From adf429ea462b6f6d25d71bbf755d39493de45cf9 Mon Sep 17 00:00:00 2001 From: nicolas Date: Fri, 12 Jan 2018 11:29:43 +0100 Subject: [PATCH 1/4] corrections of db name for dev version --- .../entity/species/VamdcInchikeyExceptions.java | 2 +- .../portal/entity/species/VamdcMarkupTypes.java | 2 +- .../species/VamdcMemberDatabaseIdentifiers.java | 2 +- .../portal/entity/species/VamdcMemberDatabases.java | 2 +- .../vamdc/portal/entity/species/VamdcSpecies.java | 2 +- .../portal/entity/species/VamdcSpeciesNames.java | 2 +- .../entity/species/VamdcSpeciesStructFormulae.java | 2 +- .../portal/entity/species/VamdcSpeciesTypes.java | 2 +- .../portal/session/queryLog/QueryStoreRequest.java | 12 +++--------- 9 files changed, 11 insertions(+), 17 deletions(-) diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcInchikeyExceptions.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcInchikeyExceptions.java index b037b2e..d049c03 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcInchikeyExceptions.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcInchikeyExceptions.java @@ -20,7 +20,7 @@ * VamdcInchikeyExceptions generated by hbm2java */ @Entity -@Table(name = "vamdc_inchikey_exceptions", catalog = "vamdc_species") +@Table(name = "vamdc_inchikey_exceptions", catalog = "vamdc_species_dev") public class VamdcInchikeyExceptions implements java.io.Serializable { private Integer id; diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMarkupTypes.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMarkupTypes.java index 736d7bb..a4c3a23 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMarkupTypes.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMarkupTypes.java @@ -17,7 +17,7 @@ * VamdcMarkupTypes generated by hbm2java */ @Entity -@Table(name = "vamdc_markup_types", catalog = "vamdc_species") +@Table(name = "vamdc_markup_types", catalog = "vamdc_species_dev") public class VamdcMarkupTypes implements java.io.Serializable { private int id; diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabaseIdentifiers.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabaseIdentifiers.java index afd4f70..e645ccc 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabaseIdentifiers.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabaseIdentifiers.java @@ -19,7 +19,7 @@ * VamdcMemberDatabaseIdentifiers generated by hbm2java */ @Entity -@Table(name = "vamdc_node_species", catalog = "vamdc_species", uniqueConstraints = @UniqueConstraint(columnNames = { +@Table(name = "vamdc_node_species", catalog = "vamdc_species_dev", uniqueConstraints = @UniqueConstraint(columnNames = { "species_id", "database_species_id", "member_database_id" })) public class VamdcMemberDatabaseIdentifiers implements java.io.Serializable { diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabases.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabases.java index 2061c0c..0526ce3 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabases.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabases.java @@ -19,7 +19,7 @@ * VamdcMemberDatabases generated by hbm2java */ @Entity -@Table(name = "vamdc_nodes", catalog = "vamdc_species") +@Table(name = "vamdc_nodes", catalog = "vamdc_species_dev") public class VamdcMemberDatabases implements java.io.Serializable { private Integer id; diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpecies.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpecies.java index 3c13f0b..d5c9910 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpecies.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpecies.java @@ -21,7 +21,7 @@ * VamdcSpecies generated by hbm2java */ @Entity -@Table(name = "vamdc_species", catalog = "vamdc_species", uniqueConstraints = @UniqueConstraint(columnNames = { +@Table(name = "vamdc_species", catalog = "vamdc_species_dev", uniqueConstraints = @UniqueConstraint(columnNames = { "inchikey" })) public class VamdcSpecies implements java.io.Serializable { diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesNames.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesNames.java index 543eaf8..d555c38 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesNames.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesNames.java @@ -22,7 +22,7 @@ * VamdcSpeciesNames generated by hbm2java */ @Entity -@Table(name = "vamdc_species_names", catalog = "vamdc_species", uniqueConstraints = @UniqueConstraint(columnNames = { +@Table(name = "vamdc_species_names", catalog = "vamdc_species_dev", uniqueConstraints = @UniqueConstraint(columnNames = { "species_id", "name", "markup_type_id" })) public class VamdcSpeciesNames implements java.io.Serializable { diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesStructFormulae.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesStructFormulae.java index 16064eb..de3fc6a 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesStructFormulae.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesStructFormulae.java @@ -22,7 +22,7 @@ * VamdcSpeciesStructFormulae generated by hbm2java */ @Entity -@Table(name = "vamdc_species_struct_formulae", catalog = "vamdc_species", uniqueConstraints = @UniqueConstraint(columnNames = { +@Table(name = "vamdc_species_struct_formulae", catalog = "vamdc_species_dev", uniqueConstraints = @UniqueConstraint(columnNames = { "species_id", "formula", "markup_type_id" })) public class VamdcSpeciesStructFormulae implements java.io.Serializable { diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesTypes.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesTypes.java index b16d27f..d6c0d99 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesTypes.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesTypes.java @@ -13,7 +13,7 @@ * VamdcSpeciesTypes generated by hbm2java */ @Entity -@Table(name = "vamdc_species_types", catalog = "vamdc_species") +@Table(name = "vamdc_species_types", catalog = "vamdc_species_dev") public class VamdcSpeciesTypes implements java.io.Serializable { private int id; diff --git a/portal.ejb/src/main/java/org/vamdc/portal/session/queryLog/QueryStoreRequest.java b/portal.ejb/src/main/java/org/vamdc/portal/session/queryLog/QueryStoreRequest.java index 577b7bf..0c84d0f 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/session/queryLog/QueryStoreRequest.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/session/queryLog/QueryStoreRequest.java @@ -79,20 +79,18 @@ private QueryStoreResponse associateRequest(String token, String userIp) { try { String request = this.getRequest(token, this.getUserEmail(), this.userIp); - // send request while no result or result is empty while ((result == null || QueryStoreResponse.STATUS_EMPTY.equals(result.getStatus())) && count < Settings.QUERYSTORE_MAX_RETRY.getInt()) { result = this.doRequest(request); + //if(result != null) Thread.sleep(Settings.QUERYSTORE_RETRY_TIMER.getInt()); count++; } - } catch (Exception e) { log.debug(e); - new QueryStoreResponse(QueryStoreResponse.STATUS_ERROR, "", "Error while querying query store"); - - } + result = new QueryStoreResponse(QueryStoreResponse.STATUS_ERROR, "", "Error while querying query store"); + } return result; } @@ -125,17 +123,14 @@ private QueryStoreResponse doRequest(String requestString) //SSLHandShakeException (IOException) occurs if missing certificate HttpResponse response = httpClient.execute(request); Integer statusCode = response.getStatusLine().getStatusCode(); - if ( statusCode == 200) { BufferedReader rd = new BufferedReader(new InputStreamReader( response.getEntity().getContent())); - String uuid; while ((uuid = rd.readLine()) != null) { result.append(uuid); } rd.close(); - } else { // empty response if (statusCode == 204) { @@ -150,7 +145,6 @@ else if (statusCode >= 400 && statusCode < 500) { return new QueryStoreResponse(QueryStoreResponse.STATUS_ERROR, "", response.getStatusLine().getReasonPhrase()); } } - // extract uuid from json response return QueryStoreResponseReader.parseResponse(result.toString()); } From 10ed8168fbe8966f106cc4c54ca19e598bdafcdc Mon Sep 17 00:00:00 2001 From: nicolas Date: Fri, 23 Mar 2018 16:32:01 +0100 Subject: [PATCH 2/4] Add a new Tools page and an entry in the main menu. --- portal.war/src/main/webapp/layout/menu.xhtml | 2 ++ portal.war/src/main/webapp/tools.xhtml | 33 ++++++++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 portal.war/src/main/webapp/tools.xhtml diff --git a/portal.war/src/main/webapp/layout/menu.xhtml b/portal.war/src/main/webapp/layout/menu.xhtml index cbcad2d..9a030c1 100644 --- a/portal.war/src/main/webapp/layout/menu.xhtml +++ b/portal.war/src/main/webapp/layout/menu.xhtml @@ -23,6 +23,8 @@ propagation="none" /> + + + + +

The VAMDC species database

+

+ Discover the content of each database in the VAMDC infrastructure +

+

+ +

+

Hitran file display and comparison

+

+ Plot data exported in HITRAN format +

+

+ +

+ + + + From 63d6e091a885cd79edbbdfcccfa7f1fe7f6525fa Mon Sep 17 00:00:00 2001 From: nicolas Date: Fri, 23 Mar 2018 16:51:45 +0100 Subject: [PATCH 3/4] query the production species database instead of the dev one, as introduced from merge with dev version --- .../vamdc/portal/entity/species/VamdcInchikeyExceptions.java | 2 +- .../org/vamdc/portal/entity/species/VamdcMarkupTypes.java | 2 +- .../entity/species/VamdcMemberDatabaseIdentifiers.java | 2 +- .../vamdc/portal/entity/species/VamdcMemberDatabases.java | 2 +- .../java/org/vamdc/portal/entity/species/VamdcSpecies.java | 2 +- .../org/vamdc/portal/entity/species/VamdcSpeciesNames.java | 2 +- .../portal/entity/species/VamdcSpeciesStructFormulae.java | 2 +- .../org/vamdc/portal/entity/species/VamdcSpeciesTypes.java | 2 +- .../portal/session/queryBuilder/forms/RadiativeForm.java | 5 ++--- 9 files changed, 10 insertions(+), 11 deletions(-) diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcInchikeyExceptions.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcInchikeyExceptions.java index d049c03..b037b2e 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcInchikeyExceptions.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcInchikeyExceptions.java @@ -20,7 +20,7 @@ * VamdcInchikeyExceptions generated by hbm2java */ @Entity -@Table(name = "vamdc_inchikey_exceptions", catalog = "vamdc_species_dev") +@Table(name = "vamdc_inchikey_exceptions", catalog = "vamdc_species") public class VamdcInchikeyExceptions implements java.io.Serializable { private Integer id; diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMarkupTypes.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMarkupTypes.java index a4c3a23..736d7bb 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMarkupTypes.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMarkupTypes.java @@ -17,7 +17,7 @@ * VamdcMarkupTypes generated by hbm2java */ @Entity -@Table(name = "vamdc_markup_types", catalog = "vamdc_species_dev") +@Table(name = "vamdc_markup_types", catalog = "vamdc_species") public class VamdcMarkupTypes implements java.io.Serializable { private int id; diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabaseIdentifiers.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabaseIdentifiers.java index e645ccc..afd4f70 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabaseIdentifiers.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabaseIdentifiers.java @@ -19,7 +19,7 @@ * VamdcMemberDatabaseIdentifiers generated by hbm2java */ @Entity -@Table(name = "vamdc_node_species", catalog = "vamdc_species_dev", uniqueConstraints = @UniqueConstraint(columnNames = { +@Table(name = "vamdc_node_species", catalog = "vamdc_species", uniqueConstraints = @UniqueConstraint(columnNames = { "species_id", "database_species_id", "member_database_id" })) public class VamdcMemberDatabaseIdentifiers implements java.io.Serializable { diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabases.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabases.java index 0526ce3..2061c0c 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabases.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabases.java @@ -19,7 +19,7 @@ * VamdcMemberDatabases generated by hbm2java */ @Entity -@Table(name = "vamdc_nodes", catalog = "vamdc_species_dev") +@Table(name = "vamdc_nodes", catalog = "vamdc_species") public class VamdcMemberDatabases implements java.io.Serializable { private Integer id; diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpecies.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpecies.java index d5c9910..3c13f0b 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpecies.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpecies.java @@ -21,7 +21,7 @@ * VamdcSpecies generated by hbm2java */ @Entity -@Table(name = "vamdc_species", catalog = "vamdc_species_dev", uniqueConstraints = @UniqueConstraint(columnNames = { +@Table(name = "vamdc_species", catalog = "vamdc_species", uniqueConstraints = @UniqueConstraint(columnNames = { "inchikey" })) public class VamdcSpecies implements java.io.Serializable { diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesNames.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesNames.java index d555c38..543eaf8 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesNames.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesNames.java @@ -22,7 +22,7 @@ * VamdcSpeciesNames generated by hbm2java */ @Entity -@Table(name = "vamdc_species_names", catalog = "vamdc_species_dev", uniqueConstraints = @UniqueConstraint(columnNames = { +@Table(name = "vamdc_species_names", catalog = "vamdc_species", uniqueConstraints = @UniqueConstraint(columnNames = { "species_id", "name", "markup_type_id" })) public class VamdcSpeciesNames implements java.io.Serializable { diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesStructFormulae.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesStructFormulae.java index de3fc6a..16064eb 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesStructFormulae.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesStructFormulae.java @@ -22,7 +22,7 @@ * VamdcSpeciesStructFormulae generated by hbm2java */ @Entity -@Table(name = "vamdc_species_struct_formulae", catalog = "vamdc_species_dev", uniqueConstraints = @UniqueConstraint(columnNames = { +@Table(name = "vamdc_species_struct_formulae", catalog = "vamdc_species", uniqueConstraints = @UniqueConstraint(columnNames = { "species_id", "formula", "markup_type_id" })) public class VamdcSpeciesStructFormulae implements java.io.Serializable { diff --git a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesTypes.java b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesTypes.java index d6c0d99..b16d27f 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesTypes.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcSpeciesTypes.java @@ -13,7 +13,7 @@ * VamdcSpeciesTypes generated by hbm2java */ @Entity -@Table(name = "vamdc_species_types", catalog = "vamdc_species_dev") +@Table(name = "vamdc_species_types", catalog = "vamdc_species") public class VamdcSpeciesTypes implements java.io.Serializable { private int id; diff --git a/portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/forms/RadiativeForm.java b/portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/forms/RadiativeForm.java index 64790aa..4b4deb1 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/forms/RadiativeForm.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/forms/RadiativeForm.java @@ -28,13 +28,12 @@ public RadiativeForm(){ addField(wlField); AbstractField field = new UnitConvRangeField(Restrictable.StateEnergy, "Upper state energy", new EnergyUnitConverter()); field.setPrefix("upper"); - addField(field); - //addField(new RangeField("upper",Restrictable.StateEnergy,"Upper state energy")); + addField(field);; field = new UnitConvRangeField(Restrictable.StateEnergy, "Lower state energy", new EnergyUnitConverter()); field.setPrefix("lower"); addField(field); - //addField(new RangeField("lower",Restrictable.StateEnergy,"Lower state energy")); addField(new RangeField(Restrictable.RadTransProbabilityA,"Probability, A")); + addField(new RangeField(Restrictable.RadTransProbabilityLineStrength,"Line strength")); } static ProxyRangeField setupWLField() { From 8677b8bd40c0a68688b38ad11d9eea962c557d57 Mon Sep 17 00:00:00 2001 From: nicolas Date: Fri, 23 Mar 2018 17:00:30 +0100 Subject: [PATCH 4/4] remove line strength from Radiative form --- .../vamdc/portal/session/queryBuilder/forms/RadiativeForm.java | 1 - 1 file changed, 1 deletion(-) diff --git a/portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/forms/RadiativeForm.java b/portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/forms/RadiativeForm.java index 4b4deb1..db5b633 100644 --- a/portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/forms/RadiativeForm.java +++ b/portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/forms/RadiativeForm.java @@ -33,7 +33,6 @@ public RadiativeForm(){ field.setPrefix("lower"); addField(field); addField(new RangeField(Restrictable.RadTransProbabilityA,"Probability, A")); - addField(new RangeField(Restrictable.RadTransProbabilityLineStrength,"Line strength")); } static ProxyRangeField setupWLField() {