qlever 0.5.2__py3-none-any.whl → 0.5.3__py3-none-any.whl

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Files changed (10) hide show
  1. qlever/Qleverfiles/Qleverfile.dblp +3 -3
  2. qlever/Qleverfiles/Qleverfile.pubchem +1 -1
  3. qlever/Qleverfiles/Qleverfile.uniprot +16 -15
  4. qlever/Qleverfiles/Qleverfile.wikidata +14 -11
  5. {qlever-0.5.2.dist-info → qlever-0.5.3.dist-info}/METADATA +1 -1
  6. {qlever-0.5.2.dist-info → qlever-0.5.3.dist-info}/RECORD +10 -10
  7. {qlever-0.5.2.dist-info → qlever-0.5.3.dist-info}/WHEEL +1 -1
  8. {qlever-0.5.2.dist-info → qlever-0.5.3.dist-info}/LICENSE +0 -0
  9. {qlever-0.5.2.dist-info → qlever-0.5.3.dist-info}/entry_points.txt +0 -0
  10. {qlever-0.5.2.dist-info → qlever-0.5.3.dist-info}/top_level.txt +0 -0
qlever/Qleverfiles/Qleverfile.dblp CHANGED
@@ -6,8 +6,8 @@
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  [data]
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  NAME = dblp
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- GET_DATA_URL = https://dblp.org/rdf/${index:INPUT_FILES}
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- GET_DATA_CMD = curl -LRC - O ${GET_DATA_URL} 2>&1 | tee ${data:NAME}.download-log.txt
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+ GET_DATA_URL = https://dblp.org/rdf/dblp.ttl.gz
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+ GET_DATA_CMD = curl -LRC - -O ${GET_DATA_URL} 2>&1 | tee ${data:NAME}.download-log.txt
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  VERSION = $$(date -r dblp.ttl.gz +"%d.%m.%Y %H:%M" || echo "NO_DATE")
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  DESCRIPTION = DBLP computer science bibliography, data from ${GET_DATA_URL} (version ${VERSION})
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@@ -19,7 +19,7 @@ SETTINGS_JSON = { "ascii-prefixes-only": false, "num-triples-per-batch": 10000
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  [server]
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  PORT = 7015
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  ACCESS_TOKEN = ${data:NAME}
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- MEMORY_FOR_QUERIES = 30G
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+ MEMORY_FOR_QUERIES = 10G
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  CACHE_MAX_SIZE = 5G
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  [runtime]
qlever/Qleverfiles/Qleverfile.pubchem CHANGED
@@ -48,7 +48,7 @@ DESCRIPTION = PubChem RDF from ${GET_DATA_URL}, version ${DATE} (all folde
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  [index]
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  INPUT_FILES = pubchem.additional-ontologies.nt.gz nt.${DATE}/*.nt.gz
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- CAT_INPUT_FILES = zcat ${FILE_NAMES}
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+ CAT_INPUT_FILES = zcat ${INPUT_FILES}
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  SETTINGS_JSON = { "languages-internal": [], "prefixes-external": [""], "ascii-prefixes-only": false, "num-triples-per-batch": 1000000 }
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  STXXL_MEMORY = 10G
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qlever/Qleverfiles/Qleverfile.uniprot CHANGED
@@ -1,37 +1,38 @@
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  # Qleverfile for UniProt, use with https://github.com/ad-freiburg/qlever-control
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  #
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- # qlever get-data # download RDFXML and convert to NT (around 1 TB each)
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- # qlever index # takes ~ 1.5 days and ~40 GB RAM (on an AMD Ryzen 9 5900X)
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- # qlever start # starts the server (takes a few second)
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+ # qlever get-data # takes ~ 30 hours and ~ 2 TB of disk (for the NT files)
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+ # qlever index # takes ~ 40 hours and ~ 60 GB RAM (on an AMD Ryzen 9 5900X)
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+ # qlever start # starts the server (takes a few seconds)
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  #
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  # Install packages: sudo apt install -y libxml2-utils parallel xz-utils pv
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  # Install manually: Apache Jena binaries (https://dlcdn.apache.org/jena/binaries)
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  #
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- # Set DATE to the date of the latest release
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- #
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- # IMPORTANT: Build on SSD, disk space required: ~ 10 T. For running the server,
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- # the uniprot.index.???.meta files can be on HDD.
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+ # Set DATE to the date of the latest release. Build on SSD (requires ~ 7 TB
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+ # during build, ~ 3 TB after build). The uniprot.index.???.meta files can be on
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+ # HDD without significant performance loss (when running the server).
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  [data]
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  NAME = uniprot
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- DATE = 2024-01-24
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+ DATE = 2024-05-29
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  DOWNLOAD_URL = https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf
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  GET_RDFXML_CMD = mkdir -p rdf.${DATE} && curl -s ${DOWNLOAD_URL}/RELEASE.meta4 | sed "s/<metalink.*/<metalink>/" | xmllint --xpath "/metalink/files/file/url[@location=\"ch\"]/text()" - | while read URL; do wget --no-verbose -P rdf.${DATE} $$URL 2>&1 | tee -a uniprot.download-log; done
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- RDFXML2NT_CMD = mkdir -p nt.${DATE} && for RDFXML in rdf.${DATE}/*.{owl,owl.xz,rdf,rdf.xz}; do echo "xzcat -f $$RDFXML | rdfxml --output=nt 2> /dev/null | xz -c > nt.${DATE}/$$(basename $$RDFXML | sed 's/\(rdf\|rdf.xz\|owl\|owl.xz\)$$/nt.xz/') && echo 'DONE converting $$RDFXML'"; done | parallel
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+ RDFXML2NT_CMD = mkdir -p nt.${DATE} && for RDFXML in rdf.${DATE}/*.{owl,owl.xz,rdf,rdf.xz}; do echo "xzcat -f $$RDFXML | rdfxml --output=nt 2> /dev/null | gzip -c > nt.${DATE}/$$(basename $$RDFXML | sed 's/\(rdf\|rdf.xz\|owl\|owl.xz\)$$/nt.gz/') && echo 'DONE converting $$RDFXML'"; done | parallel
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  GET_DATA_CMD = rdfxml --help && date > ${NAME}.get-data.begin-date && ${GET_RDFXML_CMD} && ${RDFXML2NT_CMD} && date > ${NAME}.get-data.end-date
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  DESCRIPTION = Complete UniProt data from ${DOWNLOAD_URL}, version ${DATE}
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  [index]
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- INPUT_FILES = nt.${data:DATE}/*.nt.xz
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- CAT_INPUT_FILES = parallel --tmpdir . -j 4 'xzcat -f {}' ::: nt.${data:DATE}/*.nt.xz | pv -q -B 5G
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+ INPUT_FILES = nt.${data:DATE}/*.nt.gz
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+ CAT_INPUT_FILES = parallel --tmpdir . -j 4 'zcat -f {}' ::: ${INPUT_FILES} | pv -q -B 5G
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  SETTINGS_JSON = { "languages-internal": [], "prefixes-external": [""], "locale": { "language": "en", "country": "US", "ignore-punctuation": true }, "ascii-prefixes-only": true, "num-triples-per-batch": 25000000 }
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  STXXL_MEMORY = 60G
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  [server]
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- PORT = 7018
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- ACCESS_TOKEN = ${data:NAME}_1369924040
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- MEMORY_FOR_QUERIES = 20G
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- CACHE_MAX_SIZE = 10G
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+ PORT = 7018
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+ ACCESS_TOKEN = ${data:NAME}
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+ MEMORY_FOR_QUERIES = 20G
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+ CACHE_MAX_SIZE = 10G
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+ CACHE_MAX_SIZE_SINGLE_ENTRY = 5G
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+ TIMEOUT = 300s
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  [runtime]
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  SYSTEM = docker
qlever/Qleverfiles/Qleverfile.wikidata CHANGED
@@ -1,24 +1,27 @@
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- # Qleverfile for Wikidata, use with https://github.com/ad-freiburg/qlever-control
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+ # Qleverfile for Wikidata, use with qlever script (`pip install qlever`)
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  #
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- # qlever get-data downloads two .bz2 files of total size ~100 GB
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- # qlever index takes ~7 hours and ~40 GB RAM (on an AMD Ryzen 9 5900X)
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- # qlever start starts the server (takes around 30 seconds)
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+ # qlever get-data # downloads two .bz2 files of total size ~100 GB
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+ # qlever index # takes ~4.5 hours and ~20 GB RAM (on an AMD Ryzen 9 5900X)
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+ # qlever start # starts the server (takes a few seconds)
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+
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+ [DEFAULT]
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+ NAME = wikidata
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  [data]
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- NAME = wikidata
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  GET_DATA_URL = https://dumps.wikimedia.org/wikidatawiki/entities
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- GET_DATA_CMD = curl -LO -C - ${GET_DATA_URL}/latest-all.ttl.bz2 ${GET_DATA_URL}/latest-lexemes.ttl.bz2
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- DESCRIPTION = "Full Wikidata dump from ${GET_DATA_URL} (latest-all.ttl.bz2 and latest-lexemes.ttl.bz2)"
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+ GET_DATA_CMD = curl -LRC - --remote-name-all ${GET_DATA_URL}/latest-all.ttl.bz2 ${GET_DATA_URL}/latest-lexemes.ttl.bz2 2>&1
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+ VERSION = $$(date -r latest-all.ttl.bz2 +%d.%m.%Y || echo "NO_DATE")
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+ DESCRIPTION = Full Wikidata dump from ${GET_DATA_URL} (latest-all.ttl.bz2 and latest-lexemes.ttl.bz2, version ${VERSION})
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  [index]
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- INPUT_FILES = latest-lexemes.ttl.bz2 latest-all.ttl.bz2
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- CAT_INPUT_FILES = bzcat ${FILE_NAMES}
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- SETTINGS_JSON = { "languages-internal": [], "prefixes-external": [""], "locale": { "language": "en", "country": "US", "ignore-punctuation": true }, "ascii-prefixes-only": false, "num-triples-per-batch": 5000000 }
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+ INPUT_FILES = latest-all.ttl.bz2 latest-lexemes.ttl.bz2
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+ CAT_INPUT_FILES = lbzcat -n 4 -f ${INPUT_FILES}
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+ SETTINGS_JSON = { "languages-internal": [], "prefixes-external": [""], "locale": { "language": "en", "country": "US", "ignore-punctuation": true }, "ascii-prefixes-only": true, "num-triples-per-batch": 5000000 }
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  STXXL_MEMORY = 10G
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  [server]
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  PORT = 7001
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- ACCESS_TOKEN = ${data:NAME}_372483264
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+ ACCESS_TOKEN = ${data:NAME}
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  MEMORY_FOR_QUERIES = 20G
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  CACHE_MAX_SIZE = 10G
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{qlever-0.5.2.dist-info → qlever-0.5.3.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: qlever
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- Version: 0.5.2
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+ Version: 0.5.3
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  Summary: Script for using the QLever SPARQL engine.
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  Author-email: Hannah Bast <bast@cs.uni-freiburg.de>
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  License: Apache-2.0
{qlever-0.5.2.dist-info → qlever-0.5.3.dist-info}/RECORD RENAMED
@@ -8,7 +8,7 @@ qlever/qlever_main.py,sha256=tA_xqOs_FjvqlDIvKTprwuysfTwzsUjE7at26gRhCVA,2336
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  qlever/qlever_old.py,sha256=6sHosOfJzkURpdK4wXLdGl4SUtPnlsNEUwAqUeJiRYA,62026
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  qlever/qleverfile.py,sha256=6Ll81xkzel_s2Ju9ZfBXUGlRfikaAzZM6Do-dTrdo3k,12934
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  qlever/util.py,sha256=eepj0SY9JJOUQq5kvtoPnWfoLLV9fbw_sTEWKHet66E,7147
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- qlever/Qleverfiles/Qleverfile.dblp,sha256=DjeyY0MGNrqEY-_8nRkjSsofGBBSz_wIgQ048KoRQBM,1002
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+ qlever/Qleverfiles/Qleverfile.dblp,sha256=oNT-O1a2I1ELPxgPxgB1F8T9Td3Iea7EyYizFpAHfXw,994
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  qlever/Qleverfiles/Qleverfile.dblp-plus,sha256=Dwd9pK1vPcelKfw6sA-IuyhbZ6yIxOh6_84JgPYnB9Q,1332
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  qlever/Qleverfiles/Qleverfile.default,sha256=mljl6I1RCkpIWOqMQwjzPZIsarYQx1R0mIlc583KuqU,1869
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  qlever/Qleverfiles/Qleverfile.dnb,sha256=GgnsbtRUl__yMCqUX2EN5x1oDWpW93bUalMfUxN8534,1751
@@ -19,11 +19,11 @@ qlever/Qleverfiles/Qleverfile.ohm-planet,sha256=Y_yUxdpWpUOSDo_zmVKj3caa8X-Wv-1K
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  qlever/Qleverfiles/Qleverfile.olympics,sha256=5w9BOFwEBhdSzPz-0LRxwhv-7Gj6xbF539HOXr3cqD0,1088
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  qlever/Qleverfiles/Qleverfile.osm-country,sha256=UnlkckSXJDrknZORlU-Hdj_J82U4kStl1aRctCc5n6M,1953
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  qlever/Qleverfiles/Qleverfile.osm-planet,sha256=2RilNix0fplN3GsNNyOu3GzmUss1Pq7586WKOFAQnSs,1400
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- qlever/Qleverfiles/Qleverfile.pubchem,sha256=bOhiJKUxzDiAm1UyXFPDQLYTqGc9jM8240fhobYLij0,3898
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+ qlever/Qleverfiles/Qleverfile.pubchem,sha256=a6EAP8mOfC0V6NnVCLarvRagyoQSQDItR7AnrZqL9iE,3899
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  qlever/Qleverfiles/Qleverfile.scientists,sha256=9eZ2c6P9a3E3VHa3RR7LdOQbF4k3oyyrn56Z3u4LZYs,1164
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- qlever/Qleverfiles/Qleverfile.uniprot,sha256=FS8QLHvujbjUYyU2Ma0PRgfCWlulviaGLc_1csxpuic,2201
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+ qlever/Qleverfiles/Qleverfile.uniprot,sha256=9kAKseomdUnIt7EAZge39g1MTuaLVaSW9JYLHzIMolM,2338
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  qlever/Qleverfiles/Qleverfile.vvz,sha256=ftdMj5dCC9jAlFtNt2WR7kP30w0itT_iYtj5HoUVyWU,931
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- qlever/Qleverfiles/Qleverfile.wikidata,sha256=fhWSChZTH3c2y14kgP1P5Duq1SsewTOK3wETf6RRmI8,1172
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+ qlever/Qleverfiles/Qleverfile.wikidata,sha256=vDkTY3mPSx2C8MvFWfB72zZoc4d-TMJSw3f_-FqnEqs,1275
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  qlever/Qleverfiles/Qleverfile.wikipathways,sha256=qWjfT-CVQCgRfN6fXPwBORMbjzXS_xsJ2DoCamQI7Rs,2045
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  qlever/Qleverfiles/Qleverfile.yago-4,sha256=GikYPqChCtbAyZOVqszmVUwgQxSePTcgM8xw2b_21e4,1849
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  qlever/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -42,9 +42,9 @@ qlever/commands/status.py,sha256=5S6EdapZEwFKV9cQZtNYcZhMbAXAY-FP6ggjIhfX8ek,163
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  qlever/commands/stop.py,sha256=TZs4bxKHvujlZAU8BZmFjA5eXSZNAa6EeNzvPpEZsuI,4139
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  qlever/commands/ui.py,sha256=rV8u017WLbfz0zVT_c9GC4d9v1WWwrTM3kfGONbeCvQ,2499
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  qlever/commands/warmup.py,sha256=WOZSxeV8U_F6pEEnAb6YybXLQMxZFTRJXs4BPHUhsmc,1030
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- qlever-0.5.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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- qlever-0.5.2.dist-info/METADATA,sha256=MHlNH1mplzq3hJ0ETmjUqM4Zw6zLqvends9IT60M4Io,4146
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- qlever-0.5.2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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- qlever-0.5.2.dist-info/entry_points.txt,sha256=U_gbYYi0wwdsn884eb0XoOXfvhACOsxhlO330dZ9bi0,87
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- qlever-0.5.2.dist-info/top_level.txt,sha256=kd3zsYqiFd0--Czh5XTVkfEq6XR-XgRFW35X0v0GT-c,7
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- qlever-0.5.2.dist-info/RECORD,,
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+ qlever-0.5.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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+ qlever-0.5.3.dist-info/METADATA,sha256=cBURUr5Og7ysQJOuCIZN5pKp_DGi4lm-c87CVxQhmtY,4146
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+ qlever-0.5.3.dist-info/WHEEL,sha256=mguMlWGMX-VHnMpKOjjQidIo1ssRlCFu4a4mBpz1s2M,91
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+ qlever-0.5.3.dist-info/entry_points.txt,sha256=U_gbYYi0wwdsn884eb0XoOXfvhACOsxhlO330dZ9bi0,87
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+ qlever-0.5.3.dist-info/top_level.txt,sha256=kd3zsYqiFd0--Czh5XTVkfEq6XR-XgRFW35X0v0GT-c,7
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+ qlever-0.5.3.dist-info/RECORD,,
{qlever-0.5.2.dist-info → qlever-0.5.3.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: bdist_wheel (0.43.0)
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+ Generator: setuptools (70.1.1)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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