diff options
Diffstat (limited to 'python')
21 files changed, 621 insertions, 80 deletions
diff --git a/python/fatcat_import.py b/python/fatcat_import.py index f502d4ed..2896577e 100755 --- a/python/fatcat_import.py +++ b/python/fatcat_import.py @@ -25,6 +25,7 @@ from fatcat_tools.importers import ( FilesetImporter, GrobidMetadataImporter, IngestFileResultImporter, + IngestFilesetFileResultImporter, IngestFilesetResultImporter, IngestWebResultImporter, JalcImporter, @@ -232,6 +233,30 @@ def run_ingest_fileset(args: argparse.Namespace) -> None: JsonLinePusher(ifri, args.json_file).run() +def run_ingest_fileset_file(args: argparse.Namespace) -> None: + ifri = IngestFilesetFileResultImporter( + args.api, + editgroup_description=args.editgroup_description_override, + skip_source_allowlist=args.skip_source_allowlist, + do_updates=args.do_updates, + default_link_rel=args.default_link_rel, + edit_batch_size=args.batch_size, + ) + if args.kafka_mode: + KafkaJsonPusher( + ifri, + args.kafka_hosts, + args.kafka_env, + "ingest-fileset-results", + "fatcat-{}-ingest-fileset-result".format(args.kafka_env), + kafka_namespace="sandcrawler", + consume_batch_size=args.batch_size, + force_flush=True, + ).run() + else: + JsonLinePusher(ifri, args.json_file).run() + + def run_savepapernow_file(args: argparse.Namespace) -> None: ifri = SavePaperNowFileImporter( args.api, @@ -750,6 +775,39 @@ def main() -> None: help="default URL rel for matches (eg, 'publisher', 'web')", ) + sub_ingest_fileset_file = subparsers.add_parser( + "ingest-fileset-file-results", + help="add/update file entities linked to releases based on sandcrawler dataset/fileset ingest results", + ) + sub_ingest_fileset_file.set_defaults( + func=run_ingest_fileset_file, + auth_var="FATCAT_AUTH_WORKER_CRAWL", + ) + sub_ingest_fileset_file.add_argument( + "json_file", + help="ingest_fileset JSON file to import from", + default=sys.stdin, + type=argparse.FileType("r"), + ) + sub_ingest_fileset_file.add_argument( + "--skip-source-allowlist", + action="store_true", + help="don't filter import based on request source allowlist", + ) + sub_ingest_fileset_file.add_argument( + "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" + ) + sub_ingest_fileset_file.add_argument( + "--do-updates", + action="store_true", + help="update pre-existing fileset entities if new match (instead of skipping)", + ) + sub_ingest_fileset_file.add_argument( + "--default-link-rel", + default="fileset", + help="default URL rel for matches (eg, 'publisher', 'web')", + ) + sub_savepapernow_file = subparsers.add_parser( "savepapernow-file-results", help="add file entities crawled due to async Save Paper Now request", diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py index 654be2e9..e13ab552 100644 --- a/python/fatcat_tools/importers/__init__.py +++ b/python/fatcat_tools/importers/__init__.py @@ -37,6 +37,7 @@ from .fileset_generic import FilesetImporter from .grobid_metadata import GrobidMetadataImporter from .ingest import ( IngestFileResultImporter, + IngestFilesetFileResultImporter, IngestFilesetResultImporter, IngestWebResultImporter, SavePaperNowFileImporter, diff --git a/python/fatcat_tools/importers/arxiv.py b/python/fatcat_tools/importers/arxiv.py index dd2c2284..d7d3ed97 100644 --- a/python/fatcat_tools/importers/arxiv.py +++ b/python/fatcat_tools/importers/arxiv.py @@ -18,6 +18,9 @@ latex2text = LatexNodes2Text() def latex_to_text(raw: str) -> str: + # hack: handle a single special mangled title + if raw.startswith("%CRTFASTGEEPWR"): + return raw.strip() try: return latex2text.latex_to_text(raw).strip() except AttributeError: @@ -26,6 +29,11 @@ def latex_to_text(raw: str) -> str: return raw.strip() +def test_latex_to_text() -> None: + s = "%CRTFASTGEEPWR: a SAS macro for power of the generalized estimating equations of multi-period cluster randomized trials with application to stepped wedge designs" + assert latex_to_text(s) == s + + def parse_arxiv_authors(raw: str) -> List[str]: if not raw: return [] diff --git a/python/fatcat_tools/importers/chocula.py b/python/fatcat_tools/importers/chocula.py index 8c410d3e..38802bcb 100644 --- a/python/fatcat_tools/importers/chocula.py +++ b/python/fatcat_tools/importers/chocula.py @@ -136,6 +136,9 @@ class ChoculaImporter(EntityImporter): do_update = True if ce.extra.get("webarchive_urls") and not ce.extra.get("webarchive_urls", []): do_update = True + if ce.extra.get("publisher_type") and not ce.extra.get("publisher_type"): + # many older containers were missing this metadata + do_update = True for k in ("kbart", "ia", "doaj"): # always update these fields if not equal (chocula override) if ce.extra.get(k) and ce.extra[k] != existing.extra.get(k): diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py index cd51a24c..2136d1da 100644 --- a/python/fatcat_tools/importers/common.py +++ b/python/fatcat_tools/importers/common.py @@ -916,3 +916,14 @@ def make_kafka_consumer( ) print("Consuming from kafka topic {}, group {}".format(topic_name, group)) return consumer + + +def filesets_very_similar(a: FilesetEntity, b: FilesetEntity) -> bool: + """ + This helper method checks if two Fileset entities are effectively equivalent: same set of files with comparable hashes. + + Uses a set() of SHA1 hashes to test for equivalence. + """ + a_hashes = set([f.sha1 for f in a.manifest]) + b_hashes = set([f.sha1 for f in b.manifest]) + return a_hashes == b_hashes diff --git a/python/fatcat_tools/importers/dblp_release.py b/python/fatcat_tools/importers/dblp_release.py index 5f78ca3a..b97c3976 100644 --- a/python/fatcat_tools/importers/dblp_release.py +++ b/python/fatcat_tools/importers/dblp_release.py @@ -542,18 +542,21 @@ class DblpReleaseImporter(EntityImporter): Used only in JSON dump mode, with the intent of transforming into sandcrawler ingest requests. """ - EXTID_PATTERNS = [ + SKIP_PATTERNS = [ "://doi.acm.org/", "://doi.ieeecomputersociety.org/", "doi.org/10.", "wikidata.org/entity/Q", "://arxiv.org/abs/", + "://hdl.handle.net/", + "://d-nb.info/", + "://www.base-search.net/", ] urls = [] for ee in xml_elem.find_all("ee"): url = ee.text skip = False - for pattern in EXTID_PATTERNS: + for pattern in SKIP_PATTERNS: if pattern in url: skip = True break diff --git a/python/fatcat_tools/importers/doaj_article.py b/python/fatcat_tools/importers/doaj_article.py index 8f5e7acf..64c05773 100644 --- a/python/fatcat_tools/importers/doaj_article.py +++ b/python/fatcat_tools/importers/doaj_article.py @@ -100,6 +100,10 @@ class DoajArticleImporter(EntityImporter): container_name = None break + if not container_id: + self.counts["skip-no-container"] += 1 + return None + volume = clean_str(bibjson["journal"].get("volume")) # NOTE: this schema seems to use "number" as "issue number" issue = clean_str(bibjson["journal"].get("number")) diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index 4f1cc3c4..c1fed31f 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -11,7 +11,7 @@ from fatcat_openapi_client import ( WebcaptureEntity, ) -from .common import EntityImporter, make_rel_url +from .common import EntityImporter, filesets_very_similar, make_rel_url class IngestFileResultImporter(EntityImporter): @@ -260,6 +260,16 @@ class IngestFileResultImporter(EntityImporter): edit_extra["grobid_status_code"] = row["grobid"]["status_code"] edit_extra["grobid_version"] = row["grobid"].get("grobid_version") + # fileset/platform metadata + if row.get("ingest_strategy"): + edit_extra["ingest_strategy"] = row["ingest_strategy"] + if row.get("platform_domain"): + edit_extra["platform_domain"] = row["platform_domain"] + if row.get("platform_name"): + edit_extra["platform_name"] = row["platform_name"] + if row.get("platform_id"): + edit_extra["platform_id"] = row["platform_id"] + return edit_extra def parse_record(self, row: Dict[str, Any]) -> FileEntity: @@ -518,7 +528,6 @@ class IngestWebResultImporter(IngestFileResultImporter): ) edit_extra = self.parse_edit_extra(row) - if edit_extra: wc.edit_extra = edit_extra return wc @@ -675,9 +684,9 @@ class IngestFilesetResultImporter(IngestFileResultImporter): return True def parse_fileset_urls(self, row: Dict[str, Any]) -> List[FilesetUrl]: - if not row.get("strategy"): + if not row.get("ingest_strategy"): return [] - strategy = row["strategy"] + strategy = row["ingest_strategy"] urls = [] if strategy == "archiveorg-fileset" and row.get("archiveorg_item_name"): urls.append( @@ -686,17 +695,14 @@ class IngestFilesetResultImporter(IngestFileResultImporter): rel="archive-base", ) ) - if row["strategy"].startswith("web-") and row.get("platform_base_url"): + if strategy.startswith("web-") and row.get("platform_base_url"): urls.append( fatcat_openapi_client.FilesetUrl( url=f"https://web.archive.org/web/{row['web_base_url_dt']}/{row['web_base_url']}", rel="webarchive-base", ) ) - # TODO: repository-base - # TODO: web-base - - if row["strategy"] == "archiveorg-fileset-bundle" and row.get("archiveorg_item_name"): + if strategy == "archiveorg-fileset-bundle" and row.get("archiveorg_item_name"): urls.append( fatcat_openapi_client.FilesetUrl( url=f"https://archive.org/download/{row['archiveorg_item_name']}/{row['archiveorg_bundle_path']}", @@ -704,7 +710,7 @@ class IngestFilesetResultImporter(IngestFileResultImporter): ) ) - if row["strategy"] == "web-fileset-bundle" and row.get("platform_bundle_url"): + if strategy == "web-fileset-bundle" and row.get("platform_bundle_url"): urls.append( fatcat_openapi_client.FilesetUrl( url=f"https://web.archive.org/web/{row['web_bundle_url_dt']}/{row['web_bundle_url']}", @@ -727,6 +733,15 @@ class IngestFilesetResultImporter(IngestFileResultImporter): rel="repository-base", ) ) + elif row.get("terminal"): + # fallback generic web URL + urls.append( + fatcat_openapi_client.FilesetUrl( + url=row["terminal"]["terminal_url"], + rel="web", + ) + ) + return urls def parse_record(self, row: Dict[str, Any]) -> FilesetEntity: @@ -748,12 +763,6 @@ class IngestFilesetResultImporter(IngestFileResultImporter): return None entity_extra: Dict[str, Any] = dict() - edit_extra = self.parse_edit_extra(row) - edit_extra["ingest_strategy"] = row["ingest_strategy"] - if row.get("platform"): - edit_extra["platform"] = row["platform"] - if row.get("platform_id"): - edit_extra["platform_id"] = row["platform_id"] entity_urls = self.parse_fileset_urls(row) if not entity_urls: @@ -770,33 +779,33 @@ class IngestFilesetResultImporter(IngestFileResultImporter): fsf = fatcat_openapi_client.FilesetFile( path=ingest_file["path"], size=ingest_file["size"], - md5=ingest_file["md5"], - sha1=ingest_file["sha1"], + md5=ingest_file.get("md5"), + sha1=ingest_file.get("sha1"), sha256=ingest_file.get("sha256"), - extra=dict( - mimetype=ingest_file["mimetype"], - ), + mimetype=ingest_file.get("mimetype"), + extra=dict(), ) - if not (fsf.md5 and fsf.sha1 and fsf.path and fsf.size): + if not (fsf.md5 and fsf.sha1 and fsf.path and fsf.size and fsf.mimetype): self.counts["skip-partial-file-info"] += 1 return None if ingest_file.get("platform_url"): - # XXX: should we include this? fsf.extra["original_url"] = ingest_file["platform_url"] if ingest_file.get("terminal_url") and ingest_file.get("terminal_dt"): fsf.extra[ "wayback_url" ] = f"https://web.archive.org/web/{ingest_file['terminal_dt']}/{ingest_file['terminal_url']}" + if not fsf.extra: + fsf.extra = None manifest.append(fsf) fe = fatcat_openapi_client.FilesetEntity( manifest=manifest, urls=entity_urls, release_ids=[release_ident], + extra=entity_extra or None, ) - if entity_extra: - fe.extra = entity_extra + edit_extra = self.parse_edit_extra(row) if edit_extra: fe.edit_extra = edit_extra return fe @@ -805,26 +814,29 @@ class IngestFilesetResultImporter(IngestFileResultImporter): # check for existing edits-in-progress with same URL for other in self._entity_queue: - # XXX: how to duplicate check? - if other.original_url == fse.original_url: + if filesets_very_similar(other, fse): self.counts["skip-in-queue"] += 1 + self.counts["skip"] += 1 return False # lookup sha1, or create new entity (TODO: API doesn't support this yet) # existing = None # NOTE: in lieu of existing checks (by lookup), only allow one fileset per release - release = self.api.get_release(fse.release_ids[0], expand="filesets") - if release.filesets: - # XXX: how to duplicate check filesets? + if not self.bezerk_mode: + release = self.api.get_release(fse.release_ids[0], expand="filesets") + # check if this is an existing match, or just a similar hit - for other in release.filesets: - if fse.original_url == other.original_url: - # TODO: compare very similar timestamps of same time (different formats) + for other in release.filesets or []: + if filesets_very_similar(other, fse): self.counts["exists"] += 1 return False - self.counts["skip-release-has-fileset"] += 1 - return False + + # for now, being conservative and just skipping if release has any other fileset + if release.filesets: + self.counts["skip-release-has-fileset"] += 1 + self.counts["skip"] += 1 + return False return True @@ -849,6 +861,197 @@ class IngestFilesetResultImporter(IngestFileResultImporter): ) +class IngestFilesetFileResultImporter(IngestFileResultImporter): + """ + Variant of IngestFileResultImporter for processing dataset (Fileset) ingest + results, which resulted in a single file, into File entities. + """ + + def __init__(self, api: ApiClient, **kwargs) -> None: + + eg_desc = ( + kwargs.pop("editgroup_description", None) + or "Single files crawled from web using sandcrawler ingest tool, in dataset mode" + ) + eg_extra = kwargs.pop("editgroup_extra", dict()) + eg_extra["agent"] = eg_extra.get( + "agent", "fatcat_tools.IngestFilesetFileResultImporter" + ) + kwargs["do_updates"] = False + super().__init__(api, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs) + self.max_file_count = 300 + + def want_fileset(self, row: Dict[str, Any]) -> bool: + + manifest: Optional[List[Any]] = row.get("manifest") + if not manifest or len(manifest) == 0: + self.counts["skip-empty-manifest"] += 1 + return False + + if len(manifest) > 1: + self.counts["skip-multiple-files"] += 1 + return False + + assert len(manifest) == 1 + return True + + def want(self, row: Dict[str, Any]) -> bool: + + if not self.want_ingest(row): + return False + + if row.get("status") != "success-file": + self.counts["skip-status"] += 1 + return False + + # fileset-specific filters + if row["request"].get("ingest_type") not in [ + "dataset", + ]: + self.counts["skip-ingest-type"] += 1 + return False + + if not self.want_fileset(row): + return False + + return True + + def parse_fileset_urls(self, row: Dict[str, Any]) -> List[FilesetUrl]: + if not row.get("ingest_strategy"): + return [] + strategy = row["ingest_strategy"] + urls = [] + # XXX + if strategy == "archiveorg-fileset" and row.get("archiveorg_item_name"): + urls.append( + fatcat_openapi_client.FilesetUrl( + url=f"https://archive.org/download/{row['archiveorg_item_name']}/", + rel="archive-base", + ) + ) + if strategy.startswith("web-") and row.get("platform_base_url"): + urls.append( + fatcat_openapi_client.FilesetUrl( + url=f"https://web.archive.org/web/{row['web_base_url_dt']}/{row['web_base_url']}", + rel="webarchive-base", + ) + ) + if strategy == "archiveorg-fileset-bundle" and row.get("archiveorg_item_name"): + urls.append( + fatcat_openapi_client.FilesetUrl( + url=f"https://archive.org/download/{row['archiveorg_item_name']}/{row['archiveorg_bundle_path']}", + rel="archive-bundle", + ) + ) + + if strategy == "web-fileset-bundle" and row.get("platform_bundle_url"): + urls.append( + fatcat_openapi_client.FilesetUrl( + url=f"https://web.archive.org/web/{row['web_bundle_url_dt']}/{row['web_bundle_url']}", + rel="webarchive-bundle", + ) + ) + + # add any additional / platform URLs here + if row.get("platform_bundle_url"): + urls.append( + fatcat_openapi_client.FilesetUrl( + url=row["platform_bundle_url"], + rel="repository-bundle", + ) + ) + if row.get("platform_base_url"): + urls.append( + fatcat_openapi_client.FilesetUrl( + url=row["platform_bundle_url"], + rel="repository-base", + ) + ) + elif row.get("terminal"): + # fallback generic web URL + urls.append( + fatcat_openapi_client.FilesetUrl( + url=row["terminal"]["terminal_url"], + rel="web", + ) + ) + + return urls + + def parse_record(self, row: Dict[str, Any]) -> FileEntity: + + request = row["request"] + + # double check that want() filtered request correctly + if request.get("ingest_type") not in [ + "dataset", + ]: + self.counts["skip-ingest-type"] += 1 + return None + + # identify release by fatcat ident, or extid lookup + release_ident = self.parse_ingest_release_ident(row) + + if not release_ident: + self.counts["skip-release-not-found"] += 1 + return None + + assert row["file_count"] == len(row["manifest"]) == 1 + file_meta = row["manifest"][0] + # print(file_meta) + assert file_meta["status"] == "success" + + # add file-level access URLs + entity_urls = [] + if file_meta.get("platform_url"): + entity_urls.append(FileUrl(rel="web", url=file_meta["platform_url"])) + if file_meta.get("terminal_url") and file_meta.get("terminal_dt"): + entity_urls.append( + FileUrl( + rel="webarchive", + url=f"https://web.archive.org/web/{file_meta['terminal_dt']}/{file_meta['terminal_url']}", + ) + ) + if row["ingest_strategy"] == "archiveorg-file": + entity_urls.append( + FileUrl( + rel="archive", + url=f"https://archive.org/download/{row['archiveorg_item_name']}/{file_meta['path']}", + ) + ) + + if not entity_urls: + self.counts["skip-no-access-url"] += 1 + return None + + entity_extra: Dict[str, Any] = dict() + entity_extra["path"] = file_meta["path"] + + # this is to work around a bug in old sandcrawler ingest code + if file_meta["md5"] == file_meta["sha1"]: + self.counts["skip-bad-hashes"] += 1 + return None + + fe = FileEntity( + md5=file_meta["md5"], + sha1=file_meta["sha1"], + sha256=file_meta["sha256"], + size=file_meta["size"], + mimetype=file_meta["mimetype"], + release_ids=[release_ident], + urls=entity_urls, + extra=entity_extra or None, + ) + if not (fe.md5 and fe.sha1 and fe.sha256 and (fe.size is not None) and fe.mimetype): + self.counts["skip-partial-file-info"] += 1 + return None + + edit_extra = self.parse_edit_extra(row) + if edit_extra: + fe.edit_extra = edit_extra + return fe + + class SavePaperNowFilesetImporter(IngestFilesetResultImporter): """ Like SavePaperNowFileImporter, but for fileset/dataset ingest. diff --git a/python/fatcat_tools/transforms/ingest.py b/python/fatcat_tools/transforms/ingest.py index cbf9e9bf..1a19a651 100644 --- a/python/fatcat_tools/transforms/ingest.py +++ b/python/fatcat_tools/transforms/ingest.py @@ -85,6 +85,14 @@ def release_ingest_request( url = "https://doi.org/{}".format(release.ext_ids.doi.lower()) link_source = "doi" link_source_id = release.ext_ids.doi.lower() + elif release.ext_ids.doaj: + url = "https://doaj.org/article/{}".format(release.ext_ids.doaj.lower()) + link_source = "doaj" + link_source_id = release.ext_ids.doaj.lower() + elif release.ext_ids.hdl: + url = "https://hdl.handle.net/{}".format(release.ext_ids.hdl.lower()) + link_source = "hdl" + link_source_id = release.ext_ids.hdl.lower() if not url: return None diff --git a/python/fatcat_web/routes.py b/python/fatcat_web/routes.py index 1f6602d4..4ceeac49 100644 --- a/python/fatcat_web/routes.py +++ b/python/fatcat_web/routes.py @@ -3,6 +3,7 @@ import os from typing import Any, Callable, Dict, List, Optional import citeproc_styles +import sentry_sdk from fatcat_openapi_client import EditgroupAnnotation from fatcat_openapi_client.rest import ApiException, ApiValueError from flask import ( @@ -1450,7 +1451,14 @@ def release_bibtex(ident: str) -> AnyResponse: entity = api.get_release(ident) except ApiException as ae: raise ae - csl = release_to_csl(entity) + try: + csl = release_to_csl(entity) + except ValueError as e: + # "handle" the missing author/surname path, so we don't get exception + # reports about it. these are not linked to, only show up from bots. + sentry_sdk.set_level("warning") + sentry_sdk.capture_exception(e) + abort(400, e) bibtex = citeproc_csl(csl, "bibtex") return Response(bibtex, mimetype="text/plain") @@ -1468,7 +1476,14 @@ def release_citeproc(ident: str) -> AnyResponse: entity = api.get_release(ident) except ApiException as ae: raise ae - csl = release_to_csl(entity) + try: + csl = release_to_csl(entity) + except ValueError as e: + # "handle" the missing author/surname path, so we don't get exception + # reports about it. these are not linked to, only show up from bots. + sentry_sdk.set_level("warning") + sentry_sdk.capture_exception(e) + abort(400, e) try: cite = citeproc_csl(csl, style, is_html) except citeproc_styles.StyleNotFoundError as e: diff --git a/python/fatcat_web/search.py b/python/fatcat_web/search.py index 913d6696..f85f6c89 100644 --- a/python/fatcat_web/search.py +++ b/python/fatcat_web/search.py @@ -636,7 +636,8 @@ def get_elastic_preservation_by_year(query: ReleaseQuery) -> List[Dict[str, Any] "biblio", ], ) - search = search.filter("term", container_id=query.container_id) + if query.container_id: + search = search.filter("term", container_id=query.container_id) if query.exclude_stubs: search = search.query( "bool", diff --git a/python/fatcat_web/templates/entity_macros.html b/python/fatcat_web/templates/entity_macros.html index 5f8f6e0a..4386e698 100644 --- a/python/fatcat_web/templates/entity_macros.html +++ b/python/fatcat_web/templates/entity_macros.html @@ -75,6 +75,14 @@ <a href="{{ u }}">{{ u }}</a><br> {% endfor %} </code> + {% elif key in ("manifest", "abstracts", "refs", "releases", "files", "webcaptures", "filesets", "urls", "archive_urls", "cdx", "contribs") and value and value is iterable and value is not string %} + <tr><td class="three wide right aligned"><code>{{ key }}[]</code></td> + <td class="seven wide"> + <code> + {% for m in value %} + {% if m != None %}{{ m }}{% endif %}<br> + {% endfor %} + </code> {% else %} <tr><td class="three wide right aligned"><code>{{ key }}</code></td> <td class="seven wide"><code>{% if value != None %}{{ value }}{% endif %}</code> diff --git a/python/fatcat_web/templates/fileset_view.html b/python/fatcat_web/templates/fileset_view.html index 4e8bfbad..6f3f802e 100644 --- a/python/fatcat_web/templates/fileset_view.html +++ b/python/fatcat_web/templates/fileset_view.html @@ -3,6 +3,21 @@ {% import "entity_macros.html" as entity_macros %} {% extends "entity_base.html" %} +{% macro file_mimetype_icon(mimetype) -%} + {%- if not mimetype -%}file outline + {%- elif mimetype in ["application/pdf"] -%}file pdf outline + {%- elif mimetype in ["application/x-hdf"] -%}database + {%- elif mimetype in ["text/csv", "text/tab-separated-values"] -%}table + {%- elif mimetype in ["application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"] -%}table + {%- elif mimetype in ["application/vnd.openxmlformats-officedocument.wordprocessingml.document"] -%}file alternate outline + {%- elif mimetype in ["application/zip", "application/gzip", "application/x-tar", "application/x-rar", "application/x-bzip2"] -%}file archive outline + {%- elif mimetype in ["application/octet-stream"] -%}save outline + {%- elif mimetype.startswith("text/") -%}file alternate outline + {%- elif mimetype.startswith("image/") -%}file image outline + {%- elif mimetype.startswith("video/") -%}film + {%- else -%}file outline{% endif %} +{%- endmacro %} + {% block entity_main %} <div class="ui stackable mobile reversed grid centered"> @@ -23,26 +38,64 @@ No known public URL, mirror, or archive for this File Set. {% endif %} +{% set fileset_vars = namespace(archiveorg_base=None, webarchiveorg_base=None) %} +{% for u in (entity.urls or []) %} + {% if u.rel in ["archive-base"] %} + {% set fileset_vars.archiveorg_base = u.url %} + {% elif u.rel in ["webarchive-base"] %} + {% set fileset_vars.webarchiveorg_base = u.url %} + {% endif %} +{% endfor %} + <h3>File Manifest ({{ fileset.manifest|count }})</h3> {% if fileset.manifest %} - <div class="ui celled list"> +<div style="overflow-x: auto;"> +<table class="ui compact single line table"> + <thead> + <tr> + <th class="collapsing"></th> + <th>Path</th> + <th>Type</th> + <th>Size</th> + <th class="collapsing"></th> + </tr> + </thead> + <tbody> {% for file in fileset.manifest %} - <div class="item"> - <div class="content"><code> - <div class="header"> - <i class="file outline icon"></i> {{ file.path }} ({{ file.size|filesizeformat }}{% if file.extra.mimetype %}, {{ file.extra.mimetype }}{% endif %}) - </div> - <div style="color: #666; margin-left: 1em;"><small> - {% if file.md5 %} md5:{{ file.md5 }}<br>{% endif %} - {% if file.sha1 %} sha1:{{ file.sha1 }}<br>{% endif %} - {% if file.sha256 %}sha256:{{ file.sha256 }}<br>{% endif %} + <tr> + <td><i class="{{ file_mimetype_icon(file.mimetype) }} icon" style="font-size: x-large;"></i></td> + <td> + <b><code>{{ file.path }}</code></b> + <br><div style="color: #666; margin-left: 0em;"><small> + {% if file.sha1 %} sha1:{{ file.sha1 }}<br> + {% elif file.sha256 %}sha256:{{ file.sha256 }}<br> + {% elif file.md5 %} md5:{{ file.md5 }}<br> + {% endif %} </small></div> - </code></div> - </div> + </td> + <td>{% if file.mimetype %}<code style="font-size: smaller;">{{ file.mimetype }}</code>{% endif %}</td> + <td>{{ file.size|filesizeformat }}</td> + <td> + {% if fileset_vars.archiveorg_base %} + <a href="{{ fileset_vars.archiveorg_base }}/{{ file.path }}">[archive.org]</a><br> + {% endif %} + {% if fileset_vars.webarchiveorg_base %} + <a href="{{ fileset_vars.webarchiveorg_base }}/{{ file.path }}">[web.archive.org]</a><br> + {% endif %} + {% if file.extra and file.extra.original_url %} + <a href="{{ file.extra.original_url }}">[platform]</a><br> + {% endif %} + {% if file.extra and file.extra.webarchive_url%} + <a href="{{ file.extra.webarchive_url }}">[web.archive.org]</a><br> + {% endif %} + </td> + </tr> {% endfor %} - </div> + </tbody> +</table> +</div> {% else %} -This File Set is empty (contains no files). +<p>This File Set is empty (contains no files). {% endif %} diff --git a/python/fatcat_web/templates/release_view.html b/python/fatcat_web/templates/release_view.html index f2e3f670..53ac3703 100644 --- a/python/fatcat_web/templates/release_view.html +++ b/python/fatcat_web/templates/release_view.html @@ -131,8 +131,9 @@ {% endif %} {% if entity.state == 'active' %} + +{% if entity.files != [] and entity.files != None %} <h3>Archived Files and Locations</h3> -{% if entity.files != [] %} <table class="ui compact fixed table"> <tbody> {% for file in entity.files %} @@ -151,15 +152,9 @@ {% endfor %} </tbody> </table> -{% else %} -<p>There are no accessible files associated with this release. You could check -<a href="/work/{{ release.work_id }}">other releases for this work</a> for an -accessible version. -{% endif %} {% endif %} -{% if entity.state == 'active' %} -{% if entity.filesets != [] %} +{% if entity.filesets != [] and entity.filesets != None %} <h3>File Sets</h3> <table class="ui compact fixed table"> <tbody> @@ -181,10 +176,8 @@ accessible version. </tbody> </table> {% endif %} -{% endif %} -{% if entity.state == 'active' %} -{% if entity.webcaptures != [] %} +{% if entity.webcaptures != [] and entity.webcaptures != None %} <h3>Web Captures</h3> <table class="ui single line compact fixed table"> <tbody> @@ -203,9 +196,17 @@ accessible version. </tbody> </table> {% endif %} + +{% if not (entity.files or entity.filesets or entity.webcaptures) %} +<h3>Archived Content</h3> +<p>There are no accessible files associated with this release. You could check +<a href="/work/{{ release.work_id }}">other releases for this work</a> for an +accessible version. +{% endif %} + {% endif %} -</div> +</div> <div class="column" style="flex: 0 0 24em;"> @@ -213,7 +214,7 @@ accessible version. <a href="{{ entity._es.ia_pdf_url }}" class="ui fluid huge black button" style="text-decoration: underline;"> <i class="file pdf outline icon"></i>Read Archived PDF </a> -{% elif entity.state == 'active' and entity.webcaptures != [] and entity.webcaptures[0].archive_urls != [] and entity.webcaptures[0].archive_urls[0].rel == "wayback" %} +{% elif entity.state == 'active' and entity.webcaptures != None and entity.webcaptures != [] and entity.webcaptures[0].archive_urls != [] and entity.webcaptures[0].archive_urls[0].rel == "wayback" %} <a href="{{ entity.webcaptures[0].archive_urls[0].url }}{{ entity.webcaptures[0]._wayback_suffix }}" class="ui fluid huge black button" style="text-decoration: underline;"> <i class="university icon"></i>Visit Web Archive </a> @@ -354,7 +355,7 @@ accessible version. #} {% endif %} {% if release.container._es.any_kbart == True %} - <i class="icon check green"></i> In <a href="https://keepers.issn.org/?q=api/search&search[]=MUST=allissn={{ release.container.issnl }}&search[]=MUST_EXIST=keepers">Keepers Registery</a><br> + <i class="icon check green"></i> In <a href="https://keepers.issn.org/?q=api/search&search[]=MUST=allissn={{ release.container.issnl }}&search[]=MUST_EXIST=keepers">Keepers Registry</a><br> {% elif release.container._es.any_kbart == False %} <i class="icon times grey"></i> Not in <a href="https://keepers.issn.org/?q=api/search&search[]=MUST=allissn={{ release.container.issnl }}&search[]=MUST_EXIST=keepers">Keepers Registry</a><br> {% endif %} {% endif %} diff --git a/python/tests/files/ISSN-to-ISSN-L.snip.txt b/python/tests/files/ISSN-to-ISSN-L.snip.txt index 2569c443..96cfb4c0 100644 --- a/python/tests/files/ISSN-to-ISSN-L.snip.txt +++ b/python/tests/files/ISSN-to-ISSN-L.snip.txt @@ -9,3 +9,4 @@ ISSN ISSN-L 0000-0108 0002-0108 0000-0140 0002-0140 1877-3273 1877-3273 +1234-5678 1234-5678 diff --git a/python/tests/files/example_doaj_articles.json b/python/tests/files/example_doaj_articles.json index 018a4800..5e018176 100644 --- a/python/tests/files/example_doaj_articles.json +++ b/python/tests/files/example_doaj_articles.json @@ -1,5 +1,5 @@ -{"last_updated":"2020-02-04T14:11:44Z","bibjson":{"identifier":[{"id":"0264-1275","type":"pissn"},{"id":"10.1016/j.matdes.2016.06.110","type":"DOI"}],"journal":{"volume":"108","number":"","country":"GB","license":[{"open_access":true,"title":"CC BY-NC-ND","type":"CC BY-NC-ND","url":"https://www.elsevier.com/journals/materials-and-design/0264-1275/open-access-journal"}],"issns":["0264-1275","1873-4197"],"publisher":"Elsevier","language":["EN"],"title":"Materials & Design"},"month":"10","end_page":"617","year":"2016","start_page":"608","subject":[{"code":"TA401-492","scheme":"LCC","term":"Materials of engineering and construction. Mechanics of materials"}],"author":[{"affiliation":"State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China","name":"Xinfeng Li"},{"affiliation":"Department of Geosciences, Center for Materials by Design, State University of New York, Stony Brook, NY 11794-2100, USA","name":"Jin Zhang"},{"affiliation":"School of Chemical Engineering & Technology, China University of Mining and Technology, Xuzhou 221116, China","name":"Yanfei Wang"},{"affiliation":"State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China","name":"Sicong Shen"},{"affiliation":"State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Corresponding author.","name":"Xiaolong Song"}],"link":[{"type":"fulltext","url":"http://www.sciencedirect.com/science/article/pii/S0264127516308723"}],"abstract":"The tensile properties and fracture behavior of PH 13-8 Mo steel after subjected to pre-charged hydrogen were investigated by slow strain rate tensile tests. The results suggest that hydrogen slightly increases yield strength, while decreases tensile strength. The susceptibility to hydrogen embrittlement of specimens aged at 650 °C firstly reduces and then increases as the aging time increases, reaching the lowest value at aging time 4 h. This is dominantly attributed to the highest content of austenite. Moreover, hydrogen-induced crack nucleation sites initiate from lath, packet and prior austenite grain boundaries. Crack propagation passes through lath boundaries and walks along packet, prior austenite grain boundaries. Scanning electron microscopy result indicates that hydrogen-charged specimens show quasi-cleavage fracture and intergranular fracture in annular brittle zone while dimple fracture is observed in hydrogen-free specimens. Keywords: Hydrogen embrittlement, PH 13-8 Mo steel, Aging time, Fracture behavior","title":"Effect of hydrogen on tensile properties and fracture behavior of PH 13-8 Mo steel"},"created_date":"2019-06-05T05:25:15Z","id":"e58f08a11ecb495ead55a44ad4f89808"} -{"last_updated":"2020-02-04T08:06:42Z","bibjson":{"identifier":[{"id":"2072-6694","type":"eissn"},{"id":"10.3390/cancers9080107","type":"doi"}],"journal":{"volume":"9","number":"8","country":"CH","license":[{"open_access":true,"title":"CC BY","type":"CC BY","url":"http://www.mdpi.com/journal/cancers/about"}],"issns":["2072-6694"],"publisher":"MDPI AG","language":["EN"],"title":"Cancers"},"month":"8","keywords":["ALK rearrangement, lung cancer, biology, immunohistochemistry, FISH, molecular biology."],"year":"2017","start_page":"107","subject":[{"code":"RC254-282","scheme":"LCC","term":"Neoplasms. Tumors. Oncology. Including cancer and carcinogens"}],"author":[{"affiliation":"Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, 30 avenue de la voie romaine, 06001 Nice cedex 01, France","name":"Paul Hofman"}],"link":[{"content_type":"pdf","type":"fulltext","url":"https://www.mdpi.com/2072-6694/9/8/107"}],"abstract":"Patients with advanced-stage non-small cell lung carcinoma (NSCLC) harboring an ALK rearrangement, detected from a tissue sample, can benefit from targeted ALK inhibitor treatment. Several increasingly effective ALK inhibitors are now available for treatment of patients. However, despite an initial favorable response to treatment, in most cases relapse or progression occurs due to resistance mechanisms mainly caused by mutations in the tyrosine kinase domain of ALK. The detection of an ALK rearrangement is pivotal and can be done using different methods, which have variable sensitivity and specificity depending, in particular, on the quality and quantity of the patient’s sample. This review will first highlight briefly some information regarding the pathobiology of an ALK rearrangement and the epidemiology of patients harboring this genomic alteration. The different methods used to detect an ALK rearrangement as well as their advantages and disadvantages will then be examined and algorithms proposed for detection in daily routine practice.","title":"ALK in Non-Small Cell Lung Cancer (NSCLC) Pathobiology, Epidemiology, Detection from Tumor Tissue and Algorithm Diagnosis in a Daily Practice"},"admin":{"seal":true},"created_date":"2018-10-26T07:49:34Z","id":"937c7aa790e048d4ae5f53a2ad71f0dc"} -{"last_updated":"2020-02-04T13:43:13Z","bibjson":{"identifier":[{"id":"1178-2013","type":"pissn"}],"end_page":"818","keywords":["bioconjugation","biosurfactant","cancer therapy","folic acid receptor","graphene quantum dots","theranostic tool"],"year":"2019","subject":[{"code":"R5-920","scheme":"LCC","term":"Medicine (General)"}],"author":[{"name":"Bansal S"},{"name":"Singh J"},{"name":"Kumari U"},{"name":"Kaur IP"},{"name":"Barnwal RP"},{"name":"Kumar R"},{"name":"Singh S"},{"name":"Singh G"},{"name":"Chatterjee M"}],"link":[{"content_type":"html","type":"fulltext","url":"https://www.dovepress.com/development-of-biosurfactant-based-graphene-quantum-dot-conjugate-as-a-peer-reviewed-article-IJN"}],"abstract":"Smriti Bansal,1 Joga Singh,2 Uma Kumari,3 Indu Pal Kaur,2 Ravi Pratap Barnwal,4 Ravinder Kumar,3 Suman Singh,5 Gurpal Singh,2 Mary Chatterjee1 1Biotechnology Engineering, University Institute of Engineering & Technology, Panjab University, Chandigarh, India; 2Department of Pharmaceutical Sciences, University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India; 3Department of Zoology, Panjab University, Chandigarh, India; 4Department of Biophysics, Panjab University, Chandigarh, India; 5Department of Agronomics, Central Scientific Instruments Organisation, Chandigarh, India Background: Biosurfactants are amphipathic molecules of microbial origin that reduce surface and interfacial tension at gas–liquid–solid interfaces. Earlier, the biosurfactant was isolated and characterized in our laboratory from Candida parapsilosis. The property of the biosurfactant is further explored in this study by using quantum dots (QDs) as nanocarrier.Materials and methods: Graphene quantum dots (GQDs) were synthesized by bottom-up approach through pyrolysis of citric acid. GQDs were conjugated with both biosurfactant and folic acid (FA) using carbodiimide chemistry. The prepared GQD bioconjugate was studied for diagnostic and therapeutic effects against cancer cells.Results and discussion: Photoluminescence quantum yield (QY) of plain GQDs was measured as 12.8%. QY for biosurfactant conjugated GQDs and FA-biosurfactant conjugated GQDs was measured as 10.4% and 9.02%, respectively, and it was sufficient for targeting cancer cells. MTT assay showed that more than 90% of cells remained viable at concentration of 1 mg/mL, hence GQDs seemed to be non-toxic to cells. Biosurfactant conjugated GQDs caused 50% reduction in cellular viability within 24 hours. FA conjugation further increased the specificity of bioconjugated GQDs toward tumor cells, which is clearly evident from the drug internalization studies using confocal laser scanning microscopy. A higher amount of drug uptake was observed when bioconjugated GQDs were decorated with FA.Conclusion: The ability of GQD bioconjugate could be used as a theranostic tool for cancer. It is foreseen that in near future cancer can be detected and/or treated at an early stage by utilizing biosurfactant conjugated GQDs. Therefore, the proposed study would provide a stepping stone to improve the life of cancer patients. Keywords: bioconjugation, nanomedicine, nanocarrier, cancer therapy, folic acid receptor, graphene quantum dots","title":"Development of biosurfactant-based graphene quantum dot conjugate as a novel and fluorescent theranostic tool for cancer","journal":{"volume":"Volume 14","country":"GB","license":[{"open_access":true,"title":"CC BY-NC","type":"CC BY-NC","url":"https://www.dovepress.com/author_guidelines.php?content_id=695"}],"issns":["1176-9114","1178-2013"],"publisher":"Dove Medical Press","language":["EN"],"title":"International Journal of Nanomedicine"},"month":"1","start_page":"809"},"created_date":"2019-01-29T18:43:40Z","id":"e0173c80437f4fb88ec4e02e453e13b0"} -{"last_updated":"2020-02-04T09:46:14Z","bibjson":{"identifier":[{"id":"1424-8220","type":"eissn"},{"id":"10.3390/s18124467","type":"doi"}],"journal":{"volume":"18","number":"12","country":"CH","license":[{"open_access":true,"title":"CC BY","type":"CC BY","url":"http://www.mdpi.com/journal/sensors/about"}],"issns":["1424-8220"],"publisher":"MDPI AG","language":["EN"],"title":"Sensors"},"month":"12","keywords":["multilayer sea ice temperature","low temperature","design","performance analysis"],"year":"2018","start_page":"4467","subject":[{"code":"TP1-1185","scheme":"LCC","term":"Chemical technology"}],"author":[{"affiliation":"College of Electrical and Power Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Guangyu Zuo"},{"affiliation":"College of Electrical and Power Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Yinke Dou"},{"affiliation":"College of Water Resources Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Xiaomin Chang"},{"affiliation":"College of Electrical and Power Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Yan Chen"},{"affiliation":"College of Electrical and Power Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Chunyan Ma"}],"link":[{"content_type":"pdf","type":"fulltext","url":"https://www.mdpi.com/1424-8220/18/12/4467"}],"abstract":"Temperature profiles of sea ice have been recorded more than a few decades. However, few high-precision temperature sensors can complete the observation of temperature profile of sea ice, especially in extreme environments. At present, the most widely used sea ice observation instruments can reach an accuracy of sea ice temperature measurement of 0.1 °C. In this study, a multilayer sea ice temperature sensor is developed with temperature measurement accuracy from −0.0047 °C to 0.0059 °C. The sensor system composition, structure of the thermistor string, and work mode are analyzed. The performance of the sensor system is evaluated from −50 °C to 30 °C. The temperature dependence of the constant current source, the amplification circuit, and the analog-to-digital converter (ADC) circuit are comprehensive tested and quantified. A temperature correction algorithm is designed to correct any deviation in the sensor system. A sea-ice thickness discrimination algorithm is proposed in charge of determining the thickness of sea ice automatically. The sensor system was field tested in Wuliangsuhai, Yellow River on 31 January 2018 and the second reservoir of Fen River, Yellow River on 30 January 2018. The integral practicality of this sensor system is identified and examined. The multilayer sea ice temperature sensor will provide good temperature results of sea ice and maintain stable performance in the low ambient temperature.","title":"Design and Performance Analysis of a Multilayer Sea Ice Temperature Sensor Used in Polar Region"},"admin":{"seal":true},"created_date":"2018-12-18T08:13:29Z","id":"152f83d12b9f477696e681684ba696e7"} -{"last_updated":"2020-06-02T23:02:32Z","bibjson":{"identifier":[{"id":"10.123/abc","type":"doi"},{"id":"2076-3417","type":"eissn"}],"journal":{"volume":"10","number":"3872","country":"CH","license":[{"open_access":true,"title":"CC BY","type":"CC BY","url":"http://www.mdpi.com/about/openaccess"}],"issns":["2076-3417"],"publisher":"MDPI AG","language":["EN"],"title":"Applied Sciences"},"month":"06","keywords":["Smart parking systems","survey","vehicle routing problem","vehicle detection techniques","routing algorithms"],"year":"2020","start_page":"3872","subject":[{"code":"T","scheme":"LCC","term":"Technology"},{"code":"TA1-2040","scheme":"LCC","term":"Engineering (General). Civil engineering (General)"},{"code":"QH301-705.5","scheme":"LCC","term":"Biology (General)"},{"code":"QC1-999","scheme":"LCC","term":"Physics"},{"code":"QD1-999","scheme":"LCC","term":"Chemistry"}],"author":[{"affiliation":"Institute of Computer Science. Faculty of Exact, Physical and Natural Sciences. National University of San Juan, 5400 San Juan, Argentina","name":"Mathias Gabriel Diaz OgĂ¡s"},{"affiliation":"Institute of Informatics and Applications. University of Girona, 17003 Girona, Spain","name":"Ramon Fabregat"},{"affiliation":"Institute of Computer Science. Faculty of Exact, Physical and Natural Sciences. National University of San Juan, 5400 San Juan, Argentina","name":"Silvana Aciar"}],"link":[{"content_type":"text/html","type":"fulltext","url":"https://www.mdpi.com/2076-3417/10/11/3872"}],"abstract":"The large number of vehicles constantly seeking access to congested areas in cities means that finding a public parking place is often difficult and causes problems for drivers and citizens alike. In this context, strategies that guide vehicles from one point to another, looking for the most optimal path, are needed. Most contributions in the literature are routing strategies that take into account different criteria to select the optimal route required to find a parking space. This paper aims to identify the types of smart parking systems (SPS) that are available today, as well as investigate the kinds of vehicle detection techniques (VDT) they have and the algorithms or other methods they employ, in order to analyze where the development of these systems is at today. To do this, a survey of 274 publications from January 2012 to December 2019 was conducted. The survey considered four principal features: SPS types reported in the literature, the kinds of VDT used in these SPS, the algorithms or methods they implement, and the stage of development at which they are. Based on a search and extraction of results methodology, this work was able to effectively obtain the current state of the research area. In addition, the exhaustive study of the studies analyzed allowed for a discussion to be established concerning the main difficulties, as well as the gaps and open problems detected for the SPS. The results shown in this study may provide a base for future research on the subject.","title":"Survey of Smart Parking Systems"},"admin":{"seal":true},"id":"9cf511bab39445ba9745feb43d7493dd","created_date":"2020-06-03T00:02:28Z"} +{"last_updated":"2020-02-04T14:11:44Z","bibjson":{"identifier":[{"id":"0264-1275","type":"pissn"},{"id":"10.1016/j.matdes.2016.06.110","type":"DOI"}],"journal":{"volume":"108","number":"","country":"GB","license":[{"open_access":true,"title":"CC BY-NC-ND","type":"CC BY-NC-ND","url":"https://www.elsevier.com/journals/materials-and-design/0264-1275/open-access-journal"}],"issns":["1234-5678","0264-1275","1873-4197"],"publisher":"Elsevier","language":["EN"],"title":"Materials & Design"},"month":"10","end_page":"617","year":"2016","start_page":"608","subject":[{"code":"TA401-492","scheme":"LCC","term":"Materials of engineering and construction. Mechanics of materials"}],"author":[{"affiliation":"State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China","name":"Xinfeng Li"},{"affiliation":"Department of Geosciences, Center for Materials by Design, State University of New York, Stony Brook, NY 11794-2100, USA","name":"Jin Zhang"},{"affiliation":"School of Chemical Engineering & Technology, China University of Mining and Technology, Xuzhou 221116, China","name":"Yanfei Wang"},{"affiliation":"State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China","name":"Sicong Shen"},{"affiliation":"State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Corresponding author.","name":"Xiaolong Song"}],"link":[{"type":"fulltext","url":"http://www.sciencedirect.com/science/article/pii/S0264127516308723"}],"abstract":"The tensile properties and fracture behavior of PH 13-8 Mo steel after subjected to pre-charged hydrogen were investigated by slow strain rate tensile tests. The results suggest that hydrogen slightly increases yield strength, while decreases tensile strength. The susceptibility to hydrogen embrittlement of specimens aged at 650 °C firstly reduces and then increases as the aging time increases, reaching the lowest value at aging time 4 h. This is dominantly attributed to the highest content of austenite. Moreover, hydrogen-induced crack nucleation sites initiate from lath, packet and prior austenite grain boundaries. Crack propagation passes through lath boundaries and walks along packet, prior austenite grain boundaries. Scanning electron microscopy result indicates that hydrogen-charged specimens show quasi-cleavage fracture and intergranular fracture in annular brittle zone while dimple fracture is observed in hydrogen-free specimens. Keywords: Hydrogen embrittlement, PH 13-8 Mo steel, Aging time, Fracture behavior","title":"Effect of hydrogen on tensile properties and fracture behavior of PH 13-8 Mo steel"},"created_date":"2019-06-05T05:25:15Z","id":"e58f08a11ecb495ead55a44ad4f89808"} +{"last_updated":"2020-02-04T08:06:42Z","bibjson":{"identifier":[{"id":"2072-6694","type":"eissn"},{"id":"10.3390/cancers9080107","type":"doi"}],"journal":{"volume":"9","number":"8","country":"CH","license":[{"open_access":true,"title":"CC BY","type":"CC BY","url":"http://www.mdpi.com/journal/cancers/about"}],"issns":["1234-5678","2072-6694"],"publisher":"MDPI AG","language":["EN"],"title":"Cancers"},"month":"8","keywords":["ALK rearrangement, lung cancer, biology, immunohistochemistry, FISH, molecular biology."],"year":"2017","start_page":"107","subject":[{"code":"RC254-282","scheme":"LCC","term":"Neoplasms. Tumors. Oncology. Including cancer and carcinogens"}],"author":[{"affiliation":"Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, 30 avenue de la voie romaine, 06001 Nice cedex 01, France","name":"Paul Hofman"}],"link":[{"content_type":"pdf","type":"fulltext","url":"https://www.mdpi.com/2072-6694/9/8/107"}],"abstract":"Patients with advanced-stage non-small cell lung carcinoma (NSCLC) harboring an ALK rearrangement, detected from a tissue sample, can benefit from targeted ALK inhibitor treatment. Several increasingly effective ALK inhibitors are now available for treatment of patients. However, despite an initial favorable response to treatment, in most cases relapse or progression occurs due to resistance mechanisms mainly caused by mutations in the tyrosine kinase domain of ALK. The detection of an ALK rearrangement is pivotal and can be done using different methods, which have variable sensitivity and specificity depending, in particular, on the quality and quantity of the patient’s sample. This review will first highlight briefly some information regarding the pathobiology of an ALK rearrangement and the epidemiology of patients harboring this genomic alteration. The different methods used to detect an ALK rearrangement as well as their advantages and disadvantages will then be examined and algorithms proposed for detection in daily routine practice.","title":"ALK in Non-Small Cell Lung Cancer (NSCLC) Pathobiology, Epidemiology, Detection from Tumor Tissue and Algorithm Diagnosis in a Daily Practice"},"admin":{"seal":true},"created_date":"2018-10-26T07:49:34Z","id":"937c7aa790e048d4ae5f53a2ad71f0dc"} +{"last_updated":"2020-02-04T13:43:13Z","bibjson":{"identifier":[{"id":"1178-2013","type":"pissn"}],"end_page":"818","keywords":["bioconjugation","biosurfactant","cancer therapy","folic acid receptor","graphene quantum dots","theranostic tool"],"year":"2019","subject":[{"code":"R5-920","scheme":"LCC","term":"Medicine (General)"}],"author":[{"name":"Bansal S"},{"name":"Singh J"},{"name":"Kumari U"},{"name":"Kaur IP"},{"name":"Barnwal RP"},{"name":"Kumar R"},{"name":"Singh S"},{"name":"Singh G"},{"name":"Chatterjee M"}],"link":[{"content_type":"html","type":"fulltext","url":"https://www.dovepress.com/development-of-biosurfactant-based-graphene-quantum-dot-conjugate-as-a-peer-reviewed-article-IJN"}],"abstract":"Smriti Bansal,1 Joga Singh,2 Uma Kumari,3 Indu Pal Kaur,2 Ravi Pratap Barnwal,4 Ravinder Kumar,3 Suman Singh,5 Gurpal Singh,2 Mary Chatterjee1 1Biotechnology Engineering, University Institute of Engineering & Technology, Panjab University, Chandigarh, India; 2Department of Pharmaceutical Sciences, University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India; 3Department of Zoology, Panjab University, Chandigarh, India; 4Department of Biophysics, Panjab University, Chandigarh, India; 5Department of Agronomics, Central Scientific Instruments Organisation, Chandigarh, India Background: Biosurfactants are amphipathic molecules of microbial origin that reduce surface and interfacial tension at gas–liquid–solid interfaces. Earlier, the biosurfactant was isolated and characterized in our laboratory from Candida parapsilosis. The property of the biosurfactant is further explored in this study by using quantum dots (QDs) as nanocarrier.Materials and methods: Graphene quantum dots (GQDs) were synthesized by bottom-up approach through pyrolysis of citric acid. GQDs were conjugated with both biosurfactant and folic acid (FA) using carbodiimide chemistry. The prepared GQD bioconjugate was studied for diagnostic and therapeutic effects against cancer cells.Results and discussion: Photoluminescence quantum yield (QY) of plain GQDs was measured as 12.8%. QY for biosurfactant conjugated GQDs and FA-biosurfactant conjugated GQDs was measured as 10.4% and 9.02%, respectively, and it was sufficient for targeting cancer cells. MTT assay showed that more than 90% of cells remained viable at concentration of 1 mg/mL, hence GQDs seemed to be non-toxic to cells. Biosurfactant conjugated GQDs caused 50% reduction in cellular viability within 24 hours. FA conjugation further increased the specificity of bioconjugated GQDs toward tumor cells, which is clearly evident from the drug internalization studies using confocal laser scanning microscopy. A higher amount of drug uptake was observed when bioconjugated GQDs were decorated with FA.Conclusion: The ability of GQD bioconjugate could be used as a theranostic tool for cancer. It is foreseen that in near future cancer can be detected and/or treated at an early stage by utilizing biosurfactant conjugated GQDs. Therefore, the proposed study would provide a stepping stone to improve the life of cancer patients. Keywords: bioconjugation, nanomedicine, nanocarrier, cancer therapy, folic acid receptor, graphene quantum dots","title":"Development of biosurfactant-based graphene quantum dot conjugate as a novel and fluorescent theranostic tool for cancer","journal":{"volume":"Volume 14","country":"GB","license":[{"open_access":true,"title":"CC BY-NC","type":"CC BY-NC","url":"https://www.dovepress.com/author_guidelines.php?content_id=695"}],"issns":["1234-5678","1176-9114","1178-2013"],"publisher":"Dove Medical Press","language":["EN"],"title":"International Journal of Nanomedicine"},"month":"1","start_page":"809"},"created_date":"2019-01-29T18:43:40Z","id":"e0173c80437f4fb88ec4e02e453e13b0"} +{"last_updated":"2020-02-04T09:46:14Z","bibjson":{"identifier":[{"id":"1424-8220","type":"eissn"},{"id":"10.3390/s18124467","type":"doi"}],"journal":{"volume":"18","number":"12","country":"CH","license":[{"open_access":true,"title":"CC BY","type":"CC BY","url":"http://www.mdpi.com/journal/sensors/about"}],"issns":["1234-5678","1424-8220"],"publisher":"MDPI AG","language":["EN"],"title":"Sensors"},"month":"12","keywords":["multilayer sea ice temperature","low temperature","design","performance analysis"],"year":"2018","start_page":"4467","subject":[{"code":"TP1-1185","scheme":"LCC","term":"Chemical technology"}],"author":[{"affiliation":"College of Electrical and Power Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Guangyu Zuo"},{"affiliation":"College of Electrical and Power Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Yinke Dou"},{"affiliation":"College of Water Resources Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Xiaomin Chang"},{"affiliation":"College of Electrical and Power Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Yan Chen"},{"affiliation":"College of Electrical and Power Engineering, Taiyuan University of Technology, Taiyuan 030024, China","name":"Chunyan Ma"}],"link":[{"content_type":"pdf","type":"fulltext","url":"https://www.mdpi.com/1424-8220/18/12/4467"}],"abstract":"Temperature profiles of sea ice have been recorded more than a few decades. However, few high-precision temperature sensors can complete the observation of temperature profile of sea ice, especially in extreme environments. At present, the most widely used sea ice observation instruments can reach an accuracy of sea ice temperature measurement of 0.1 °C. In this study, a multilayer sea ice temperature sensor is developed with temperature measurement accuracy from −0.0047 °C to 0.0059 °C. The sensor system composition, structure of the thermistor string, and work mode are analyzed. The performance of the sensor system is evaluated from −50 °C to 30 °C. The temperature dependence of the constant current source, the amplification circuit, and the analog-to-digital converter (ADC) circuit are comprehensive tested and quantified. A temperature correction algorithm is designed to correct any deviation in the sensor system. A sea-ice thickness discrimination algorithm is proposed in charge of determining the thickness of sea ice automatically. The sensor system was field tested in Wuliangsuhai, Yellow River on 31 January 2018 and the second reservoir of Fen River, Yellow River on 30 January 2018. The integral practicality of this sensor system is identified and examined. The multilayer sea ice temperature sensor will provide good temperature results of sea ice and maintain stable performance in the low ambient temperature.","title":"Design and Performance Analysis of a Multilayer Sea Ice Temperature Sensor Used in Polar Region"},"admin":{"seal":true},"created_date":"2018-12-18T08:13:29Z","id":"152f83d12b9f477696e681684ba696e7"} +{"last_updated":"2020-06-02T23:02:32Z","bibjson":{"identifier":[{"id":"10.123/abc","type":"doi"},{"id":"2076-3417","type":"eissn"}],"journal":{"volume":"10","number":"3872","country":"CH","license":[{"open_access":true,"title":"CC BY","type":"CC BY","url":"http://www.mdpi.com/about/openaccess"}],"issns":["1234-5678","2076-3417"],"publisher":"MDPI AG","language":["EN"],"title":"Applied Sciences"},"month":"06","keywords":["Smart parking systems","survey","vehicle routing problem","vehicle detection techniques","routing algorithms"],"year":"2020","start_page":"3872","subject":[{"code":"T","scheme":"LCC","term":"Technology"},{"code":"TA1-2040","scheme":"LCC","term":"Engineering (General). Civil engineering (General)"},{"code":"QH301-705.5","scheme":"LCC","term":"Biology (General)"},{"code":"QC1-999","scheme":"LCC","term":"Physics"},{"code":"QD1-999","scheme":"LCC","term":"Chemistry"}],"author":[{"affiliation":"Institute of Computer Science. Faculty of Exact, Physical and Natural Sciences. National University of San Juan, 5400 San Juan, Argentina","name":"Mathias Gabriel Diaz OgĂ¡s"},{"affiliation":"Institute of Informatics and Applications. University of Girona, 17003 Girona, Spain","name":"Ramon Fabregat"},{"affiliation":"Institute of Computer Science. Faculty of Exact, Physical and Natural Sciences. National University of San Juan, 5400 San Juan, Argentina","name":"Silvana Aciar"}],"link":[{"content_type":"text/html","type":"fulltext","url":"https://www.mdpi.com/2076-3417/10/11/3872"}],"abstract":"The large number of vehicles constantly seeking access to congested areas in cities means that finding a public parking place is often difficult and causes problems for drivers and citizens alike. In this context, strategies that guide vehicles from one point to another, looking for the most optimal path, are needed. Most contributions in the literature are routing strategies that take into account different criteria to select the optimal route required to find a parking space. This paper aims to identify the types of smart parking systems (SPS) that are available today, as well as investigate the kinds of vehicle detection techniques (VDT) they have and the algorithms or other methods they employ, in order to analyze where the development of these systems is at today. To do this, a survey of 274 publications from January 2012 to December 2019 was conducted. The survey considered four principal features: SPS types reported in the literature, the kinds of VDT used in these SPS, the algorithms or methods they implement, and the stage of development at which they are. Based on a search and extraction of results methodology, this work was able to effectively obtain the current state of the research area. In addition, the exhaustive study of the studies analyzed allowed for a discussion to be established concerning the main difficulties, as well as the gaps and open problems detected for the SPS. The results shown in this study may provide a base for future research on the subject.","title":"Survey of Smart Parking Systems"},"admin":{"seal":true},"id":"9cf511bab39445ba9745feb43d7493dd","created_date":"2020-06-03T00:02:28Z"} diff --git a/python/tests/files/example_fileset_file_ingest_result.json b/python/tests/files/example_fileset_file_ingest_result.json new file mode 100644 index 00000000..94ae4cc6 --- /dev/null +++ b/python/tests/files/example_fileset_file_ingest_result.json @@ -0,0 +1,20 @@ 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Thyroid surgery has been considered as a risk factor for the management of difficult airway. Method: We review the relevant literature related to the difficult airway and thyroid surgery. Comments: Endothoracic goiter, deformity of the airway, compression of the airway and thyroid cancer do not appear to have an influence on the difficulty for intubation. Classical parameters have a better predictive value: mouth opening less than 35 mm, Mallampati II-IV, short neck, neck movility less than 80 degrees, thyromental distance less than 60 mm, retrognathia, Cormack index III-IV, macroglossia, inability to protude the teeth and body mass index (BMI) greater than 35 Kg/m2. Conclusions: According to the literature, thyroid disease does not increase the risk for a difficult airway (ventilation / intubation). The risk of an unexpected difficult airway (false negative) cannot be eliminated. 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diff --git a/python/tests/import_doaj.py b/python/tests/import_doaj.py index 9c4ba552..81f17d7c 100644 --- a/python/tests/import_doaj.py +++ b/python/tests/import_doaj.py @@ -144,8 +144,7 @@ def test_doaj_dict_parse(doaj_importer): assert r.pages == "608-617" assert r.version is None assert r.language == "en" - # matched by ISSN, so wouldn't be defined normally - assert r.extra["container_name"] == "Materials & Design" + assert r.container_id assert len(r.abstracts) == 1 assert len(r.abstracts[0].content) == 1033 assert len(r.contribs) == 5 diff --git a/python/tests/import_ingest.py b/python/tests/import_ingest.py index d9e7d294..65549d1d 100644 --- a/python/tests/import_ingest.py +++ b/python/tests/import_ingest.py @@ -5,6 +5,8 @@ from fixtures import * from fatcat_tools.importers import ( IngestFileResultImporter, + IngestFilesetFileResultImporter, + IngestFilesetResultImporter, IngestWebResultImporter, JsonLinePusher, ) @@ -20,6 +22,16 @@ def ingest_web_importer(api): yield IngestWebResultImporter(api) +@pytest.fixture(scope="function") +def ingest_fileset_importer(api): + yield IngestFilesetResultImporter(api) + + +@pytest.fixture(scope="function") +def ingest_fileset_file_importer(api): + yield IngestFilesetFileResultImporter(api) + + # TODO: use API to check that entities actually created... def test_ingest_importer_basic(ingest_importer): with open("tests/files/example_ingest.json", "r") as f: @@ -58,7 +70,6 @@ def test_ingest_importer_xml(ingest_importer): with open("tests/files/example_ingest_xml.json", "r") as f: ingest_importer.bezerk_mode = True counts = JsonLinePusher(ingest_importer, f).run() - print(counts) assert counts["insert"] == 1 assert counts["exists"] == 0 assert counts["skip"] == 0 @@ -86,7 +97,6 @@ def test_ingest_importer_web(ingest_web_importer): with open("tests/files/example_ingest_html.json", "r") as f: ingest_web_importer.bezerk_mode = True counts = JsonLinePusher(ingest_web_importer, f).run() - print(counts) assert counts["insert"] == 1 assert counts["exists"] == 0 assert counts["skip"] == 0 @@ -139,7 +149,6 @@ def test_ingest_importer_stage(ingest_importer, api): ingest_importer.reset() ingest_importer.push_record(raw) counts = ingest_importer.finish() - print(counts) assert counts["total"] == 1 assert counts[row["status"]] == 1 @@ -182,3 +191,118 @@ def test_ingest_dict_parse_old(ingest_importer): if u.rel == "webarchive": assert u.url.startswith("https://web.archive.org/") assert len(f.release_ids) == 1 + + +def test_ingest_fileset_dict_parse(ingest_fileset_importer): + with open("tests/files/example_fileset_ingest_result.json", "r") as f: + raw = json.loads(f.readline()) + fs = ingest_fileset_importer.parse_record(raw) + assert len(fs.manifest) == 3 + assert fs.manifest[0].sha1 == "c0669e84e7b9052cc0f342e8ce7d31d59956326a" + assert fs.manifest[0].md5 == "caf4d9fc2c6ebd0d9251ac84e0b6b006" + assert fs.manifest[0].mimetype == "application/x-hdf" + assert fs.manifest[0].size == 16799750 + assert fs.manifest[0].path == "N2 on food R_2010_03_25__10_53_27___4___1_features.hdf5" + assert ( + fs.manifest[0].extra["original_url"] + == "https://zenodo.org/api/files/563203f6-6de5-46d9-b305-ba42604f2508/N2%20on%20food%20R_2010_03_25__10_53_27___4___1_features.hdf5" + ) + assert len(fs.urls) == 2 + matched = 0 + for u in fs.urls: + if u.rel == "web": + assert u.url == "https://zenodo.org/record/1028059" + matched += 1 + if u.rel == "archive-base": + assert u.url == "https://archive.org/download/zenodo.org-1028059/" + matched += 1 + assert matched == 2 + assert len(fs.release_ids) == 1 + + +def test_ingest_fileset_importer(ingest_fileset_importer): + last_index = ingest_fileset_importer.api.get_changelog(limit=1)[0].index + with open("tests/files/example_fileset_ingest_result.json", "r") as f: + ingest_fileset_importer.bezerk_mode = True + counts = JsonLinePusher(ingest_fileset_importer, f).run() + assert counts["insert"] == 7 + assert counts["exists"] == 0 + assert counts["skip"] == 13 + assert counts["skip-release-not-found"] == 13 + + # fetch most recent editgroup + change = ingest_fileset_importer.api.get_changelog_entry(index=last_index + 1) + eg = change.editgroup + assert eg.description + assert "filesets crawled from web" in eg.description.lower() + assert eg.extra["git_rev"] + assert "fatcat_tools.IngestFilesetResultImporter" in eg.extra["agent"] + + # re-insert; should skip + with open("tests/files/example_fileset_ingest_result.json", "r") as f: + ingest_fileset_importer.reset() + ingest_fileset_importer.bezerk_mode = False + counts = JsonLinePusher(ingest_fileset_importer, f).run() + + assert counts["insert"] == 0 + assert counts["exists"] == 7 + assert counts["skip"] == 13 + assert counts["skip-release-not-found"] == 13 + + +def test_ingest_fileset_file_dict_parse(ingest_fileset_file_importer): + with open("tests/files/example_fileset_file_ingest_result.json", "r") as f: + raw = json.loads(f.readline()) + fe = ingest_fileset_file_importer.parse_record(raw) + assert fe.sha1 == "6fb020064da66bb7a666c17555611cf6820fc9ae" + assert fe.md5 == "dfc41b617564f99a12e6077a6208876f" + assert fe.sha256 == "2febad53ff0f163a18d7cbb913275bf99ed2544730cda191458837e2b0da9d18" + assert fe.mimetype == "image/tiff" + assert fe.size == 410631015 + assert fe.extra["path"] == "NDVI_Diff_1990_2018_T06.tif" + assert len(fe.urls) == 2 + matched = 0 + for u in fe.urls: + if u.rel == "web": + assert u.url == "https://ndownloader.figshare.com/files/14460875" + matched += 1 + if u.rel == "archive": + assert ( + u.url + == "https://archive.org/download/springernature.figshare.com-7767695-v1/NDVI_Diff_1990_2018_T06.tif" + ) + matched += 1 + assert matched == 2 + assert len(fe.release_ids) == 1 + + +def test_ingest_fileset_file_importer(ingest_fileset_file_importer): + """ + Similar to the above, but specifically tests 'file'/'success-file' import pathway + """ + last_index = ingest_fileset_file_importer.api.get_changelog(limit=1)[0].index + with open("tests/files/example_fileset_file_ingest_result.json", "r") as f: + ingest_fileset_file_importer.bezerk_mode = True + counts = JsonLinePusher(ingest_fileset_file_importer, f).run() + assert counts["insert"] == 16 + assert counts["exists"] == 0 + assert counts["skip"] == 4 + assert counts["skip-bad-hashes"] == 4 + + # fetch most recent editgroup + change = ingest_fileset_file_importer.api.get_changelog_entry(index=last_index + 1) + eg = change.editgroup + assert eg.description + assert "crawled from web" in eg.description.lower() + assert eg.extra["git_rev"] + assert "fatcat_tools.IngestFilesetFileResultImporter" in eg.extra["agent"] + + # re-insert; should skip + with open("tests/files/example_fileset_file_ingest_result.json", "r") as f: + ingest_fileset_file_importer.reset() + ingest_fileset_file_importer.bezerk_mode = False + counts = JsonLinePusher(ingest_fileset_file_importer, f).run() + assert counts["insert"] == 0 + assert counts["exists"] == 16 + assert counts["skip"] == 4 + assert counts["skip-bad-hashes"] == 4 diff --git a/python/tests/web_citation_csl.py b/python/tests/web_citation_csl.py index e3dbec2b..9dfe94f6 100644 --- a/python/tests/web_citation_csl.py +++ b/python/tests/web_citation_csl.py @@ -54,8 +54,8 @@ def test_release_bibtex(app, api): rv = app.get("/release/{}".format(r1edit.ident)) assert rv.status_code == 200 assert b"BibTeX" not in rv.data - with pytest.raises(ValueError): - rv = app.get("/release/{}.bib".format(r1edit.ident)) + rv = app.get("/release/{}.bib".format(r1edit.ident)) + assert rv.status_code == 400 # create release can have citeproc run on it (no authors) eg = quick_eg(api) |