.jumpCallForward(1)

        # Load draft
        draft = d.get_or_create_draft(draft_id)

        # Fill draft with values from recjson
        record_to_draft(
            record, draft=draft, post_process=post_process, producer=producer
        )

        d.update()

        # Stop API request
        if getattr(request, 'is_api_request', False):
            d.set_render_context(dict(
                response=d.marshal(),
                status=201,
            ))
            eng.halt("API request")