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Merge pull request #1030 from HL7/2025-01-gg-no-ftp-uploads
2025 01 gg no ftp uploads
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| * Loader: Add missing packages to CQL list | ||
| * Loader: fix up language/local loading sequence | ||
| * Loader: fix bug for cross-version extension containing escaped [x] | ||
| * Validator: Add check for duplicate ids on contained resources | ||
| * Validator: fix bug looking up code system | ||
| * Validator: Look for cs on other server in missed location | ||
| * Validator: fix bug accessing code system from other terminology server if no version specified | ||
| * Validator: validate displaylanguage when validating codes | ||
| * Renderer: Possible fix for an NPE reported bu a user with no context | ||
| * QA: fix bug parsing `script` tag in xhtml - handling `<` characters | ||
| * QA: Tighted up handling of errors when HTML pages can't be parsed | ||
| * Publication Process: remove FTP support in -go-publish (it's all git now) | ||
| * Publication Process: radd support for creation phase |
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164 changes: 164 additions & 0 deletions
164
...ir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/utils/HL7OrgFhirFixer.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,164 @@ | ||
| package org.hl7.fhir.igtools.publisher.utils; | ||
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Set; | ||
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| import org.hl7.fhir.utilities.TextFile; | ||
| import org.hl7.fhir.utilities.Utilities; | ||
| import org.hl7.fhir.utilities.json.model.JsonElement; | ||
| import org.hl7.fhir.utilities.json.model.JsonObject; | ||
| import org.hl7.fhir.utilities.json.parser.JsonParser; | ||
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| public class HL7OrgFhirFixer { | ||
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| public static void main(String[] args) throws IOException { | ||
| File folder = new File("/Users/grahamegrieve/web/www.hl7.org.fhir"); | ||
| new HL7OrgFhirFixer().execute(folder.getAbsolutePath().length(), folder, true); | ||
| } | ||
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| private void execute(int rootLen, File folder, boolean root) throws IOException { | ||
| boolean isSpec = isSpec(folder); | ||
| if (isSpec) { | ||
| System.out.print("Found Spec at "+folder.getAbsolutePath()); | ||
| processSpec(rootLen, folder); | ||
| } | ||
| boolean isEmpty = true; | ||
| for (File f : folder.listFiles()) { | ||
| if (f.isDirectory()) { | ||
| isEmpty = false; | ||
| execute(rootLen, f, false); | ||
| } else if (f.getName().endsWith(".asp")) { | ||
| f.delete(); | ||
| } else { | ||
| isEmpty = false; | ||
| } | ||
| } | ||
| if (isEmpty) { | ||
| folder.delete(); | ||
| } | ||
| } | ||
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| private boolean isSpec(File folder) throws IOException { | ||
| if (new File(Utilities.path(folder.getAbsolutePath(), "package.tgz")).exists()) { | ||
| return true; | ||
| } | ||
| if (new File(Utilities.path(folder.getAbsolutePath(), "patient.html")).exists()) { | ||
| return true; | ||
| } | ||
| if (new File(Utilities.path(folder.getAbsolutePath(), "patient.htm")).exists()) { | ||
| return true; | ||
| } | ||
| return false; | ||
| } | ||
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| private void processSpec(int rootLen, File folder) throws IOException { | ||
| Map<String, Map<String, String>> list = new HashMap<>(); | ||
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| scanFolder(rootLen, folder, list); | ||
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| int size = 0; | ||
| for (String t : list.keySet()) { | ||
| size += list.get(t).size(); | ||
| String tf = Utilities.noString(t) ? folder.getAbsolutePath() : Utilities.path(folder.getAbsolutePath(), t); | ||
| Utilities.createDirectoryNC(tf); | ||
| Map<String, String> map = list.get(t); | ||
| for (String id : map.keySet()) { | ||
| String idf = Utilities.path(tf, id); | ||
| Utilities.createDirectoryNC(idf); | ||
| String rf = Utilities.path(idf, "index.php"); | ||
| TextFile.stringToFile(genRedirect(map.get(id)), rf); | ||
| } | ||
| } | ||
| System.out.println(" "+size+" resources"); | ||
| } | ||
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| private String genRedirect(String url) { | ||
| String ub = url.replace(".json", ""); | ||
| return "<?php\r\n"+ | ||
| "function Redirect($url)\r\n"+ | ||
| "{\r\n"+ | ||
| " header('Location: ' . $url, true, 302);\r\n"+ | ||
| " exit();\r\n"+ | ||
| "}\r\n"+ | ||
| "\r\n"+ | ||
| "$accept = $_SERVER['HTTP_ACCEPT'];\r\n"+ | ||
| "if (strpos($accept, 'application/json+fhir') !== false)\r\n"+ | ||
| " Redirect('/fhir"+ub+".json2');\r\n"+ | ||
| "elseif (strpos($accept, 'application/fhir+json') !== false)\r\n"+ | ||
| " Redirect('/fhir"+ub+".json1');\r\n"+ | ||
| "elseif (strpos($accept, 'json') !== false)\r\n"+ | ||
| " Redirect('/fhir"+ub+".json');\r\n"+ | ||
| "elseif (strpos($accept, 'application/xml+fhir') !== false)\r\n"+ | ||
| " Redirect('/fhir"+ub+".xml2');\r\n"+ | ||
| "elseif (strpos($accept, 'application/fhir+xml') !== false)\r\n"+ | ||
| " Redirect('/fhir"+ub+".xml1');\r\n"+ | ||
| "elseif (strpos($accept, 'html') !== false)\r\n"+ | ||
| " Redirect('/fhir"+ub+".html');\r\n"+ | ||
| "else \r\n"+ | ||
| " Redirect('/fhir"+ub+".json');\r\n"+ | ||
| "?>\r\n"+ | ||
| "\r\n"+ | ||
| "You should not be seeing this page. If you do, PHP has failed badly.\r\n"+ | ||
| "\r\n"; | ||
| } | ||
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| private void scanFolder(int rootLen, File folder, Map<String, Map<String, String>> list) throws IOException { | ||
| for (File f : folder.listFiles()) { | ||
| if (f.getName().equals("web.config")) { | ||
| f.delete(); | ||
| } else if (f.getName().endsWith(".asp")) { | ||
| f.delete(); | ||
| } else if (f.isDirectory()) { | ||
| if (!isSpec(folder)) { | ||
| scanFolder(rootLen, f, list); | ||
| } | ||
| } else if (f.getName().endsWith(".json") && !f.getName().contains(".canonical.")) { | ||
| try { | ||
| JsonElement je = JsonParser.parse(f); | ||
| if (je.isJsonObject()) { | ||
| JsonObject j = je.asJsonObject(); | ||
| if (j.has("resourceType") && j.has("id")) { | ||
| String rt = j.asString("resourceType"); | ||
| String id = j.asString("id"); | ||
| String link = f.getAbsolutePath().substring(rootLen); | ||
| Map<String, String> ft = makeMapForType(list, rt); | ||
| ft.put(id, link); | ||
| if (j.has("url")) { | ||
| String url = j.asString("url"); | ||
| if (url.startsWith("http://hl7.org/fhir/")) { | ||
| String tail = url.substring(20); | ||
| if (j.has("version")) { | ||
| ft.put(id+"|"+j.asString("version"), link); | ||
| } | ||
| if (!tail.contains("/") && !tail.contains(".")) { | ||
| ft = makeMapForType(list, ""); | ||
| ft.put(tail, link); | ||
| if (j.has("version")) { | ||
| ft.put(tail+"|"+j.asString("version"), link); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } catch (Exception e) { | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| public Map<String, String> makeMapForType(Map<String, Map<String, String>> list, String rt) { | ||
| Map<String, String> ft = list.get(rt); | ||
| if (ft == null) { | ||
| ft = new HashMap<String, String>(); | ||
| list.put(rt, ft); | ||
| } | ||
| return ft; | ||
| } | ||
| } |
107 changes: 107 additions & 0 deletions
107
...core/src/main/java/org/hl7/fhir/igtools/publisher/utils/HL7OrgFhirFixerForExtensions.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| package org.hl7.fhir.igtools.publisher.utils; | ||
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| import org.hl7.fhir.r5.model.CanonicalResource; | ||
| import org.hl7.fhir.r5.model.Resource; | ||
| import org.hl7.fhir.utilities.TextFile; | ||
| import org.hl7.fhir.utilities.Utilities; | ||
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| public class HL7OrgFhirFixerForExtensions { | ||
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| public static void main(String[] args) throws IOException { | ||
| File folderRoot = new File("/Users/grahamegrieve/web/www.hl7.org.fhir"); | ||
| File folderExt = new File("/Users/grahamegrieve/web/www.hl7.org.fhir/extensions"); | ||
| new HL7OrgFhirFixerForExtensions().execute(folderRoot, folderExt); | ||
| } | ||
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| private void execute(File folderRoot, File folderExt) throws IOException { | ||
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| scanForEmptyFolders(folderRoot); | ||
| } | ||
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| private void scanForEmptyFolders(File ff) throws IOException { | ||
| boolean indexed = false; | ||
| for (File f : ff.listFiles()) { | ||
| if (f.isDirectory()) { | ||
| if (!Utilities.existsInList(f.getName(), "assets", "assets-hist", "dist", "dist-hist", "less", "images", "less-glyphicons", "less-joyo", "html", "css", | ||
| "quick", "qicore", "external", "examples", "sid", ".git", "ehrsrle")) { | ||
| scanForEmptyFolders(f); | ||
| } | ||
| } else { | ||
| if (Utilities.existsInList(f.getName(), "index.html", "index.php", "web.config", ".no.index")) { | ||
| indexed = true; | ||
| } | ||
| if (f.getName().equals(".no.index")) { | ||
| f.delete(); | ||
| } | ||
| if (f.getName().equals("web.config")) { | ||
| String s = TextFile.fileToString(f); | ||
| String url = s.substring(s.indexOf("destination=")+13); | ||
| url = url.substring(0, url.indexOf("\"")); | ||
| String rf = genRedirect(url.replace("http://hl7.org/fhir", "")); | ||
| String dst = Utilities.path(ff, "index.php"); | ||
| TextFile.stringToFile(rf, dst); | ||
| f.delete(); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| private boolean lowerCaseHtmlExists(File ff) throws IOException { | ||
| String path = Utilities.path(ff.getParentFile(), ff.getName().toLowerCase()+".html"); | ||
| return new File(path).exists(); | ||
| } | ||
|
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| private String genRedirect(String url) { | ||
| return "<?php\r\n"+ | ||
| "function Redirect($url)\r\n"+ | ||
| "{\r\n"+ | ||
| " header('Location: ' . $url, true, 302);\r\n"+ | ||
| " exit();\r\n"+ | ||
| "}\r\n"+ | ||
| "\r\n"+ | ||
| "$accept = $_SERVER['HTTP_ACCEPT'];\r\n"+ | ||
| "if (strpos($accept, 'html') !== false)\r\n"+ | ||
| " Redirect('/fhir"+url+"');\r\n"+ | ||
| "else \r\n"+ | ||
| " header($_SERVER[\"SERVER_PROTOCOL\"].\" 404 Not Found\");\r\n"+ | ||
| "?>\r\n"+ | ||
| "\r\n"+ | ||
| "{ \"message\" : \"not-found\" }\r\n"+ | ||
| "\r\n"; | ||
| } | ||
|
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| private boolean isResourceName(String name) { | ||
| return Utilities.existsInList(name, | ||
| "Account", "ActivityDefinition", "ActorDefinition", "AdministrableProductDefinition", "AdverseEvent", "AllergyIntolerance", "Appointment", "AppointmentResponse", "ArtifactAssessment", "AuditEvent", | ||
| "Basic", "Binary", "BiologicallyDerivedProduct", "BiologicallyDerivedProductDispense", "BodySite", "BodyStructure", "Bundle", "CanonicalResource", "CapabilityStatement", "CarePlan", "CareTeam", | ||
| "CatalogEntry", "ChargeItem", "ChargeItemDefinition", "Citation", "Claim", "ClaimResponse", "ClinicalImpression", "ClinicalUseDefinition", "CodeSystem", "Communication", "CommunicationRequest", | ||
| "CompartmentDefinition", "Composition", "ConceptMap", "Condition", "ConditionDefinition", "Conformance", "Consent", "Contract", "Coverage", "CoverageEligibilityRequest", "CoverageEligibilityResponse", | ||
| "DataElement", "DetectedIssue", "Device", "DeviceAssociation", "DeviceComponent", "DeviceDefinition", "DeviceDispense", "DeviceMetric", "DeviceRequest", "DeviceUsage", "DeviceUseRequest", | ||
| "DeviceUseStatement", "DiagnosticOrder", "DiagnosticReport", "DocumentManifest", "DocumentReference", "DomainResource", "EffectEvidenceSynthesis", "EligibilityRequest", "EligibilityResponse", | ||
| "Encounter", "EncounterHistory", "Endpoint", "EnrollmentRequest", "EnrollmentResponse", "EpisodeOfCare", "EventDefinition", "Evidence", "EvidenceReport", "EvidenceVariable", "ExampleScenario", | ||
| "ExpansionProfile", "ExplanationOfBenefit", "FamilyMemberHistory", "Flag", "FormularyItem", "GenomicStudy", "Goal", "GraphDefinition", "Group", "GuidanceResponse", "HealthcareService", "ImagingManifest", | ||
| "ImagingObjectSelection", "ImagingSelection", "ImagingStudy", "Immunization", "ImmunizationEvaluation", "ImmunizationRecommendation", "ImplementationGuide", "Ingredient", "InsurancePlan", "InventoryItem", | ||
| "InventoryReport", "Invoice", "Library", "Linkage", "List", "Location", "ManufacturedItemDefinition", "Measure", "MeasureReport", "Media", "Medication", "MedicationAdministration", "MedicationDispense", | ||
| "MedicationKnowledge", "MedicationOrder", "MedicationPrescription", "MedicationRequest", "MedicationStatement", "MedicationUsage", "MedicinalProduct", "MedicinalProductAuthorization", "MedicinalProductContraindication", | ||
| "MedicinalProductDefinition", "MedicinalProductIndication", "MedicinalProductIngredient", "MedicinalProductInteraction", "MedicinalProductManufactured", "MedicinalProductPackaged", | ||
| "MedicinalProductPharmaceutical", "MedicinalProductUndesirableEffect", "MessageDefinition", "MessageHeader", "MetadataResource", "MolecularSequence", "NamingSystem", "NutritionIntake", "NutritionOrder", | ||
| "NutritionProduct", "Observation", "ObservationDefinition", "OperationDefinition", "OperationOutcome", "Order", "OrderResponse", "Organization", "OrganizationAffiliation", "PackagedProductDefinition", | ||
| "Parameters", "Patient", "PaymentNotice", "PaymentReconciliation", "Permission", "Person", "PlanDefinition", "Practitioner", "PractitionerRole", "Procedure", "ProcedureRequest", "ProcessRequest", | ||
| "ProcessResponse", "Provenance", "Questionnaire", "QuestionnaireResponse", "ReferralRequest", "RegulatedAuthorization", "RelatedPerson", "RequestGroup", "RequestOrchestration", "Requirements", | ||
| "ResearchDefinition", "ResearchElementDefinition", "ResearchStudy", "ResearchSubject", "Resource", "RiskAssessment", "RiskEvidenceSynthesis", "Schedule", "SearchParameter", "Sequence", "ServiceDefinition", | ||
| "ServiceRequest", "Slot", "Specimen", "SpecimenDefinition", "StructureDefinition", "StructureMap", "Subscription", "SubscriptionStatus", "SubscriptionTopic", "Substance", "SubstanceDefinition", | ||
| "SubstanceNucleicAcid", "SubstancePolymer", "SubstanceProtein", "SubstanceReferenceInformation", "SubstanceSourceMaterial", "SubstanceSpecification", "SupplyDelivery", "SupplyRequest", "Task", | ||
| "TerminologyCapabilities", "TestPlan", "TestReport", "TestScript", "Transport", "ValueSet", "VerificationResult", "VisionPrescription", | ||
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| "Supply", "Contraindication", "CapabilityStatement2", "ClinicalUseIssue", "DiagnosticRequest", "NutritionRequest", | ||
| "DecisionSupportServiceModule", "ModuleDefinition", "GuidanceRequest", "DecisionSupportRule", "ModuleMetadata", "OrderSet", "ModuleDefinition", "GuidanceRequest", "EvidenceFocus","ItemInstance" | ||
| ); | ||
| } | ||
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|
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| } |
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