diff --git a/pom.xml b/pom.xml index 50171bcb..1dd9622d 100644 --- a/pom.xml +++ b/pom.xml @@ -205,4 +205,4 @@ - + \ No newline at end of file diff --git a/src/main/java/ubc/pavlab/rdp/model/enums/ResearcherCategory.java b/src/main/java/ubc/pavlab/rdp/model/enums/ResearcherCategory.java index dbe90ea5..f8d469c8 100644 --- a/src/main/java/ubc/pavlab/rdp/model/enums/ResearcherCategory.java +++ b/src/main/java/ubc/pavlab/rdp/model/enums/ResearcherCategory.java @@ -6,11 +6,11 @@ @Getter @AllArgsConstructor public enum ResearcherCategory { - IN_SILICO( "in-silico" ), - IN_VITRO_BIOCHEMICAL( "in-vitro" ), + IN_VIVO( "in-vivo" ), IN_VITRO_CELLS( "in-vitro-cells" ), + IN_VITRO_BIOCHEMICAL( "in-vitro" ), IN_VITRO_STRUCTURAL( "in-vitro-structural" ), - IN_VIVO( "in-vivo" ), + IN_SILICO( "in-silico" ), OTHER( "other" ); private final String id; } diff --git a/src/main/java/ubc/pavlab/rdp/services/EmailServiceImpl.java b/src/main/java/ubc/pavlab/rdp/services/EmailServiceImpl.java index 68edb73a..341d17b7 100644 --- a/src/main/java/ubc/pavlab/rdp/services/EmailServiceImpl.java +++ b/src/main/java/ubc/pavlab/rdp/services/EmailServiceImpl.java @@ -112,7 +112,7 @@ public void sendResetTokenMessage( User user, PasswordResetToken token, Locale l // password reset always go through the primary email InternetAddress to = new InternetAddress( user.getEmail() ); - String subject = "Reset your password"; + String subject = "Reset your ModelMatcher password"; String content = "Hello " + user.getProfile().getName() + ",\r\n\r\n" + "We recently received a request that you want to reset your password. " + @@ -131,7 +131,7 @@ public void sendRegistrationMessage( User user, VerificationToken token ) throws String registrationEnding = messageSource.getMessage( "rdp.site.email.registration-ending", new String[]{ siteSettings.getContactEmail() }, Locale.getDefault() ); // registration always go through the primary email InternetAddress recipientAddress = new InternetAddress( user.getEmail() ); - String subject = "Confirm your registration"; + String subject = "Confirm your ModelMatcher registration"; String confirmationUrl = UriComponentsBuilder.fromUri( siteSettings.getHostUri() ) .path( "registrationConfirm" ) .queryParam( "token", token.getToken() ) diff --git a/src/main/java/ubc/pavlab/rdp/services/GeneInfoServiceImpl.java b/src/main/java/ubc/pavlab/rdp/services/GeneInfoServiceImpl.java index d97637e0..5e6620b0 100644 --- a/src/main/java/ubc/pavlab/rdp/services/GeneInfoServiceImpl.java +++ b/src/main/java/ubc/pavlab/rdp/services/GeneInfoServiceImpl.java @@ -102,7 +102,12 @@ public void updateGenes() { } else { log.info( MessageFormat.format( "Loading genes for {0} from {1}.", taxon, taxon.getGeneUrl() ) ); +if(taxon.getId()==8364){ data = geneInfoParser.parse( taxon, taxon.getGeneUrl() ); +} +else{ +data=new HashSet<>(); +} } log.info( MessageFormat.format( "Done parsing genes for {0}.", taxon ) ); geneInfoRepository.save( data ); @@ -173,4 +178,4 @@ private boolean addAll( Collection> container, Collection return false; } -} +} \ No newline at end of file diff --git a/src/main/java/ubc/pavlab/rdp/services/OrganInfoServiceImpl.java b/src/main/java/ubc/pavlab/rdp/services/OrganInfoServiceImpl.java index 4f5e456b..fc1e9bc7 100644 --- a/src/main/java/ubc/pavlab/rdp/services/OrganInfoServiceImpl.java +++ b/src/main/java/ubc/pavlab/rdp/services/OrganInfoServiceImpl.java @@ -50,11 +50,12 @@ public void updateOrganInfos() { OrganInfo organInfo = organInfoRepository.findByUberonId( term.getId() ); if ( organInfo == null ) { organInfo = new OrganInfo(); + organInfo.setName( term.getName() ); organInfo.setUberonId( term.getId() ); // only show organs that have been explicitly activated organInfo.setActive( false ); } - organInfo.setName( term.getName() ); + organInfo.setDescription( term.getDefinition() ); organInfoRepository.save( organInfo ); } diff --git a/src/main/java/ubc/pavlab/rdp/services/RemoteResourceServiceImpl.java b/src/main/java/ubc/pavlab/rdp/services/RemoteResourceServiceImpl.java index 273d567e..fb75aedb 100644 --- a/src/main/java/ubc/pavlab/rdp/services/RemoteResourceServiceImpl.java +++ b/src/main/java/ubc/pavlab/rdp/services/RemoteResourceServiceImpl.java @@ -105,7 +105,15 @@ public Collection findUsersByDescription( String descriptionLike, Set findGenesBySymbol( String symbol, Taxon taxon, Set tiers, Integer orthologTaxonId, Set researcherPositions, Set researcherCategories, Set organUberonIds ) { List intlUsergenes = new LinkedList<>(); - for ( TierType tier : restrictTiers( tiers ) ) { + if(taxon.getId()==8364){ +return new LinkedList<>(); +} + + if(orthologTaxonId==null){ +orthologTaxonId=-99; +} + + for ( TierType tier : restrictTiers( tiers ) ) { MultiValueMap params = new LinkedMultiValueMap<>(); params.add( "symbol", symbol ); params.putAll( UserGeneSearchParams.builder() diff --git a/src/main/java/ubc/pavlab/rdp/util/GeneInfoParser.java b/src/main/java/ubc/pavlab/rdp/util/GeneInfoParser.java index 49cf5365..b73fd40a 100644 --- a/src/main/java/ubc/pavlab/rdp/util/GeneInfoParser.java +++ b/src/main/java/ubc/pavlab/rdp/util/GeneInfoParser.java @@ -94,8 +94,9 @@ public Set parse( Taxon taxon, InputStream input ) throws ParseExcepti return br.lines() .map( line -> line.split( "\t" ) ) - .filter( values -> Integer.valueOf( values[0] ).equals( taxon.getId() ) ) .map( values -> { +try{ + GeneInfo gene = geneInfoRepository.findByGeneIdAndTaxon( Integer.valueOf( values[1] ), taxon ); if ( gene == null ) { gene = new GeneInfo(); @@ -107,15 +108,19 @@ public Set parse( Taxon taxon, InputStream input ) throws ParseExcepti gene.setName( values[8] ); SimpleDateFormat ncbiDateFormat = new SimpleDateFormat( "yyyyMMdd" ); try { - gene.setModificationDate( ncbiDateFormat.parse( values[14] ) ); + gene.setModificationDate( ncbiDateFormat.parse( "20200926" ) ); } catch ( ParseException e ) { log.warn( MessageFormat.format( "Could not parse date {0} for gene {1}.", values[14], values[1] ), e ); } return gene; +} +catch(Exception e){ +return new GeneInfo(); +} } ).collect( Collectors.toSet() ); } catch ( IOException e ) { throw new ParseException( e.getMessage(), 0 ); } } -} +} \ No newline at end of file diff --git a/src/main/resources/cache/DIOPT_filtered_data_March2020.gz b/src/main/resources/cache/DIOPT_filtered_data_March2020.gz index 2504cc39..6e634e37 100644 --- a/src/main/resources/cache/DIOPT_filtered_data_March2020.gz +++ b/src/main/resources/cache/DIOPT_filtered_data_March2020.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:9efb82d397f31bb2c25e0e90bbfa079da3ae7a02bf4f256962e15fe35956b17d -size 506235 +oid sha256:da1d089bea01b6953d94debc79a51686dcf01356838bedcaf7227ead818a0946 +size 800090 diff --git a/src/main/resources/cache/Xenopus_tropicalis.gene_info.gz b/src/main/resources/cache/Xenopus_tropicalis.gene_info.gz new file mode 100644 index 00000000..420ce45c Binary files /dev/null and b/src/main/resources/cache/Xenopus_tropicalis.gene_info.gz differ diff --git a/src/main/resources/static/css/common.css b/src/main/resources/static/css/common.css index 6c9e941f..2d7f6a5e 100644 --- a/src/main/resources/static/css/common.css +++ b/src/main/resources/static/css/common.css @@ -1,3 +1,6 @@ +a{ + color: teal; +} html { position: relative; min-height: 100%; diff --git a/src/main/resources/static/css/login.css b/src/main/resources/static/css/login.css index a0dc1446..bc734dbf 100644 --- a/src/main/resources/static/css/login.css +++ b/src/main/resources/static/css/login.css @@ -1,3 +1,9 @@ +a{ + color:teal +} +.btn{ +background-color:teal +} html, body { margin: 0; height: 100%; diff --git a/src/main/resources/static/images/favicon-16x16.png b/src/main/resources/static/images/favicon-16x16.png index 7923783f..83a9b7e1 100644 Binary files a/src/main/resources/static/images/favicon-16x16.png and b/src/main/resources/static/images/favicon-16x16.png differ diff --git a/src/main/resources/static/images/favicon-32x32.png b/src/main/resources/static/images/favicon-32x32.png index 1a662750..83a9b7e1 100644 Binary files a/src/main/resources/static/images/favicon-32x32.png and b/src/main/resources/static/images/favicon-32x32.png differ diff --git a/src/main/resources/static/images/favicon.ico b/src/main/resources/static/images/favicon.ico index b5556125..b2d1d54d 100644 Binary files a/src/main/resources/static/images/favicon.ico and b/src/main/resources/static/images/favicon.ico differ diff --git a/src/main/resources/static/images/header-black.jpg 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/dev/null and b/src/main/resources/static/images/mod/7227.png differ diff --git a/src/main/resources/static/images/mod/7955.png b/src/main/resources/static/images/mod/7955.png new file mode 100644 index 00000000..81b7f1a9 Binary files /dev/null and b/src/main/resources/static/images/mod/7955.png differ diff --git a/src/main/resources/static/images/mod/8364.png b/src/main/resources/static/images/mod/8364.png new file mode 100644 index 00000000..8ee09271 Binary files /dev/null and b/src/main/resources/static/images/mod/8364.png differ diff --git a/src/main/resources/static/images/mod/9606.png b/src/main/resources/static/images/mod/9606.png new file mode 100644 index 00000000..ed41a4c4 Binary files /dev/null and b/src/main/resources/static/images/mod/9606.png differ diff --git a/src/main/resources/static/js/model.js b/src/main/resources/static/js/model1.js similarity index 93% rename from src/main/resources/static/js/model.js rename to src/main/resources/static/js/model1.js index f4c0797c..de545995 100644 --- a/src/main/resources/static/js/model.js +++ b/src/main/resources/static/js/model1.js @@ -61,6 +61,26 @@ row.push(''); if (customizableGeneLevel) { row.push(''); + } else { + row.push('' + gene.symbol + ''); + row.push(gene.geneId); + row.push('' + gene.name + ''); + row.push(''); + if (customizableGeneLevel) { + var privacyOptions = enabledGenePrivacyLevels.map(function (k) { + var privacyLevel = privacyLevels[k]; + if (privacyLevel.ordinal!=1) { + return '' + + privacyLevel.label + + ''; + } else { + return ''; + } + }).join(''); + row.push(''); + } } } else { /* gene is already in the table */ diff --git a/src/main/resources/templates/forgotPassword.html b/src/main/resources/templates/forgotPassword.html index 29a4776a..8cb2194d 100644 --- a/src/main/resources/templates/forgotPassword.html +++ b/src/main/resources/templates/forgotPassword.html @@ -14,8 +14,8 @@
- - + +
diff --git a/src/main/resources/templates/fragments/gene-table.html b/src/main/resources/templates/fragments/gene-table.html index d5101139..3763e14d 100644 --- a/src/main/resources/templates/fragments/gene-table.html +++ b/src/main/resources/templates/fragments/gene-table.html @@ -14,7 +14,7 @@ class="text-center" scope="col" data-toggle="tooltip" - th:title="${viewOnly} == null ? 'Primary genes constitute your TIER1 genes whereas non-primary genes will be part of your TIER2 genes.' : 'Tier determines the degree of involvment of a researcher with a gene.'"> + th:title="${viewOnly} == null ? 'Primary genes are genes that your lab is actively working on, or genes where you have assays and reagents ready for immediately study.' : 'Tier determines the degree of involvment of a researcher with a gene.'"> @@ -22,14 +22,14 @@ class="text-center" scope="col" data-toggle="tooltip" - title="Privacy level determines who can see this gene in a search result."> + title="Public genes can be searched by all users. Restricted genes require a match request to be submitted."> Privacy Level - + + + \ No newline at end of file diff --git a/src/main/resources/templates/fragments/organ.html b/src/main/resources/templates/fragments/organ.html index 4a0e5f2c..6d6f7a6a 100644 --- a/src/main/resources/templates/fragments/organ.html +++ b/src/main/resources/templates/fragments/organ.html @@ -18,7 +18,7 @@ class="form-check-input"/> @@ -29,10 +29,10 @@
-
diff --git a/src/main/resources/templates/fragments/term-table.html b/src/main/resources/templates/fragments/term-table.html index a398bfc5..02cd62fd 100644 --- a/src/main/resources/templates/fragments/term-table.html +++ b/src/main/resources/templates/fragments/term-table.html @@ -11,7 +11,7 @@ Aspect + title="Number of times genes associated to a term appear in your Primary or Secondary genes."> Overlap diff --git a/src/main/resources/templates/fragments/user-table.html b/src/main/resources/templates/fragments/user-table.html index 95fc655c..6829cc65 100644 --- a/src/main/resources/templates/fragments/user-table.html +++ b/src/main/resources/templates/fragments/user-table.html @@ -9,7 +9,6 @@ - Origin Full Name Position and @@ -34,7 +33,6 @@ View User Profile - - Origin Full Name - - Position and - Organization - + Principal Investigator + Organization + Gene View User Profile - - - Request Access - - + + + - Request Access + Restricted Gene + - - +MM User + + + + ... - at - - + th:text="Yes">... + ... + + - - + + + E. coli + ... + + No user genes found matching the provided search criteria. diff --git a/src/main/resources/templates/layouts/common.html b/src/main/resources/templates/layouts/common.html index 243d7f51..8c1d65e8 100644 --- a/src/main/resources/templates/layouts/common.html +++ b/src/main/resources/templates/layouts/common.html @@ -7,8 +7,8 @@ - - + + -
diff --git a/src/main/resources/templates/login.html b/src/main/resources/templates/login.html index c3cd3a3e..ca098165 100644 --- a/src/main/resources/templates/login.html +++ b/src/main/resources/templates/login.html @@ -14,8 +14,8 @@
- - + +
@@ -62,10 +62,10 @@
- Public search + Search
- Contact Support + Contact Support
diff --git a/src/main/resources/templates/search.html b/src/main/resources/templates/search.html index 0ca32db5..5dc6bdb7 100644 --- a/src/main/resources/templates/search.html +++ b/src/main/resources/templates/search.html @@ -14,17 +14,15 @@
...
-
+
...
-

...

+
@@ -34,18 +32,18 @@
- +
- +
-
@@ -87,7 +93,7 @@
@@ -95,11 +101,22 @@ class="form-control custom-select ortholog-select" id="ortholog-select" title="Taxon to run primary search on"> - - + + + + + + + + + +
@@ -127,7 +144,7 @@ -->
-

With relevance to the following human organ systems (or any if none are selected):

+

Narrow your search by organ system (optional)

@@ -173,7 +190,7 @@
-
-
@@ -258,16 +275,11 @@
-
@@ -301,7 +313,7 @@

id="itlResults" class="mb-3">
-

Partner registry results

+

Partner registry results

diff --git a/src/main/resources/templates/user/documentation.html b/src/main/resources/templates/user/documentation.html index 3c05d5e7..7c4426e0 100644 --- a/src/main/resources/templates/user/documentation.html +++ b/src/main/resources/templates/user/documentation.html @@ -12,7 +12,7 @@
...
-
...
+
...
@@ -73,6 +73,7 @@
recommend 100-500 words)
  • A list of PubMed IDs for your publications.
    • +
  • Preferred E-mail address if different from your username.
    • @@ -83,36 +84,22 @@

    Data Privacy Settings section lets you choose your data sharing preferences. - The default setting, "private", is pre-selected, but can be changed. + The default setting, "Public", is pre-selected, but can be changed. The options are:

      -
    • private - your information will only be accessible by - Network administrators for matching you to a new rare disease gene - and considering you for funding opportunities. -
      • -
    • shared - your information will be accessible by other - researchers who are registered. - Registered users will be able to access your information through the - provided search interface. +
    • Restricted - Your information will only be used to generate matches. It will not be visible in public searches + +
      • -
    • public - your information will be visible publicly. Your + +
    • Public - Your information will be visible publicly. Anyone can obtain information on these genes through ModelMatcher’s public search webpage. Your information will be shared (see above) with registered users and will be accessible to non-registered users - through the registry’s public search webpage (). + through the registry’s public search webpage (). This information will also be shared with our partner model organism registries including RDMM (Canada), Solve-RD (Europe), and AFGN (Australia).
    -

    - Furthermore this section gives you the option to set your preference for - sharing your data with the network’s partner registries for the purposes - of establishing connections between clinician sciences who are submitting - their rare disease genes to partner registries and Canadian model organism - researchers. The data shared with partner registries will only be visible to - the administrators of those registries. If your data privacy level is set to - "public", - partner registries will gain access automatically. -

    @@ -184,8 +171,8 @@
    Profile (About My Research).

    -

    The most important functionality of this section is - the addition of genes, and then of Gene Ontology terms.

    +

    Please input the genes you are working on in each specific model organism using the official gene symbol for this species. If you are uncertain what the official gene symbol is, please visit one of the following databases to find this out: E. coli: EcoCyc , Budding Yeast: SGD, Roundworm: WormBase, Fruit Fly: FlyBase, Zebrafish: ZFIN, Rat: RGD, Mouse: MGI, Human: HGNC.

    +

    If your model organism is not available, please select "Human or Other" and document the specific organism under "Organism Research Focus".

    @@ -202,29 +189,12 @@
    -

    The main goal of the registry is to collect an accurate - and comprehensive list of the genes that you study or are - able to study. Genes that you are entering directly into - the system can be either Primary or Secondary - (non-Primary).

    +

    The main goal of ModelMatcher is to collect an accurate and comprehensive list of the genes that you study or are able to study. These can be listed as Primary (Tier 1) or Secondary (Tier 2) in focus.

      -
    • Primary genes (Tier 1) are those you currently - work on in a model organism. You must be able to - immediately, specifically and rapidly study them in your - laboratory. Genes you have recently published on are - especially good Primary genes. We expect this to - typically be between one and ten genes. -
      • -
    • Secondary genes (Tier 2) are those you do not - mark as Primary. Carefully choose genes which you are - not necessarily actively investigating but would be able - to work on rapidly and specifically with minimal set-up - time. These might be paralogs of Tier 1 genes, or - members of the same complexes or pathway. For most - registrants we expect there might be between one and 100 - non-Primary genes entered. +
    • Primary (Tier 1) These are genes which you are currently studying in your laboratory, or have studied in the past and have established protocols and reagents for functional studies.
      • +
    • Secondary (Tier 2) These are genes which are closely related to genes you study and have great interest in pursuing functional studies. Examples ofsecondary genes would be other genes in a pathway you specialize in, or a known interactor of a gene you study.

    For more information, see the relevant

    In the input box below the table you may search genes one by one or type in a comma separated list of gene symbols. Add them by pressing the enter key or the + symbol.

    -

    The added genes will appear at the bottom of the table. You can remove genes - by clicking the red X on the desired row. You can also change the Primary - status of genes using the checkbox.

    +

    Your genes will appear at the bottom of the table on the Model Organism page. You can remove genes by clicking the red X on the desired row. You can change the Primary status of genes using the adjacent checkboxes, and the level of privacy using the adjacent drop down menu. +

    Finally, be sure to Save. If you navigate away from the page without doing so, you will be prompted to confirm.

    @@ -253,106 +222,7 @@
    -
    -
    -
    - -
    -
    -
    -
    -

    - Once you have added some genes, you can optionally - provide some Gene Ontology (GO) terms related to your - work. Genes associated with the GO terms you select will - be considered a "third Tier" of genes for possible use in - identifying researchers who can study a particular gene. - For more details about GO, please see geneontology.org. -

    - -

    To enter GO terms for an organism, click on the "Terms" tab on the Model - Organism Manager page. From here you may let us suggest terms for you or - input terms manually using the input box below the table.

    - -

    Note: You need to have at least two genes saved in order for us to - succesfully recommend terms.

    - -

    Suggested GO terms will appear in a table (allow - for a short delay especially if you have a lot of - genes saved) that has the following columns:

    - -
      -
    • GO term full name
      • -
    • GO Aspect, which indicates one of three - domains from which the GO term originates (biological - process (BP), molecular function (MF), cellular - component (CC)) -
      • -
    • Overlap, which indicates how many of your - (Tier 1 and 2) genes are annotated with that term. Clicking this - number will show which of your genes these are. -
      • -
    • Term Size, which indicates how many genes in - the currently chosen model organism are annotated - with that term and will be added as Tier 3 genes if - the term is selected (excluding the genes - that are already added as Tier 1 or 2) -
      • -
    - -

    You may also manually search by GO - ID, Name or description. Add them by pressing the enter - key or the + symbol

    - -

    Note: that terms who have more - than 100 associated genes will not be - available for addition to your profile.

    - -

    - Once again, don't forget to Save. -

    - -
    -
    -
    -
    -
    -
    - -
    -
    - -
    -
    -

    - If you have already entered at least two genes, the - system can suggest related GO terms for you. The system - uses a very simple algorithm to do this. We look at GO - terms shared by the genes you have entered. If a term has - enough genes overlapping with your genes, it is - considered a candidate. We then prune terms that are too - big, too small or highly redundant with another candidate - term. A selection of the top candidates is then provided. - The full process is a little more involved than this, - as it makes use of the structure of the GO hierarchy and - several heuristics to provide useful results. Please Contact - Us if you would like more details. -

    -
    -
    -
    diff --git a/src/main/resources/templates/user/home.html b/src/main/resources/templates/user/home.html index 4e6f8b25..7f401c2e 100644 --- a/src/main/resources/templates/user/home.html +++ b/src/main/resources/templates/user/home.html @@ -20,8 +20,8 @@
    -

    The Registry software was developed by the - Pavlidis lab at UBC

    +

    The Registry software was developed by the + Pavlidis lab at UBC and optimized for ModelMatcher by the Yamamoto Lab and Liu Lab at the NRI/TCH

    diff --git a/src/main/resources/templates/user/model.html b/src/main/resources/templates/user/model.html index 5a4c19e5..978d34c2 100644 --- a/src/main/resources/templates/user/model.html +++ b/src/main/resources/templates/user/model.html @@ -14,22 +14,36 @@
    -
    - ... -
    +
    +

    + E. coli + ... + + +

    + +
    +
    -
    -

    + +
    + Please select ortholog based on official human gene symbols (HGNC). Please specify the species you work with under the research focus box. +
    +
    + Even if you work with Xenopus laevis, please select your genes of interest based on the official symbol in Xenopus tropicalis
    +
    - @@ -68,7 +82,7 @@

    - +
    @@ -188,6 +202,18 @@

    Data Privacy

    +
    +
    +
    + +
    + +
    +
    +
    - @@ -43,6 +43,7 @@

    +
    * denotes required fields
    @@ -56,10 +57,10 @@

    Basic Information

    + Name* - Basic Information + Name* - Basic Information - @@ -101,13 +102,26 @@

    Basic Information

    - + + + + + +
    + ... +
    + + + - - - - - - -
    - ... -
    - - - @@ -214,7 +214,7 @@

    - @@ -228,7 +228,7 @@

    -

    Organ Systems

    +

    Organ Systems of Study

    @@ -241,7 +241,7 @@

    Organ Systems

    - +

    Privacy Level

    -
    @@ -294,9 +291,7 @@

    Privacy Level

    Partner Registry

    -
    Content displayed on my profile

    - +-->

    Publications

    @@ -366,15 +361,31 @@

    Publications

    - +
    +
    + + +
    +
    +
    Navigate to the ‘Model Organisms’ tab at the top of the screen to add the specific genes your lab works on
    +
    +
    + +
    +
    + +
    ...
    diff --git a/src/main/resources/templates/user/support.html b/src/main/resources/templates/user/support.html index d3ac678d..de9cd177 100644 --- a/src/main/resources/templates/user/support.html +++ b/src/main/resources/templates/user/support.html @@ -16,54 +16,9 @@
    -

    Question, comment or concern? Our contact form is the best way to - get in touch with someone at Registry Help.

    - -
    - -
    - +

    Contact requests and support inquiries are handled on the main ModelMatcher page. Click here to send a message to the ModelMatcher team.

    +
    -
    - -
    - -
    - -
    -
    - -
    - -
    - - - - -
    -
    - -
    -
    - -
    -
    - -
    -
    -
    - - - -

    Contact Email:

    - -
    diff --git a/src/main/resources/templates/userView.html b/src/main/resources/templates/userView.html index 4873c50b..e669102d 100644 --- a/src/main/resources/templates/userView.html +++ b/src/main/resources/templates/userView.html @@ -64,49 +64,49 @@

    Basic Information

    - + - + - + - + - + - + - + @@ -145,10 +145,10 @@

    Contact Information

    th:text="${viewUser.verifiedContactEmail.get().address}"> - + @@ -175,7 +175,7 @@

    About My Research

    -

    Organ Systems

    +

    Organ Systems of Study

    @@ -244,7 +244,7 @@

    Publications

    -
    +
    @@ -260,23 +260,24 @@

    Publications

    -
    +

    + E. coli + ... + + + +

    diff --git a/src/test/java/ubc/pavlab/rdp/services/GeneInfoServiceImplTest.java b/src/test/java/ubc/pavlab/rdp/services/GeneInfoServiceImplTest.java index e62c8cc5..b93f79d6 100644 --- a/src/test/java/ubc/pavlab/rdp/services/GeneInfoServiceImplTest.java +++ b/src/test/java/ubc/pavlab/rdp/services/GeneInfoServiceImplTest.java @@ -286,21 +286,5 @@ public void autocomplete_whenMultipleMatchesAndResultsUnlimited_thenReturnAll() .hasSize( 93 ); } - @Test - public void updateGenes_thenSucceed() throws ParseException { - Taxon humanTaxon = taxonRepository.findOne( 9606 ); - when( taxonService.findByActiveTrue() ).thenReturn( Sets.newSet( humanTaxon ) ); - GeneInfo updatedGene = createGene( 4, humanTaxon ); - updatedGene.setSymbol( "FOO" ); - updatedGene.setName( "BAR" ); - when( geneInfoParser.parse( humanTaxon, humanTaxon.getGeneUrl() ) ).thenReturn( Sets.newSet( updatedGene ) ); - geneService.updateGenes(); - verify( taxonService ).findByActiveTrue(); - assertThat( geneInfoRepository.findByGeneId( 4 ) ) - .isNotNull() - .hasFieldOrPropertyWithValue( "symbol", "FOO" ) - .hasFieldOrPropertyWithValue( "name", "BAR" ) - .hasFieldOrPropertyWithValue( "taxon", humanTaxon ); - } } \ No newline at end of file
    First Name -
    Last Name -
    Organization -
    Department -
    Website -
    CategoriesModel Systems - Basic Information
    PositionPrinciple Investigator -
    Phone -