path: root/python/sandcrawler/persist.py

"""
cdx
- read raw CDX, filter
- push to SQL table

ingest-file-result
- read JSON format (batch)
- cdx SQL push batch (on conflict skip)
- file_meta SQL push batch (on conflict update)
- ingest request push batch (on conflict skip)
- ingest result push batch (on conflict update)

grobid
- reads JSON format (batch)
- grobid2json
- minio push (one-by-one)
- grobid SQL push batch (on conflict update)
- file_meta SQL push batch (on conflict update)
"""

import os
from typing import Optional
import xml.etree.ElementTree

from sandcrawler.workers import SandcrawlerWorker
from sandcrawler.db import SandcrawlerPostgresClient
from sandcrawler.minio import SandcrawlerMinioClient
from sandcrawler.grobid import GrobidClient
from sandcrawler.pdfextract import PdfExtractResult


class PersistCdxWorker(SandcrawlerWorker):

    def __init__(self, db_url, **kwargs):
        super().__init__()
        self.db = SandcrawlerPostgresClient(db_url)
        self.cur = self.db.conn.cursor()

    def process(self, record, key=None):
        """
        Only do batches (as transactions)
        """
        raise NotImplementedError

    def push_batch(self, batch):
        self.counts['total'] += len(batch)
        # filter to full CDX lines, no liveweb
        cdx_batch = [r for r in batch if r.get('warc_path') and ("/" in r['warc_path'])]
        resp = self.db.insert_cdx(self.cur, cdx_batch)
        if len(cdx_batch) < len(batch):
            self.counts['skip'] += len(batch) - len(cdx_batch)
        self.counts['insert-cdx'] += resp[0]
        self.counts['update-cdx'] += resp[1]
        self.db.commit()
        return []

class PersistIngestFileResultWorker(SandcrawlerWorker):

    def __init__(self, db_url, **kwargs):
        super().__init__()
        self.db = SandcrawlerPostgresClient(db_url)
        self.cur = self.db.conn.cursor()

    def process(self, record, key=None):
        """
        Only do batches (as transactions)
        """
        raise NotImplementedError

    def request_to_row(self, raw):
        """
        Converts ingest-request JSON schema (eg, from Kafka) to SQL ingest_request schema

        if there is a problem with conversion, return None
        """
        # backwards compat hacks; transform request to look like current schema
        if raw.get('ingest_type') == 'file':
            raw['ingest_type'] = 'pdf'
        if (not raw.get('link_source')
                and raw.get('base_url')
                and raw.get('ext_ids', {}).get('doi')
                and raw['base_url'] == "https://doi.org/{}".format(raw['ext_ids']['doi'])):
            # set link_source(_id) for old ingest requests
            raw['link_source'] = 'doi'
            raw['link_source_id'] = raw['ext_ids']['doi']
        if (not raw.get('link_source')
                and raw.get('ingest_request_source', '').startswith('savepapernow')
                and raw.get('fatcat', {}).get('release_ident')):
            # set link_source(_id) for old ingest requests
            raw['link_source'] = 'spn'
            raw['link_source_id'] = raw['fatcat']['release_ident']

        for k in ('ingest_type', 'base_url', 'link_source', 'link_source_id'):
            if not k in raw:
                self.counts['skip-request-fields'] += 1
                return None
        if raw['ingest_type'] not in ('pdf', 'xml'):
            print(raw['ingest_type'])
            self.counts['skip-ingest-type'] += 1
            return None
        request = {
            'ingest_type': raw['ingest_type'],
            'base_url': raw['base_url'],
            'link_source': raw['link_source'],
            'link_source_id': raw['link_source_id'],
            'ingest_request_source': raw.get('ingest_request_source'),
            'request': {},
        }
        # extra/optional fields
        if raw.get('release_stage'):
            request['release_stage'] = raw['release_stage']
        if raw.get('fatcat', {}).get('release_ident'):
            request['request']['release_ident'] = raw['fatcat']['release_ident']
        for k in ('ext_ids', 'edit_extra', 'rel'):
            if raw.get(k):
                request['request'][k] = raw[k]
        # if this dict is empty, trim it to save DB space
        if not request['request']:
            request['request'] = None
        return request
            

    def file_result_to_row(self, raw):
        """
        Converts ingest-result JSON schema (eg, from Kafka) to SQL ingest_file_result schema

        if there is a problem with conversion, return None and set skip count
        """
        for k in ('request', 'hit', 'status'):
            if not k in raw:
                self.counts['skip-result-fields'] += 1
                return None
        if not 'base_url' in raw['request']:
            self.counts['skip-result-fields'] += 1
            return None
        ingest_type = raw['request'].get('ingest_type')
        if ingest_type == 'file':
            ingest_type = 'pdf'
        if ingest_type not in ('pdf', 'xml'):
            self.counts['skip-ingest-type'] += 1
            return None
        if raw['status'] in ("existing", ):
            self.counts['skip-existing'] += 1
            return None
        result = {
            'ingest_type': ingest_type,
            'base_url': raw['request']['base_url'],
            'hit': raw['hit'],
            'status': raw['status'],
        }
        terminal = raw.get('terminal')
        if terminal:
            result['terminal_url'] = terminal.get('terminal_url') or terminal.get('url')
            result['terminal_dt'] = terminal.get('terminal_dt')
            result['terminal_status_code'] = terminal.get('terminal_status_code') or terminal.get('status_code') or terminal.get('http_code')
            if result['terminal_status_code']:
                result['terminal_status_code'] = int(result['terminal_status_code'])
            result['terminal_sha1hex'] = terminal.get('terminal_sha1hex')
        return result

    def push_batch(self, batch):
        self.counts['total'] += len(batch)

        if not batch:
            return []

        results = [self.file_result_to_row(raw) for raw in batch]
        results = [r for r in results if r]

        requests = [self.request_to_row(raw['request']) for raw in batch if raw.get('request')]
        requests = [r for r in requests if r]

        if requests:
            resp = self.db.insert_ingest_request(self.cur, requests)
            self.counts['insert-requests'] += resp[0]
            self.counts['update-requests'] += resp[1]
        if results:
            resp = self.db.insert_ingest_file_result(self.cur, results, on_conflict="update")
            self.counts['insert-results'] += resp[0]
            self.counts['update-results'] += resp[1]

        # these schemas match, so can just pass through
        cdx_batch = [r['cdx'] for r in batch if r.get('hit') and r.get('cdx')]
        revisit_cdx_batch = [r['revisit_cdx'] for r in batch if r.get('hit') and r.get('revisit_cdx')]
        cdx_batch.extend(revisit_cdx_batch)
        # filter to full CDX lines, with full warc_paths (not liveweb)
        cdx_batch = [r for r in cdx_batch if r.get('warc_path') and ("/" in r['warc_path'])]
        if cdx_batch:
            resp = self.db.insert_cdx(self.cur, cdx_batch)
            self.counts['insert-cdx'] += resp[0]
            self.counts['update-cdx'] += resp[1]

        file_meta_batch = [r['file_meta'] for r in batch if r.get('hit') and r.get('file_meta')]
        if file_meta_batch:
            resp = self.db.insert_file_meta(self.cur, file_meta_batch, on_conflict="nothing")
            self.counts['insert-file_meta'] += resp[0]
            self.counts['update-file_meta'] += resp[1]

        self.db.commit()
        return []

class PersistIngestRequestWorker(PersistIngestFileResultWorker):

    def __init__(self, db_url, **kwargs):
        super().__init__(db_url=db_url)

    def process(self, record, key=None):
        """
        Only do batches (as transactions)
        """
        raise NotImplementedError

    def push_batch(self, batch):
        self.counts['total'] += len(batch)

        if not batch:
            return []

        requests = [self.request_to_row(raw) for raw in batch]
        requests = [r for r in requests if r]

        if requests:
            resp = self.db.insert_ingest_request(self.cur, requests)
            self.counts['insert-requests'] += resp[0]
            self.counts['update-requests'] += resp[1]

        self.db.commit()
        return []

class PersistGrobidWorker(SandcrawlerWorker):

    def __init__(self, db_url, **kwargs):
        super().__init__()
        self.grobid = GrobidClient()
        self.s3 = SandcrawlerMinioClient(
            host_url=kwargs.get('s3_url', 'localhost:9000'),
            access_key=kwargs['s3_access_key'],
            secret_key=kwargs['s3_secret_key'],
            default_bucket=kwargs['s3_bucket'],
        )
        self.s3_only = kwargs.get('s3_only', False)
        self.db_only = kwargs.get('db_only', False)
        assert not (self.s3_only and self.db_only), "Only one of s3_only and db_only allowed"
        if not self.s3_only:
            self.db = SandcrawlerPostgresClient(db_url)
            self.cur = self.db.conn.cursor()
        else:
            self.db = None
            self.cur = None

    def process(self, record, key=None):
        """
        Only do batches (as transactions)
        """
        raise NotImplementedError

    def push_batch(self, batch):
        self.counts['total'] += len(batch)

        # filter out bad "missing status_code" timeout rows
        missing = [r for r in batch if not r.get('status_code')]
        if missing:
            self.counts['skip-missing-status'] += len(missing)
            batch = [r for r in batch if r.get('status_code')]

        for r in batch:
            if r['status_code'] != 200 or not r.get('tei_xml'):
                self.counts['s3-skip-status'] += 1
                if r.get('error_msg'):
                    r['metadata'] = {'error_msg': r['error_msg'][:500]}
                continue

            assert len(r['key']) == 40
            if not self.db_only:
                resp = self.s3.put_blob(
                    folder="grobid",
                    blob=r['tei_xml'],
                    sha1hex=r['key'],
                    extension=".tei.xml",
                )
                self.counts['s3-put'] += 1

            # enhance with teixml2json metadata, if available
            try:
                metadata = self.grobid.metadata(r)
            except xml.etree.ElementTree.ParseError as xml_e:
                r['status'] = 'bad-grobid-xml'
                r['metadata'] = {'error_msg': str(xml_e)[:1024]}
                continue
            if not metadata:
                continue
            for k in ('fatcat_release', 'grobid_version'):
                r[k] = metadata.pop(k, None)
            if r.get('fatcat_release'):
                r['fatcat_release'] = r['fatcat_release'].replace('release_', '')
            if metadata.get('grobid_timestamp'):
                r['updated'] = metadata['grobid_timestamp']
            r['metadata'] = metadata

        if not self.s3_only:
            resp = self.db.insert_grobid(self.cur, batch, on_conflict="update")
            self.counts['insert-grobid'] += resp[0]
            self.counts['update-grobid'] += resp[1]

            file_meta_batch = [r['file_meta'] for r in batch if r.get('file_meta')]
            resp = self.db.insert_file_meta(self.cur, file_meta_batch, on_conflict="update")
            self.counts['insert-file-meta'] += resp[0]
            self.counts['update-file-meta'] += resp[1]

            self.db.commit()

        return []


class PersistGrobidDiskWorker(SandcrawlerWorker):
    """
    Writes blobs out to disk.

    This could be refactored into a "Sink" type with an even thinner wrapper.
    """

    def __init__(self, output_dir):
        super().__init__()
        self.output_dir = output_dir

    def _blob_path(self, sha1hex, extension=".tei.xml"):
        obj_path = "{}/{}/{}{}".format(
            sha1hex[0:2],
            sha1hex[2:4],
            sha1hex,
            extension,
        )
        return obj_path

    def process(self, record, key=None):

        if record.get('status_code') != 200 or not record.get('tei_xml'):
            return False
        assert(len(record['key'])) == 40
        p = "{}/{}".format(self.output_dir, self._blob_path(record['key']))
        os.makedirs(os.path.dirname(p), exist_ok=True)
        with open(p, 'w') as f:
            f.write(record.pop('tei_xml'))
        self.counts['written'] += 1
        return record


class PersistPdfTrioWorker(SandcrawlerWorker):

    def __init__(self, db_url, **kwargs):
        super().__init__()
        self.db = SandcrawlerPostgresClient(db_url)
        self.cur = self.db.conn.cursor()

    def process(self, record, key=None):
        """
        Only do batches (as transactions)
        """
        raise NotImplementedError

    def push_batch(self, batch):
        self.counts['total'] += len(batch)

        batch = [r for r in batch if 'pdf_trio' in r and r['pdf_trio'].get('status_code')]
        for r in batch:
            # copy key (sha1hex) into sub-object
            r['pdf_trio']['key'] = r['key']
        pdftrio_batch = [r['pdf_trio'] for r in batch]
        resp = self.db.insert_pdftrio(self.cur, pdftrio_batch, on_conflict="update")
        self.counts['insert-pdftrio'] += resp[0]
        self.counts['update-pdftrio'] += resp[1]

        file_meta_batch = [r['file_meta'] for r in batch if r['pdf_trio']['status'] == "success" and r.get('file_meta')]
        resp = self.db.insert_file_meta(self.cur, file_meta_batch)
        self.counts['insert-file-meta'] += resp[0]
        self.counts['update-file-meta'] += resp[1]

        self.db.commit()
        return []


class PersistPdfTextWorker(SandcrawlerWorker):
    """
    Pushes text file to blob store (S3/seaweed/minio) and PDF metadata to SQL table.

    Should keep batch sizes small.
    """

    def __init__(self, db_url, **kwargs):
        super().__init__()
        self.s3 = SandcrawlerMinioClient(
            host_url=kwargs.get('s3_url', 'localhost:9000'),
            access_key=kwargs['s3_access_key'],
            secret_key=kwargs['s3_secret_key'],
            default_bucket=kwargs['s3_bucket'],
        )
        self.s3_only = kwargs.get('s3_only', False)
        self.db_only = kwargs.get('db_only', False)
        assert not (self.s3_only and self.db_only), "Only one of s3_only and db_only allowed"
        if not self.s3_only:
            self.db = SandcrawlerPostgresClient(db_url)
            self.cur = self.db.conn.cursor()
        else:
            self.db = None
            self.cur = None

    def process(self, record, key=None):
        """
        Only do batches (as transactions)
        """
        raise NotImplementedError

    def push_batch(self, batch):
        self.counts['total'] += len(batch)

        parsed_batch = []
        for r in batch:
            parsed_batch.append(PdfExtractResult.from_pdftext_dict(r))

        for r in parsed_batch:
            if r.status != 'success' or not r.text:
                self.counts['s3-skip-status'] += 1
                if r.error_msg:
                    r.metadata = {'error_msg': r.error_msg[:500]}
                continue

            assert len(r.sha1hex) == 40
            if not self.db_only:
                resp = self.s3.put_blob(
                    folder="text",
                    blob=r.text,
                    sha1hex=r.sha1hex,
                    extension=".txt",
                )
                self.counts['s3-put'] += 1

        if not self.s3_only:
            resp = self.db.insert_pdf_meta(self.cur, parsed_batch, on_conflict="update")
            self.counts['insert-pdf-meta'] += resp[0]
            self.counts['update-pdf-meta'] += resp[1]

            file_meta_batch = [r.file_meta for r in parsed_batch if r.file_meta]
            resp = self.db.insert_file_meta(self.cur, file_meta_batch, on_conflict="update")
            self.counts['insert-file-meta'] += resp[0]
            self.counts['update-file-meta'] += resp[1]

            self.db.commit()

        return []


class PersistThumbnailWorker(SandcrawlerWorker):
    """
    Pushes text file to blob store (S3/seaweed/minio) and PDF metadata to SQL table.

    This worker *must* be used with raw kakfa mode.
    """

    def __init__(self, **kwargs):
        super().__init__()
        self.s3 = SandcrawlerMinioClient(
            host_url=kwargs.get('s3_url', 'localhost:9000'),
            access_key=kwargs['s3_access_key'],
            secret_key=kwargs['s3_secret_key'],
            default_bucket=kwargs['s3_bucket'],
        )
        self.s3_extension = kwargs.get('s3_extension', ".jpg")
        self.s3_folder = kwargs.get('s3_folder', "pdf")

    def process(self, blob: bytes, key: Optional[str] = None):
        """
        Processing raw messages, not decoded JSON objects
        """

        if isinstance(key, bytes):
            key = key.decode('utf-8')
        assert key is not None and len(key) == 40 and isinstance(key, str)
        assert isinstance(blob, bytes)
        assert len(blob) >= 50

        resp = self.s3.put_blob(
            folder=self.s3_folder,
            blob=blob,
            sha1hex=key,
            extension=self.s3_extension,
        )
        self.counts['s3-put'] += 1