{ "_id": "6a215d8ecd65a98ecbd2f90b", "Package": "fhircrackr", "Type": "Package", "Title": "Handling HL7 FHIR® Resources in R", "Version": "2.4.0", "Date": "2026-06-04", "Authors@R": "c(\nperson( given = \"Thomas\",\nfamily = \"Peschel\",\nemail = \"thomas.peschel@imise.uni-leipzig.de\",\nrole = c(\"aut\")),\nperson( given = \"Julia\",\nfamily = \"Palm\",\nemail = \"julia.palm@med.uni-jena.de\",\nrole = c(\"aut\",\"cre\"),\ncomment=c(ORCID = \"0000-0003-1568-5893\")),\nperson( given = \"Jens\",\nfamily = \"Przybilla\",\nemail = \"jprzybilla@imise.uni-leipzig.de\",\nrole = \"aut\"),\nperson( given = \"Frank\",\nfamily = \"Meineke\",\nemail = \"frank.meineke@imise.uni-leipzig.de\",\nrole = \"aut\",\ncomment=c(ORCID = \"0000-0002-9256-7543\")))", "Description": "Useful tools for conveniently downloading FHIR resources\nin xml format and converting them to R data.frames. Uses\nFHIR-search to download bundles from a FHIR server, provides\nfunctions to save and read xml-files containing such bundles\nand allows flattening the bundles to data.frames using XPath\nexpressions. FHIR® is the registered trademark of HL7 and is\nused with the permission of HL7. Use of the FHIR trademark does\nnot constitute endorsement of this product by HL7.", "BugReports": "https://github.com/POLAR-fhiR/fhircrackr/issues", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "Collate": "'fhir_body.R' 'fhir_resource.R' 'fhir_url.R' 'fhir_bundle.R'\n'fhir_bundle_list.R' 'build_resources.R' 'design.R'\n'download_resources.R' 'fhir_xpath_expression.R'\n'fhir_columns.R' 'fhir_resource_type.R'\n'fhir_table_description.R' 'fhir_design.R' 'fhir_style.R'\n'fhir_table_list.R' 'fhir_tree.R' 'flatten_resources.R'\n'miscellaneous.R' 'multiple_entries.R' 'sample_resources.R'", "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev", "Repository": "https://polar-fhir.r-universe.dev", "Date/Publication": "2026-06-04 08:04:07 UTC", "RemoteUrl": "https://github.com/polar-fhir/fhircrackr", "RemoteRef": "HEAD", "RemoteSha": "5480069af69a168d19dfa11bf1febd17f97c45b6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 11:06:07 UTC", "User": "root" }, "Author": "Thomas Peschel [aut],\nJulia Palm [aut, cre] (ORCID: ),\nJens Przybilla [aut],\nFrank Meineke [aut] (ORCID: )", "Maintainer": "Julia Palm ", "MD5sum": "ab8f21d5a3dd3c4b8eb2b6dbbcc974d5", "_user": "polar-fhir", "_type": "src", "_file": "fhircrackr_2.4.0.tar.gz", "_fileid": "73e54c8fc320e8e2c1c8763cb080d8fd107e3a39e04608c635ac69464938c82f", "_filesize": 604888, "_sha256": "73e54c8fc320e8e2c1c8763cb080d8fd107e3a39e04608c635ac69464938c82f", "_created": "2026-06-04T11:06:07.000Z", "_published": "2026-06-04T11:12:14.051Z", "_distro": "noble", "_jobs": [ { "job": 79505434417, "time": 132, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7409863172" }, { "job": 79505434390, "time": 124, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7409859942" }, { "job": 79505434384, "time": 114, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7409925702" }, { "job": 79505434399, "time": 85, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7409853713" }, { "job": 79504962992, "time": 176, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7409821637" }, { "job": 79505434538, "time": 103, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7409854132" }, { "job": 79505434426, "time": 133, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7409867332" }, { "job": 79505434498, "time": 87, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7409849078" }, { "job": 79505434561, "time": 120, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7409859514" } ], "_buildurl": "https://github.com/r-universe/polar-fhir/actions/runs/26947762218", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/polar-fhir/fhircrackr", "_commit": { "id": "5480069af69a168d19dfa11bf1febd17f97c45b6", "author": "Julia Palm ", "committer": "Julia Palm ", "message": "prepare cran submission\n", "time": 1780560247 }, "_maintainer": { "name": "Julia Palm", "email": "julia.palm@med.uni-jena.de", "login": "palmjulia", "description": "", "uuid": 51789135, "orcid": "0000-0003-1568-5893" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "xml2", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "polar-fhir", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-23", "n": 2 } ], "_tags": [], "_topics": [ "fhir", "fhir-client" ], "_stars": 39, "_contributors": [ { "user": "palmjulia", "count": 546, "uuid": 51789135 }, { "user": "tpeschel", "count": 43, "uuid": 25242528 }, { "user": "jeprzybilla", "count": 14, "uuid": 61840319 }, { "user": "astruebi", "count": 10, "uuid": 5671404 }, { "user": "flow191", "count": 5, "uuid": 79848862 } ], "_userbio": { "uuid": 66358896, "type": "organization", "name": "POLAR-fhir" }, "_downloads": { "count": 266, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fhircrackr" }, "_devurl": "https://github.com/polar-fhir/fhircrackr", "_searchresults": 61, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/fhircrackr.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/polar-fhir/fhircrackr", "_realowner": "polar-fhir", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2020-07-10" }, { "version": "0.1.1", "date": "2020-07-22" }, { "version": "0.2.0", "date": "2020-10-19" }, { "version": "0.2.1", "date": "2020-11-24" }, { "version": "1.0.0", "date": "2021-06-16" }, { "version": "1.0.1", "date": "2021-06-17" }, { "version": "2.0.0", "date": "2022-07-14" }, { "version": "2.1.0", "date": "2022-11-19" }, { "version": "2.1.1", "date": "2023-02-10" }, { "version": "2.2.0", "date": "2024-03-21" }, { "version": "2.3.0", "date": "2025-04-07" } ], "_exports": [ "as_fhir", "fhir_authenticate", "fhir_body", "fhir_build_bundle", "fhir_build_resource", "fhir_bundle_list", "fhir_bundle_xml", "fhir_canonical_design", "fhir_capability_statement", "fhir_cast", "fhir_collapse", "fhir_columns", "fhir_common_columns", "fhir_count_resource", "fhir_crack", "fhir_current_request", "fhir_design", "fhir_get_resource_ids", "fhir_get_resources_by_ids", "fhir_is_empty", "fhir_load", "fhir_load_design", "fhir_melt", "fhir_melt_all", "fhir_next_bundle_url", "fhir_post", "fhir_put", "fhir_recent_http_error", "fhir_request", "fhir_resource_type", "fhir_resource_xml", "fhir_rm_div", "fhir_rm_indices", "fhir_rm_tag", "fhir_sample_resources", "fhir_sample_resources_by_ids", "fhir_save", "fhir_save_design", "fhir_search", "fhir_serialize", "fhir_style", "fhir_table_description", "fhir_tree", "fhir_unserialize", "fhir_url", "fhir_xpath_expression", "paste_paths", "pastep" ], "_datasets": [ { "name": "example_bundles_empty", "title": "Toy example bundles for multiple entries", "object": "example_bundles_empty", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_bundles1", "title": "Toy example bundles for multiple entries", "object": "example_bundles1", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_bundles2", "title": "Toy example bundles for multiple entries", "object": "example_bundles2", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_bundles3", "title": "Toy example bundles for multiple entries", "object": "example_bundles3", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_bundles4", "title": "Toy example bundles for multiple entries", "object": "example_bundles4", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_bundles5", "title": "Toy example bundles for multiple entries", "object": "example_bundles5", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_bundles6", "title": "Toy example bundles for multiple entries", "object": "example_bundles6", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_bundles7", "title": "Toy example bundles for multiple entries", "object": "example_bundles7", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_resource1", "title": "Toy examples to POST/PUT on a server", "object": "example_resource1", "class": [ "fhir_resource_serialized" ], "fields": [], "table": false, "tojson": true }, { "name": "example_resource2", "title": "Toy examples to POST/PUT on a server", "object": "example_resource2", "class": [ "fhir_resource_serialized" ], "fields": [], "table": false, "tojson": true }, { "name": "example_resource3", "title": "Toy examples to POST/PUT on a server", "object": "example_resource3", "class": [ "fhir_resource_serialized" ], "fields": [], "table": false, "tojson": true }, { "name": "medication_bundles", "title": "Exemplary FHIR bundles", "object": "medication_bundles", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "patient_bundles", "title": "Exemplary FHIR bundles", "object": "patient_bundles", "class": [ "fhir_bundle_list" ], "fields": [], "table": false, "tojson": true }, { "name": "transaction_bundle_example", "title": "Toy examples to POST/PUT on a server", "object": "transaction_bundle_example", "class": [ "fhir_bundle_serialized" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "as_fhir", "title": "Coerce character vector to fhir_bundle_list", "topics": [ "as_fhir" ] }, { "page": "datasets_selfmade", "title": "Toy example bundles for multiple entries", "topics": [ "example_bundles1", "example_bundles2", "example_bundles3", "example_bundles4", "example_bundles5", "example_bundles6", "example_bundles7", "example_bundles_empty" ] }, { "page": "fhir_authenticate", "title": "Create token for Authentication", "topics": [ "fhir_authenticate" ] }, { "page": "fhir_body-methods", "title": "Create fhir_body object", "topics": [ "fhir_body", "fhir_body,character,character-method", "fhir_body,character,character-methods", "fhir_body,list,character-method", "fhir_body,list,character-methods", "fhir_body,list,missing-method", "fhir_body,list,missing-methods" ] }, { "page": "fhir_body-class", "title": "An s4 class to represent a body for a POST to a FHIR server", "topics": [ "fhir_body-class" ] }, { "page": "fhir_build_bundle-methods", "title": "Build a FHIR bundle", "topics": [ "fhir_build_bundle", "fhir_build_bundle,data.frame-method", "fhir_build_bundle,list-method" ] }, { "page": "fhir_build_resource", "title": "Build a single FHIR resource", "topics": [ "fhir_build_resource" ] }, { "page": "fhir_bundle_list", "title": "Create fhir_bundle_list object", "topics": [ "fhir_bundle_list" ] }, { "page": "fhir_bundle_list-class", "title": "S4 class to represent a list of FHIR bundles", "topics": [ "fhir_bundle_list-class" ] }, { "page": "fhir_bundle_serialized-class", "title": "An S4 class to represent a FHIR bundle in serialized form", "topics": [ "fhir_bundle_serialized-class" ] }, { "page": "fhir_bundle_xml", "title": "Create fhir_bundle_xml object", "topics": [ "fhir_bundle_xml" ] }, { "page": "fhir_bundle_xml-class", "title": "An S4 class to represent a FHIR bundle in xml form", "topics": [ "fhir_bundle_xml-class" ] }, { "page": "fhir_bundle-class", "title": "An S4 class to represent FHIR bundles", "topics": [ "fhir_bundle-class" ] }, { "page": "fhir_canonical_design", "title": "Retrieve design of last call to fhir_crack", "topics": [ "fhir_canonical_design" ] }, { "page": "fhir_capability_statement", "title": "Get capability statement", "topics": [ "fhir_capability_statement" ] }, { "page": "fhir_cast", "title": "Cast table with multiple entries This function divides multiple entries in a compact indexed table as produced by 'fhir_crack()' into separate columns.", "topics": [ "fhir_cast" ] }, { "page": "fhir_collapse", "title": "Collapse multiple entries", "topics": [ "fhir_collapse" ] }, { "page": "fhir_columns-methods", "title": "Create fhir_columns object", "topics": [ "fhir_columns", "fhir_columns,character,character-method", "fhir_columns,character,missing-method", "fhir_columns,list,missing-method", "fhir_columns,missing,missing-method", "fhir_columns,NULL,missing-method" ] }, { "page": "fhir_columns-class", "title": "A S4 class to represent columns in a fhir_table_description", "topics": [ "fhir_columns-class" ] }, { "page": "fhir_common_columns", "title": "Find common columns", "topics": [ "fhir_common_columns" ] }, { "page": "fhir_count_resource", "title": "Get Resources' Counts", "topics": [ "fhir_count_resource" ] }, { "page": "fhir_crack-methods", "title": "Flatten list of FHIR bundles", "topics": [ "fhir_crack", "fhir_crack,ANY,fhir_design-method", "fhir_crack,ANY,fhir_table_description-method", "fhir_crack,fhir_design-method", "fhir_crack,fhir_table_description-method" ] }, { "page": "fhir_current_request", "title": "Return FHIR search request used in last call to 'fhir_search()' or 'fhir_url()'", "topics": [ "fhir_current_request" ] }, { "page": "fhir_design-methods", "title": "Create a fhir_design object", "topics": [ "fhir_design", "fhir_design,fhir_table_description-method", "fhir_design,fhir_table_list-method", "fhir_design,list-method" ] }, { "page": "fhir_design-class", "title": "A S4 class containing a design for 'fhir_crack()'", "topics": [ "fhir_design-class" ] }, { "page": "fhir_df_list-class", "title": "List of data.frames as returned by 'fhir_crack()'", "topics": [ "fhir_df_list-class" ] }, { "page": "fhir_dt_list-class", "title": "List of data.tables as returned by 'fhir_crack()'", "topics": [ "fhir_dt_list-class" ] }, { "page": "fhir_get_resource_ids", "title": "Get Resources' IDs", "topics": [ "fhir_get_resource_ids" ] }, { "page": "fhir_get_resources_by_ids", "title": "Get Resources by their IDs", "topics": [ "fhir_get_resources_by_ids" ] }, { "page": "fhir_is_empty-methods", "title": "Check if Bundle/Bundlelist is empty", "topics": [ "fhir_is_empty", "fhir_is_empty,fhir_bundle_list-method", "fhir_is_empty,fhir_bundle_xml-method" ] }, { "page": "fhir_load", "title": "Load bundles from xml-files", "topics": [ "fhir_load" ] }, { "page": "fhir_load_design", "title": "Load design from xml", "topics": [ "fhir_load_design" ] }, { "page": "fhir_melt", "title": "Melt multiple entries", "topics": [ "fhir_melt" ] }, { "page": "fhir_melt_all", "title": "Melt all columns with multiple entries", "topics": [ "fhir_melt_all" ] }, { "page": "fhir_melt_internal", "title": "Internal function to melt multiple entries in a data.table", "topics": [ "fhir_melt_internal" ] }, { "page": "fhir_next_bundle_url", "title": "Next Bundle's URL", "topics": [ "fhir_next_bundle_url" ] }, { "page": "fhir_post-methods", "title": "POST to a FHIR server", "topics": [ "fhir_post", "fhir_post,ANY,fhir_body-method", "fhir_post,ANY,fhir_bundle_xml-method", "fhir_post,ANY,fhir_resource-method", "fhir_post,fhir_body-method", "fhir_post,fhir_bundle_xml-method", "fhir_post,fhir_resource-method" ] }, { "page": "fhir_put", "title": "PUT to a FHIR server", "topics": [ "fhir_put" ] }, { "page": "fhir_recent_http_error", "title": "Return most recent http error from 'fhir_search()'", "topics": [ "fhir_recent_http_error" ] }, { "page": "fhir_request", "title": "fhir_request", "topics": [ "fhir_request" ] }, { "page": "fhir_resource_serialized-class", "title": "An S4 class to represent a FHIR resource in serialized form", "topics": [ "fhir_resource_serialized-class" ] }, { "page": "fhir_resource_type", "title": "Create fhir_resource_type object", "topics": [ "fhir_resource_type" ] }, { "page": "fhir_resource_type-class", "title": "A representation of a FHIR resource type", "topics": [ "fhir_resource_type-class" ] }, { "page": "fhir_resource_xml-methods", "title": "Create fhir_resource_xml object", "topics": [ "fhir_resource_xml", "fhir_resource_xml,character-method", "fhir_resource_xml,xml_document-method", "fhir_resource_xml,xml_node-method" ] }, { "page": "fhir_resource_xml-class", "title": "An S4 class to represent a FHIR resource in xml form", "topics": [ "fhir_resource_xml-class" ] }, { "page": "fhir_resource-class", "title": "An S4 class to represent FHIR resources", "topics": [ "fhir_resource-class" ] }, { "page": "fhir_rm_div", "title": "Remove html elements", "topics": [ "fhir_rm_div" ] }, { "page": "fhir_rm_indices", "title": "Remove indices from data.frame/data.table", "topics": [ "fhir_rm_indices" ] }, { "page": "fhir_rm_tag-methods", "title": "Remove a certain xml tag", "topics": [ "fhir_rm_tag", "fhir_rm_tag,character-method", "fhir_rm_tag,fhir_bundle_list-method", "fhir_rm_tag,fhir_bundle_xml-method" ] }, { "page": "fhir_sample_resources", "title": "Randomly sample resources from a FHIR server", "topics": [ "fhir_sample_resources" ] }, { "page": "fhir_sample_resources_by_ids", "title": "Download a random sample of resources from a vector of resource IDs.", "topics": [ "fhir_sample_resources_by_ids" ] }, { "page": "fhir_save", "title": "Save FHIR bundles as xml-files", "topics": [ "fhir_save" ] }, { "page": "fhir_save_design", "title": "Write design to xml", "topics": [ "fhir_save_design" ] }, { "page": "fhir_search", "title": "Download FHIR search result", "topics": [ "fhir_search" ] }, { "page": "fhir_serialize-methods", "title": "Serialize a fhir_bundle, fhir_bundle_list or fhir_resource", "topics": [ "fhir_serialize", "fhir_serialize,fhir_bundle_list-method", "fhir_serialize,fhir_bundle_serialized-method", "fhir_serialize,fhir_bundle_xml-method", "fhir_serialize,fhir_resource_serialized-method", "fhir_serialize,fhir_resource_xml-method" ] }, { "page": "fhir_table_description", "title": "Create fhir_table_description object", "topics": [ "fhir_table_description" ] }, { "page": "fhir_table_description-class", "title": "A S4 class describing the form of a table produced by 'fhir_crack()'", "topics": [ "fhir_table_description-class" ] }, { "page": "fhir_tree", "title": "Represent a wide cast table as a tree", "topics": [ "fhir_tree" ] }, { "page": "fhir_unserialize-methods", "title": "Unserialize a fhir_bundle, fhir_bundle_list or fhir_resource", "topics": [ "fhir_unserialize", "fhir_unserialize,fhir_bundle_list-method", "fhir_unserialize,fhir_bundle_serialized-method", "fhir_unserialize,fhir_bundle_xml-method", "fhir_unserialize,fhir_resource_serialized-method", "fhir_unserialize,fhir_resource_xml-method" ] }, { "page": "fhir_url-methods", "title": "Create FHIR URL", "topics": [ "fhir_url", "fhir_url,character,character,character-method", "fhir_url,character,character,list-method", "fhir_url,character,character,missing-method", "fhir_url,character,missing,missing-method" ] }, { "page": "fhir_url-class", "title": "An S4 object to represent a URL for a FHIR server", "topics": [ "fhir_url-class" ] }, { "page": "fhir_xpath_expression", "title": "Create fhir_xpath_expression", "topics": [ "fhir_xpath_expression" ] }, { "page": "fhir_xpath_expression-class", "title": "An S4 class for xpath_expressions Objects of this class are essentially character vectors, but can only be valid XPath (1.0) expressions. They are mostly used in the 'fhir_columns' class.", "topics": [ "fhir_xpath_expression-class" ] }, { "page": "datasets_real", "title": "Exemplary FHIR bundles", "topics": [ "medication_bundles", "patient_bundles" ] }, { "page": "paste_paths", "title": "Concatenate two paths", "topics": [ "paste_paths" ] }, { "page": "pastep", "title": "Concatenate paths", "topics": [ "pastep" ] }, { "page": "datasets_for_post", "title": "Toy examples to POST/PUT on a server", "topics": [ "example_resource1", "example_resource2", "example_resource3", "transaction_bundle_example" ] } ], "_readme": "https://github.com/polar-fhir/fhircrackr/raw/HEAD/docs/README.md", "_rundeps": [ "askpass", "cli", "curl", "data.table", "glue", "httr", "jsonlite", "lifecycle", "magrittr", "mime", "openssl", "R6", "rlang", "stringi", "stringr", "sys", "vctrs", "xml2" ], "_vignettes": [ { "source": "fhircrackr_intro.Rmd", "filename": "fhircrackr_intro.html", "title": "fhircrackr Intro: Handling HL7® FHIR® Resources in R", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Downloading resources", "Flattening resources", "Multiple entries", "Process Tables with multiple Entries", "Melt tables with multiple entries", "Remove indices", "Save and load downloaded bundles", "Save and load bundles as R objects", "Save and load bundles as xml files", "Acknowledgments" ], "created": "2021-03-12 15:03:05", "modified": "2024-03-21 13:51:35", "commits": 7 }, { "source": "downloadResources.Rmd", "filename": "downloadResources.html", "title": "fhircrackr: Download FHIR resources", "engine": "knitr::rmarkdown", "headings": [ "FHIR search requests", "Accessing the current request", "Download FHIR resources from a server", "Basic request", "More than one resource type", "Authentication", "Search via POST", "Deal with HTTP Errors", "Save the downloaded bundles", "Save bundles as R objects", "Save and load bundles as xml files", "Dealing with large data sets", "Saving memory", "1. Download trimmed resources using _elements", "2. Batch process bundles by saving them to hard drive", "3. 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