diff --git a/README.md b/README.md index e687f6e..07453e9 100644 --- a/README.md +++ b/README.md @@ -1,219 +1,5 @@ [![Build Status](https://travis-ci.org/agduncan94/gdc-viewer.svg?branch=develop)](https://travis-ci.org/agduncan94/gdc-viewer) # GDC JBrowse Plugin -A plugin for [JBrowse](https://jbrowse.org/) for viewing [GDC](https://gdc.cancer.gov/) data. For any bugs, issues, or feature recommendations please create an issue through GitHub. +A plugin for [JBrowse](https://jbrowse.org/) for viewing [GDC](https://gdc.cancer.gov/) data. For any bugs, issues, or feature recommendations please create an issue or PR through GitHub. -# Installation and Setup -## 1. Install JBrowse -Quick setup of JBrowse - https://github.com/GMOD/jbrowse/#install-jbrowse-from-github-for-developers - -## 2. Install Plugin -See [JBrowse - Installing Plugins](https://jbrowse.org/docs/plugins.html) for a general approach to installing plugins. - -For installing gdc-viewer plugin: -1. Copy the gdc-viewer folder into the JBrowse `plugins` directory. -2. Add 'gdc-viewer' to the array of plugins in the `jbrowse_conf.json`. - -## 3. Install Reference Sequence Data -Now setup the reference sequence used. GDC requires the GRCh38 Human reference files. - -Download the GRCh38 `.fa` and `.fa.fai` files online (ex. http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch38/). Then put the following in `./data/tracks.conf` (note files may be named something else). - -``` -refSeqs=GRCh38.genome.fa.fai - -[tracks.refseqs] -urlTemplate=GRCh38.genome.fa -``` - -## 4. Adding new tracks -We have some basic example tracks in `data/tracks.conf`. You can also add new tracks by using the GDC dialog accessible within JBrowse. These are present in the menu under `GDC`. See [Dynamic Track Generation](#dynamic-track-generation) for more details. - -## 5. Run JBrowse -You'll have to run the following commands: - -``` -./setup.sh -utils/jb_run.js -p 3000 -``` - -JBrowse should now be running with the GDC Plugin working! - -# JBrowse configuration -## Faceted Track Selector -Add the following to your jbrowse.conf to use the faceted track selector. -``` -[trackSelector] -type = Faceted -displayColumns = - + label - + key - + datatype - + case - + project - + primarySite -``` - -Note that this will only show preloaded tracks as well as tracks you have added using the various dialogs. It does not dynamically create tracks based on what is available from the GDC. - -# Available Store SeqFeature -## A note on filters -All SeqFeatures support filters as they are defined in the [GDC API Documentation](https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-query). - -Note that filters should have the filter type prepended to the front. Ex. Case filters use `cases.`, SSM filters use `ssms.`, and Gene filters use `genes.`. GraphQL is used to retrieve results, so if the filters work there, they work with these Store classes. - -The following shows a filter for cases by ethnicity: -``` -{ - "op":"in", - "content":{ - "field":"cases.demographic.ethnicity", - "value":[ - "hispanic or latino" - ] - } -} -``` - -You can view/edit the filters associated with a track by clicking the down arrow for the track menu and selecting `View Applied Filters`. Be careful, there are currently no checks to see if the filters are valid before applying them. - -## Genes -A simple view of all of the genes seen across all cases. - -You can view case specific genes by setting the `case` field. - -You can apply filters to the track too, in the same format as GDC. The below example only shows Genes whose biotype is not 'protein_coding'. - -``` -{ - "op":"!=", - "content":{ - "field":"cases.biotype", - "value":"protein_coding" - } -} -``` - -To put it in the track config you may want to minimize it as such: -``` -filters={"op":"!=","content":{"field":"cases.biotype","value":"protein_coding"}} -``` - -Example Track: -``` -[tracks.GDC_Genes] -storeClass=gdc-viewer/Store/SeqFeature/Genes -type=JBrowse/View/Track/GeneTrack -key=GDC Genes -metadata.datatype=Gene -filters={"op":"!=","content":{"field":"cases.biotype","value":"protein_coding"}} -``` - -![GDC Genes](images/GDC-genes-protein-coding.png) - -### Extra notes -You can set the max number of genes to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear. - -## SSMs -A simple view of all of the simple somatic mutations seen across all cases. - -You can view case specific SSMs by setting the `case` field. - -You can apply filters to the track too, in the same format as GDC. The below example only shows SSMs whose reference allele is 'G'. -``` -{ - "op":"=", - "content":{ - "field":"ssms.reference_allele", - "value":"G" - } -} -``` - -To put it in the track config you may want to minimize it as such: -``` -filters={"op":"=","content":{"field":"ssms.reference_allele","value":"G"}} -``` - -Example Track: -``` -[tracks.GDC_SSM] -storeClass=gdc-viewer/Store/SeqFeature/SimpleSomaticMutations -type=gdc-viewer/View/Track/SSMVariants -key=GDC SSM -metadata.datatype=SSM -filters={"op":"=","content":{"field":"ssms.reference_allele","value":"G"}} -``` - -![GDC SSMs](images/GDC-mutations-base-g.png) - -### Extra notes -You can set the max number of SSMs to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear. - -## CNVs -A simple view of all of the CNVs seen across all cases. - -You can view case specific CNVs by setting the `case` field. - -You can apply filters to the track too, in the same format as GDC. The below example only shows CNVs that are 'Gains'. -``` -{ - "op":"=", - "content":{ - "field":"cnv_change", - "value":[ - "Gain" - ] - } -} -``` - -To put it in the track config you may want to minimize it as such: -``` -filters={"op":"=","content":{"field":"cnv_change","value":["Gain"]}} -``` - -Example Track: -``` -[tracks.GDC_CNV] -storeClass=gdc-viewer/Store/SeqFeature/CNVs -type=gdc-viewer/View/Track/CNVTrack -key=GDC CNV -metadata.datatype=CNV - -``` - -![GDC CNVs](images/GDC-cnv-gain.png) - -### Extra notes -You can set the max number of CNVs to return with the `size` field (per panel). It defaults to 500. The smaller the number, the faster the results will appear. - -# Dynamic Track Generation -## Explore cases, genes and mutations -This dialog is similar to the Exploration section of the GDC data portal. As you apply facets on the left-hand side, updated results will be shown on the right side. You can create donor specific SSM, Gene, and CNV tracks, along with GDC-wide SSM, Gene and CNV tracks. -![GDC Portal](images/GDC-portal-explore.png) - -## Explore Projects -This dialog shows the projects present on the GDC Data Portal. You can add SSM, Gene, and CNV tracks for each project. -![GDC projects](images/GDC-project-browser.png) - -## Explore Primary Sites -This dialog shows the primary sites present on the GDC Data Portal. You can add SSM, Gene, and CNV tracks for each primary site. -![GDC primary sites](images/GDC-primary-sites.png) - -# Export Types -The following export types are supported by both GDC Genes and SSMs. To export, select `Save track data` in the track dropdown. Note that not all track information is carried over to the exported file. -* BED -* GFF3 -* Sequin Table -* CSV -* Track Config - -# Automated testing -Cypress.io is used for testing this plugin. The following steps show how to run the tests locally. -1. Install JBrowse but don't install chromosome files. -2. Download Chr 1 fasta from `http://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz`. There should be the fasta index file in `cypress/data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.fai`. Put these files into `jbrowse/data/`. -3. Install Cypress.io with `npm install`. -4. Place `cypress/data/tracks.conf` into your `jbrowse/data/` directory. Make sure no other tracks are present. -5. Run `npx cypress open` or `npx cypress run` or `npm run e2e` - -**Note** while some tests have mocked endpoints, not all endpoints are mocked. This could lead to breakage of tests in the future. \ No newline at end of file +Check out [our documentation](https://agduncan94.github.io/gdc-viewer/) for information on installation, available features, and more. \ No newline at end of file diff --git a/cypress/fixtures/ExportGenes/GeneProjects.json b/cypress/fixtures/ExportGenes/GeneProjects.json deleted file mode 100644 index 93b1c29..0000000 --- a/cypress/fixtures/ExportGenes/GeneProjects.json +++ /dev/null @@ -1 +0,0 @@ -{"data":{"projectsViewer":{"projects":{"hits":{"edges":[{"node":{"disease_type":["Myeloid Leukemias","Not Applicable"],"id":"UHJvamVjdDpUQVJHRVQtQU1M","primary_site":["Unknown","Hematopoietic and reticuloendothelial systems"],"project_id":"TARGET-AML"}},{"node":{"disease_type":["Neuroepitheliomatous Neoplasms"],"id":"UHJvamVjdDpUQVJHRVQtTkJM","primary_site":["Heart, mediastinum, and pleura","Stomach","Bones, joints and articular cartilage of other and unspecified sites","Lymph nodes","Liver and intrahepatic bile ducts","Unknown","Uterus, NOS","Skin","Meninges","Other endocrine glands and related structures","Adrenal gland","Renal pelvis","Connective, subcutaneous and other soft tissues","Other and ill-defined sites","Bones, joints and articular cartilage of limbs","Spinal cord, cranial nerves, and other parts of central nervous system","Retroperitoneum and peritoneum","Peripheral nerves and autonomic nervous system","Hematopoietic and reticuloendothelial systems","Kidney"],"project_id":"TARGET-NBL"}},{"node":{"disease_type":["Gliomas"],"id":"UHJvamVjdDpUQ0dBLUxHRw==","primary_site":["Brain"],"project_id":"TCGA-LGG"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLVJFQUQ=","primary_site":["Rectosigmoid junction","Unknown","Rectum","Colon","Connective, subcutaneous and other soft tissues"],"project_id":"TCGA-READ"}},{"node":{"disease_type":["Epithelial Neoplasms, NOS","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLVRIQ0E=","primary_site":["Thyroid gland"],"project_id":"TCGA-THCA"}},{"node":{"disease_type":["Myeloid Leukemias"],"id":"UHJvamVjdDpCRUFUQU1MMS4wLUNSRU5PTEFOSUI=","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"BEATAML1.0-CRENOLANIB"}},{"node":{"disease_type":["Mesothelial Neoplasms"],"id":"UHJvamVjdDpUQ0dBLU1FU08=","primary_site":["Heart, mediastinum, and pleura","Bronchus and lung"],"project_id":"TCGA-MESO"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUFDQw==","primary_site":["Adrenal gland"],"project_id":"TCGA-ACC"}},{"node":{"disease_type":["Myomatous Neoplasms","Soft Tissue Tumors and Sarcomas, NOS","Fibromatous Neoplasms","Lipomatous Neoplasms","Nerve Sheath Tumors","Synovial-like Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVNBUkM=","primary_site":["Corpus uteri","Stomach","Other and unspecified parts of tongue","Meninges","Other and unspecified male genital organs","Colon","Connective, subcutaneous and other soft tissues","Bones, joints and articular cartilage of limbs","Ovary","Retroperitoneum and peritoneum","Peripheral nerves and autonomic nervous system","Uterus, NOS","Kidney"],"project_id":"TCGA-SARC"}},{"node":{"disease_type":["Complex Mixed and Stromal Neoplasms"],"id":"UHJvamVjdDpUQVJHRVQtQ0NTSw==","primary_site":["Kidney"],"project_id":"TARGET-CCSK"}},{"node":{"disease_type":["Adnexal and Skin Appendage Neoplasms","Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas","Basal Cell Neoplasms","Epithelial Neoplasms, NOS","Squamous Cell Neoplasms","Fibroepithelial Neoplasms","Ductal and Lobular Neoplasms","Complex Epithelial Neoplasms"],"id":"UHJvamVjdDpUQ0dBLUJSQ0E=","primary_site":["Breast"],"project_id":"TCGA-BRCA"}},{"node":{"disease_type":["Not Reported","Cystic, Mucinous and Serous Neoplasms"],"id":"UHJvamVjdDpUQ0dBLU9W","primary_site":["Ovary"],"project_id":"TCGA-OV"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUNIT0w=","primary_site":["Other and unspecified parts of biliary tract","Gallbladder","Liver and intrahepatic bile ducts"],"project_id":"TCGA-CHOL"}},{"node":{"disease_type":["Unknown","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpPUkdBTk9JRC1QQU5DUkVBVElD","primary_site":["Pancreas"],"project_id":"ORGANOID-PANCREATIC"}},{"node":{"disease_type":["Epithelial Neoplasms, NOS","Squamous Cell Neoplasms"],"id":"UHJvamVjdDpWQVJFUE9QLUFQT0xMTw==","primary_site":["Bronchus and lung"],"project_id":"VAREPOP-APOLLO"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas","Gliomas"],"id":"UHJvamVjdDpIQ01JLUNNREM=","primary_site":["Brain","Rectum","Colon"],"project_id":"HCMI-CMDC"}},{"node":{"disease_type":["Not Reported","Gliomas"],"id":"UHJvamVjdDpUQ0dBLUdCTQ==","primary_site":["Brain"],"project_id":"TCGA-GBM"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUtJUkM=","primary_site":["Kidney"],"project_id":"TCGA-KIRC"}},{"node":{"disease_type":["Nevi and Melanomas"],"id":"UHJvamVjdDpUQ0dBLVNLQ00=","primary_site":["Skin"],"project_id":"TCGA-SKCM"}},{"node":{"disease_type":["Not Reported","Cystic, Mucinous and Serous Neoplasms","Epithelial Neoplasms, NOS","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLVVDRUM=","primary_site":["Corpus uteri","Uterus, NOS"],"project_id":"TCGA-UCEC"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLVNUQUQ=","primary_site":["Stomach"],"project_id":"TCGA-STAD"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpDUFRBQy0z","primary_site":["Kidney","Uterus, NOS","Bronchus and lung"],"project_id":"CPTAC-3"}},{"node":{"disease_type":["Squamous Cell Neoplasms"],"id":"UHJvamVjdDpUQ0dBLUxVU0M=","primary_site":["Bronchus and lung"],"project_id":"TCGA-LUSC"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas","Ductal and Lobular Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVBSQUQ=","primary_site":["Prostate gland"],"project_id":"TCGA-PRAD"}},{"node":{"disease_type":["Myeloid Leukemias","Other Hematologic Disorders","Unknown","Precursor Cell Lymphoblastic Lymphoma","Myelodysplastic Syndromes","Other Leukemias","Chronic Myeloproliferative Disorders","Plasma Cell Tumors","Leukemias, NOS"],"id":"UHJvamVjdDpCRUFUQU1MMS4wLUNPSE9SVA==","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"BEATAML1.0-COHORT"}},{"node":{"disease_type":["Not Reported","Mature B-Cell Lymphomas"],"id":"UHJvamVjdDpUQ0dBLURMQkM=","primary_site":["Heart, mediastinum, and pleura","Testis","Stomach","Lymph nodes","Bones, joints and articular cartilage of other and unspecified sites","Brain","Thyroid gland","Small intestine","Colon","Connective, subcutaneous and other soft tissues","Other and unspecified major salivary glands","Retroperitoneum and peritoneum","Hematopoietic and reticuloendothelial systems","Breast"],"project_id":"TCGA-DLBC"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUtJQ0g=","primary_site":["Kidney"],"project_id":"TCGA-KICH"}},{"node":{"disease_type":["Germ Cell Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVRHQ1Q=","primary_site":["Testis"],"project_id":"TCGA-TGCT"}},{"node":{"disease_type":["Nevi and Melanomas"],"id":"UHJvamVjdDpUQ0dBLVVWTQ==","primary_site":["Eye and adnexa"],"project_id":"TCGA-UVM"}},{"node":{"disease_type":["Myeloid Leukemias"],"id":"UHJvamVjdDpUQ0dBLUxBTUw=","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"TCGA-LAML"}},{"node":{"disease_type":["Not Applicable","Myeloid Leukemias","Lymphoid Leukemias","Leukemias, NOS","Other Leukemias"],"id":"UHJvamVjdDpUQVJHRVQtQUxMLVAz","primary_site":["Unknown","Hematopoietic and reticuloendothelial systems"],"project_id":"TARGET-ALL-P3"}},{"node":{"disease_type":["Mature B-Cell Lymphomas"],"id":"UHJvamVjdDpDR0NJLUJMR1NQ","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"CGCI-BLGSP"}},{"node":{"disease_type":["Thymic Epithelial Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVRIWU0=","primary_site":["Heart, mediastinum, and pleura","Thymus"],"project_id":"TCGA-THYM"}},{"node":{"disease_type":["Lymphoid Leukemias"],"id":"UHJvamVjdDpUQVJHRVQtQUxMLVAy","primary_site":["Hematopoietic and reticuloendothelial systems","Blood"],"project_id":"TARGET-ALL-P2"}},{"node":{"disease_type":["Germ Cell Neoplasms","Acinar Cell Neoplasms","Miscellaneous Tumors","Thymic Epithelial Neoplasms","Gliomas","Not Reported","Neuroepitheliomatous Neoplasms","Ductal and Lobular Neoplasms","Complex Mixed and Stromal Neoplasms","Complex Epithelial Neoplasms","Adnexal and Skin Appendage Neoplasms","Mesothelial Neoplasms","Basal Cell Neoplasms","Mucoepidermoid Neoplasms","Specialized Gonadal Neoplasms","Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas","Epithelial Neoplasms, NOS","Squamous Cell Neoplasms","Transitional Cell Papillomas and Carcinomas","Paragangliomas and Glomus Tumors","Nevi and Melanomas","Meningiomas"],"id":"UHJvamVjdDpGTS1BRA==","primary_site":["Kidney","Testis","Gallbladder","Unknown","Other and unspecified parts of biliary tract","Adrenal gland","Thyroid gland","Spinal cord, cranial nerves, and other parts of central nervous system","Peripheral nerves and autonomic nervous system","Stomach","Cervix uteri","Bladder","Small intestine","Breast","Bronchus and lung","Other and ill-defined sites","Other and unspecified major salivary glands","Rectum","Retroperitoneum and peritoneum","Pancreas","Heart, mediastinum, and pleura","Prostate gland","Liver and intrahepatic bile ducts","Other and unspecified female genital organs","Thymus","Penis","Nasopharynx","Ovary","Uterus, NOS","Vulva","Other and unspecified urinary organs","Trachea","Ureter","Other endocrine glands and related structures","Not Reported","Colon","Anus and anal canal","Vagina","Skin","Esophagus","Eye and adnexa","Other and ill-defined digestive organs"],"project_id":"FM-AD"}},{"node":{"disease_type":["Squamous Cell Neoplasms"],"id":"UHJvamVjdDpUQ0dBLUhOU0M=","primary_site":["Other and ill-defined sites in lip, oral cavity and pharynx","Palate","Other and unspecified parts of tongue","Hypopharynx","Tonsil","Oropharynx","Larynx","Other and unspecified parts of mouth","Gum","Floor of mouth","Bones, joints and articular cartilage of other and unspecified sites","Lip","Base of tongue"],"project_id":"TCGA-HNSC"}},{"node":{"disease_type":["Complex Mixed and Stromal Neoplasms"],"id":"UHJvamVjdDpUQVJHRVQtUlQ=","primary_site":["Lip","Kidney","Liver and intrahepatic bile ducts"],"project_id":"TARGET-RT"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Epithelial Neoplasms, NOS","Adenomas and Adenocarcinomas","Complex Epithelial Neoplasms"],"id":"UHJvamVjdDpUQ0dBLUNPQUQ=","primary_site":["Rectosigmoid junction","Colon"],"project_id":"TCGA-COAD"}},{"node":{"disease_type":["Osseous and Chondromatous Neoplasms"],"id":"UHJvamVjdDpUQVJHRVQtT1M=","primary_site":["Not Reported","Bones, joints and articular cartilage of other and unspecified sites","Bones, joints and articular cartilage of limbs"],"project_id":"TARGET-OS"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUxJSEM=","primary_site":["Liver and intrahepatic bile ducts"],"project_id":"TCGA-LIHC"}},{"node":{"disease_type":["Mature B-Cell Lymphomas","Lymphoid Neoplasm Diffuse Large B-cell Lymphoma"],"id":"UHJvamVjdDpDVFNQLURMQkNMMQ==","primary_site":["Unknown","Lymph Nodes"],"project_id":"CTSP-DLBCL1"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas","Squamous Cell Neoplasms"],"id":"UHJvamVjdDpUQ0dBLUVTQ0E=","primary_site":["Esophagus","Stomach"],"project_id":"TCGA-ESCA"}},{"node":{"disease_type":["Complex Mixed and Stromal Neoplasms"],"id":"UHJvamVjdDpUQVJHRVQtV1Q=","primary_site":["Kidney"],"project_id":"TARGET-WT"}},{"node":{"disease_type":["Lymphoid Neoplasm Diffuse Large B-cell Lymphoma"],"id":"UHJvamVjdDpOQ0lDQ1ItRExCQ0w=","primary_site":["Lymph Nodes"],"project_id":"NCICCR-DLBCL"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Acinar Cell Neoplasms","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUxVQUQ=","primary_site":["Bronchus and lung"],"project_id":"TCGA-LUAD"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Epithelial Neoplasms, NOS","Adenomas and Adenocarcinomas","Ductal and Lobular Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVBBQUQ=","primary_site":["Pancreas"],"project_id":"TCGA-PAAD"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas","Complex 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b/cypress/fixtures/ExportSSMs/ProjectTable.json index 4166ea1..a048897 100644 --- a/cypress/fixtures/ExportSSMs/ProjectTable.json +++ b/cypress/fixtures/ExportSSMs/ProjectTable.json @@ -1 +1 @@ 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unspecified urinary organs","Trachea","Ureter","Other endocrine glands and related structures","Not Reported","Colon","Gallbladder","Vagina","Skin","Esophagus","Eye and adnexa","Other and ill-defined digestive organs"],"project_id":"FM-AD"}},{"node":{"disease_type":["Not Reported","Cystic, Mucinous and Serous Neoplasms","Epithelial Neoplasms, NOS","Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLVVDRUM=","primary_site":["Corpus uteri","Uterus, NOS"],"project_id":"TCGA-UCEC"}},{"node":{"disease_type":["Not Applicable","Leukemias, NOS","Lymphoid Leukemias","Myeloid Leukemias","Other Leukemias"],"id":"UHJvamVjdDpUQVJHRVQtQUxMLVAz","primary_site":["Unknown","Hematopoietic and reticuloendothelial systems"],"project_id":"TARGET-ALL-P3"}},{"node":{"disease_type":["Mature B-Cell Lymphomas"],"id":"UHJvamVjdDpDR0NJLUJMR1NQ","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"CGCI-BLGSP"}},{"node":{"disease_type":["Lymphoid Leukemias"],"id":"UHJvamVjdDpUQVJHRVQtQUxMLVAy","primary_site":["Hematopoietic and reticuloendothelial systems","Blood"],"project_id":"TARGET-ALL-P2"}},{"node":{"disease_type":["Myeloid Leukemias"],"id":"UHJvamVjdDpUQ0dBLUxBTUw=","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"TCGA-LAML"}},{"node":{"disease_type":["Not Reported","Mature B-Cell Lymphomas"],"id":"UHJvamVjdDpUQ0dBLURMQkM=","primary_site":["Heart, mediastinum, and pleura","Testis","Stomach","Lymph nodes","Bones, joints and articular cartilage of other and unspecified sites","Brain","Thyroid gland","Small intestine","Colon","Breast","Other and unspecified major salivary glands","Retroperitoneum and peritoneum","Hematopoietic and reticuloendothelial systems","Connective, subcutaneous and other soft tissues"],"project_id":"TCGA-DLBC"}},{"node":{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUtJQ0g=","primary_site":["Kidney"],"project_id":"TCGA-KICH"}},{"node":{"disease_type":["Thymic Epithelial Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVRIWU0=","primary_site":["Heart, mediastinum, and pleura","Thymus"],"project_id":"TCGA-THYM"}},{"node":{"disease_type":["Nevi and Melanomas"],"id":"UHJvamVjdDpUQ0dBLVVWTQ==","primary_site":["Eye and adnexa"],"project_id":"TCGA-UVM"}},{"node":{"disease_type":["Cystic, Mucinous and Serous Neoplasms","Adenomas and Adenocarcinomas","Ductal and Lobular Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVBSQUQ=","primary_site":["Prostate gland"],"project_id":"TCGA-PRAD"}},{"node":{"disease_type":["Squamous Cell Neoplasms"],"id":"UHJvamVjdDpUQ0dBLUxVU0M=","primary_site":["Bronchus and lung"],"project_id":"TCGA-LUSC"}},{"node":{"disease_type":["Germ Cell Neoplasms"],"id":"UHJvamVjdDpUQ0dBLVRHQ1Q=","primary_site":["Testis"],"project_id":"TCGA-TGCT"}},{"node":{"disease_type":["Adenomas and 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\ No newline at end of file diff --git a/cypress/integration/ExploreGDC.js b/cypress/integration/ExploreGDC.js index 6f5c5ce..c280c4e 100644 --- a/cypress/integration/ExploreGDC.js +++ b/cypress/integration/ExploreGDC.js @@ -93,15 +93,15 @@ describe('Explore GDC', function() { /** * Checks that each results tab has the expected information - * Assumes donor tab is already selected - * @param {*} donorArray array of strings to check for on donor tab + * Assumes case tab is already selected + * @param {*} caseArray array of strings to check for on case tab * @param {*} geneArray array of strings to check for on gene tab * @param {*} mutationArray array of strings to check for on mutation tab */ - var checkAllResultsTab = function(donorArray, geneArray, mutationArray) { + var checkAllResultsTab = function(caseArray, geneArray, mutationArray) { cy.wait(3000) // wait a few seconds for results to load - // Validate donor results - checkResultsTab(donorArray) + // Validate case results + checkResultsTab(caseArray) // Validate gene results selectResultsTab(1) @@ -116,11 +116,11 @@ describe('Explore GDC', function() { // Select ethnicity -> hispanic or latino cy.get('.dijitDialog').within(() => { cy.contains('Explore data available on the GDC Data Portal') - selectFacetTab(0, 0, 0) + selectFacetTab(0, 0, 2) }) checkAllResultsTab( - ['Showing 1 to 20 of 1,492', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'], + ['Showing 1 to 20 of 3,107', 'TCGA-A5-A1OF', 'TCGA-AJ-A3EK'], ['Showing 1 to 20 of 21,168', 'TP53', 'TTN'], ['Showing 1 to 20 of 120,824', 'chr2:g.208248388C>T', 'chr17:g.7673803G>A'] ) @@ -140,9 +140,9 @@ describe('Explore GDC', function() { // Add tracks and check that they were added cy.get('.dijitTabContainer').eq(1).within(() => { - cy.contains('All Genes for Donor').eq(0).click() - cy.contains('All SSMs for Donor').eq(0).click() - cy.contains('All CNVs for Donor').eq(0).click() + cy.contains('All Genes').eq(0).click() + cy.contains('All Mutations').eq(0).click() + cy.contains('All CNVs').eq(0).click() }) closePopup() diff --git a/cypress/integration/ExportGeneTrack.js b/cypress/integration/ExportGeneTrack.js index 363b291..3f19d6f 100644 --- a/cypress/integration/ExportGeneTrack.js +++ b/cypress/integration/ExportGeneTrack.js @@ -13,18 +13,11 @@ describe('Gene track', function() { response: 'fixture:ExportGenes/GenesTable.json' }).as('getGeneTable') - cy - .route({ - method: 'POST', - url: 'v0/graphql/gene-projects', - response: 'fixture:ExportGenes/GeneProjects.json' - }).as('getGeneProjects') - cy .route({ method: 'POST', url: 'v0/graphql/projectsTable', - response: 'fixture:ExportGenes/ProjectTable.json' + response: 'fixture:ExportGenes/GeneProjects.json' }).as('getProjectsTable') // Open track menu @@ -58,7 +51,7 @@ describe('Gene track', function() { if (radioIndex === 2) { cy.wait('@getGeneTable').then(() => { cy.wait(3000) // Give time to process results - cy.wait(['@getGeneProjects.all', '@getProjectsTable.all']).then(() => { + cy.wait(['@getProjectsTable.all']).then(() => { cy.wait(3000) // Give time to process results for (var text of textValues) { cy.get('textarea').should('to.include.value', text) @@ -81,7 +74,7 @@ describe('Gene track', function() { it('Should be able to export Genes in various export formats', function() { testExport(2, 'GFF3', ['##gff-version 3', '##sequence-region', 'Gene']) testExport(3, 'BED', ['track name="GDC_Genes" useScore=0', '1 152302175 152325203 ENSG00000143631 -']) - testExport(4, 'CSV', ['type,start,end,strand,id,gene name,biotype,symbol,synonyms', 'Gene,152302175,152325203,-1,,filaggrin,protein_coding,FLG']) + testExport(4, 'CSV', ['id,type,start,end,chromosome,strand,gene name,biotype,symbol,synonyms', 'ENSG00000143631,Gene,152302175,152325203,1,-1,filaggrin,protein_coding,FLG']) testExport(5, 'Sequin Table', ['>Feature 1', '152325203 152302176 Gene']) cy.fixture('ExportGenes/track-conf-export.conf').then((json) => { testExport(6, 'Track Config', [json]) diff --git a/cypress/integration/ExportSSMTrack.js b/cypress/integration/ExportSSMTrack.js index fdc63fc..322cb24 100644 --- a/cypress/integration/ExportSSMTrack.js +++ b/cypress/integration/ExportSSMTrack.js @@ -12,13 +12,6 @@ describe('SSM track', function() { url: 'v0/graphql/SsmsTable', response: 'fixture:ExportSSMs/SsmsTable.json' }).as('getSSMTable') - - cy - .route({ - method: 'POST', - url: 'v0/graphql/ssm-projects', - response: 'fixture:ExportSSMs/SSMProjects.json' - }).as('getSSMProjects') cy .route({ @@ -58,7 +51,7 @@ describe('SSM track', function() { if (radioIndex === 2) { cy.wait('@getSSMTable').then(() => { cy.wait(3000) // Give time to process results - cy.wait(['@getSSMProjects.all', '@getProjectsTable.all']).then(() => { + cy.wait(['@getProjectsTable.all']).then(() => { cy.wait(3000) // Give time to process results for (var text of textValues) { cy.get('textarea').should('to.include.value', text) @@ -81,7 +74,7 @@ describe('SSM track', function() { it('Should be able to export SSMs in various export formats', function() { testExport(2, 'GFF3', ['##gff-version 3', '##sequence-region', 'Simple Somatic Mutation']) testExport(3, 'BED', ['track name="GDC_SSM" useScore=0', '1 56496417 56496417 ec690998-d555-5ed3-ab18-55e8685b2bfd']) - testExport(4, 'CSV', ['type,start,end,strand,id,reference allele,dna change,subtype', 'Simple Somatic Mutation,56496417,56496417,,,T,chr1:g.56496417delT,Small deletion']) + testExport(4, 'CSV', ['id,type,start,end,chromosome,reference allele,dna change,subtype', 'ec690998-d555-5ed3-ab18-55e8685b2bfd,Simple Somatic Mutation,56496417,56496417,,T,chr1:g.56496417delT,Small deletion']) testExport(5, 'Sequin Table', ['>Feature 1', '56496418 56496417 Simple Somatic Mutation']) cy.fixture('ExportSSMs/track-conf-export.conf').then((json) => { testExport(6, 'Track Config', [json]) diff --git a/cypress/integration/PrimarySites.js b/cypress/integration/PrimarySites.js index 827e968..3ddbef5 100644 --- a/cypress/integration/PrimarySites.js +++ b/cypress/integration/PrimarySites.js @@ -40,7 +40,7 @@ describe('Primary sites dialog', function() { it('Should be able to view primary sites', function() { // Open track menu cy.get('#dropdownbutton_gdc').type('{enter}') - cy.contains('Explore Primary Sites').click() + cy.contains('Explore primary sites').click() cy.wait('@getPrimarySites') @@ -51,13 +51,13 @@ describe('Primary sites dialog', function() { // Add SSM, Gene, and CNV tracks for primary site bronchus and lung (assume first in list) cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}') - cy.contains('SSMs for Primary Site').click() + cy.contains('All Mutations').click() cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}') - cy.contains('Genes for Primary Site').click() + cy.contains('All Genes').click() cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}') - cy.contains('CNVs for Primary Site').click() + cy.contains('All CNVs').click() cy.contains('GDC Primary Site Browser').parent().within(() => { cy.get('.dijitDialogCloseIcon').click() diff --git a/cypress/integration/projects.js b/cypress/integration/projects.js index e3eda06..d219e1c 100644 --- a/cypress/integration/projects.js +++ b/cypress/integration/projects.js @@ -41,7 +41,7 @@ describe('Project dialog', function() { it('Should be able to view projects', function() { // Open track menu cy.get('#dropdownbutton_gdc').type('{enter}') - cy.contains('Explore Projects').click() + cy.contains('Explore projects').click() cy.wait('@getProjects') @@ -53,13 +53,13 @@ describe('Project dialog', function() { // Add SSM, Gene, and CNV tracks for project FM-AD (assume first in list) // Note that even though we select FM-AD, we are mocking TCGA-BRCA cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}') - cy.contains('SSMs for Project').click() + cy.contains('All Mutations').click() cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}') - cy.contains('Genes for Project').click() + cy.contains('All Genes').click() cy.get('#dijit_form_ComboButton_0_arrow').should('be.visible').type('{enter}') - cy.contains('CNVs for Project').click() + cy.contains('All CNVs').click() cy.contains('GDC Project Browser').parent().within(() => { cy.get('.dijitDialogCloseIcon').click() @@ -72,12 +72,6 @@ describe('Project dialog', function() { cy.contains('GDC_CNVs_FM-AD') // Stub some responses for viewing a mutation - cy - .route({ - method: 'POST', - url: 'v0/graphql/ssm-projects', - response: 'fixture:projects/mutation-projects.json' - }).as('getProjectsForMutation') cy .route({ @@ -93,7 +87,6 @@ describe('Project dialog', function() { // Ensure mutation has right data cy.get('.popup-dialog').within(() => { - cy.wait('@getProjectsForMutation') cy.contains('Simple Somatic Mutation') cy.contains('chr1:g.52055208delT') cy.contains('7ffb5e22-05d6-5664-a0b0-908184bacbb9') @@ -117,12 +110,6 @@ describe('Project dialog', function() { }) // Stub some responses for viewing a gene - cy - .route({ - method: 'POST', - url: 'v0/graphql/gene-projects', - response: 'fixture:projects/gene-projects.json' - }).as('getProjectsForGene') cy .route({ @@ -138,7 +125,6 @@ describe('Project dialog', function() { // Ensure gene has right data cy.get('.popup-dialog').within(() => { - cy.wait('@getProjectsForGene') cy.contains('Gene') cy.contains('The protein encoded by this gene is expressed in the brain, predominantly in the parietal and frontal cortex as well as in dorsal root ganglia.') cy.contains('protein_coding') diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 0000000..45c1505 --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1,3 @@ +_site +.sass-cache +.jekyll-metadata diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..c472b4e --- /dev/null +++ b/docs/404.html @@ -0,0 +1,24 @@ +--- +layout: default +--- + + + +
+

404

+ +

Page not found :(

+

The requested page could not be found.

+
diff --git a/docs/Gemfile b/docs/Gemfile new file mode 100644 index 0000000..cb1de77 --- /dev/null +++ b/docs/Gemfile @@ -0,0 +1,31 @@ +source "https://rubygems.org" + +# Hello! This is where you manage which Jekyll version is used to run. +# When you want to use a different version, change it below, save the +# file and run `bundle install`. Run Jekyll with `bundle exec`, like so: +# +# bundle exec jekyll serve +# +# This will help ensure the proper Jekyll version is running. +# Happy Jekylling! +gem "jekyll", "~> 3.7.3" + +# This is the default theme for new Jekyll sites. You may change this to anything you like. +gem "minima", "~> 2.0" + +# If you want to use GitHub Pages, remove the "gem "jekyll"" above and +# uncomment the line below. To upgrade, run `bundle update github-pages`. +# gem "github-pages", group: :jekyll_plugins + +# If you have any plugins, put them here! +group :jekyll_plugins do + gem "jekyll-feed", "~> 0.6" +end + +# Windows does not include zoneinfo files, so bundle the tzinfo-data gem +gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby] + +# Performance-booster for watching directories on Windows +gem "wdm", "~> 0.1.0" if Gem.win_platform? + +gem "just-the-docs" diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock new file mode 100644 index 0000000..ab849bd --- /dev/null +++ b/docs/Gemfile.lock @@ -0,0 +1,77 @@ +GEM + remote: https://rubygems.org/ + specs: + addressable (2.7.0) + public_suffix (>= 2.0.2, < 5.0) + colorator (1.1.0) + concurrent-ruby (1.1.6) + em-websocket (0.5.1) + eventmachine (>= 0.12.9) + http_parser.rb (~> 0.6.0) + eventmachine (1.2.7) + ffi (1.12.2) + forwardable-extended (2.6.0) + http_parser.rb (0.6.0) + i18n (0.9.5) + concurrent-ruby (~> 1.0) + jekyll (3.7.4) + addressable (~> 2.4) + colorator (~> 1.0) + em-websocket (~> 0.5) + i18n (~> 0.7) + jekyll-sass-converter (~> 1.0) + jekyll-watch (~> 2.0) + kramdown (~> 1.14) + liquid (~> 4.0) + mercenary (~> 0.3.3) + pathutil (~> 0.9) + rouge (>= 1.7, < 4) + safe_yaml (~> 1.0) + jekyll-feed (0.13.0) + jekyll (>= 3.7, < 5.0) + jekyll-sass-converter (1.5.2) + sass (~> 3.4) + jekyll-seo-tag (2.6.1) + jekyll (>= 3.3, < 5.0) + jekyll-watch (2.2.1) + listen (~> 3.0) + just-the-docs (0.1.6) + jekyll (~> 3.3) + rake (~> 10.0) + kramdown (1.17.0) + liquid (4.0.3) + listen (3.2.1) + rb-fsevent (~> 0.10, >= 0.10.3) + rb-inotify (~> 0.9, >= 0.9.10) + mercenary (0.3.6) + minima (2.5.1) + jekyll (>= 3.5, < 5.0) + jekyll-feed (~> 0.9) + jekyll-seo-tag (~> 2.1) + pathutil (0.16.2) + forwardable-extended (~> 2.6) + public_suffix (4.0.3) + rake (10.5.0) + rb-fsevent (0.10.3) + rb-inotify (0.10.1) + ffi (~> 1.0) + rouge (3.17.0) + safe_yaml (1.0.5) + sass (3.7.4) + sass-listen (~> 4.0.0) + sass-listen (4.0.0) + rb-fsevent (~> 0.9, >= 0.9.4) + rb-inotify (~> 0.9, >= 0.9.7) + +PLATFORMS + ruby + +DEPENDENCIES + jekyll (~> 3.7.3) + jekyll-feed (~> 0.6) + just-the-docs + minima (~> 2.0) + tzinfo-data + +BUNDLED WITH + 2.1.4 diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 0000000..5aadf08 --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1,43 @@ +# Welcome to Jekyll! +# +# This config file is meant for settings that affect your whole blog, values +# which you are expected to set up once and rarely edit after that. If you find +# yourself editing this file very often, consider using Jekyll's data files +# feature for the data you need to update frequently. +# +# For technical reasons, this file is *NOT* reloaded automatically when you use +# 'bundle exec jekyll serve'. If you change this file, please restart the server process. + +# Site settings +# These are used to personalize your new site. If you look in the HTML files, +# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on. +# You can create any custom variable you would like, and they will be accessible +# in the templates via {{ site.myvariable }}. +title: GDC Viewer +description: >- # this means to ignore newlines until "baseurl:" + A JBrowse plugin for interacting with the GDC portal +baseurl: "" # the subpath of your site, e.g. /blog +url: "https://agduncan94.github.io/gdc-viewer/" # the base hostname & protocol for your site, e.g. http://example.com + +# Build settings +markdown: kramdown +theme: just-the-docs +remote_theme: pmarsceill/just-the-docs +plugins: + - jekyll-feed + +aux_links: + "GDC Viewer on GitHub": + - "//github.com/agduncan94/gdc-viewer" + +# Exclude from processing. +# The following items will not be processed, by default. Create a custom list +# to override the default setting. +# exclude: +# - Gemfile +# - Gemfile.lock +# - node_modules +# - vendor/bundle/ +# - vendor/cache/ +# - vendor/gems/ +# - vendor/ruby/ diff --git a/docs/developers.md b/docs/developers.md new file mode 100644 index 0000000..1fcf8ea --- /dev/null +++ b/docs/developers.md @@ -0,0 +1,22 @@ +--- +layout: default +title: Developers +nav_order: 4 +--- +# Extra Notes for Developers +This section just goes over some areas of the code to help new developers navigate. + +## js/Model +These files override the function for printing to the feature dialog. It overrides the get function to display content that requires extra API calls (on top of the call to grab the whole track). For example, this is used to generate the projects table shown on Mutations and gene feature dialogs. + +## js/Store/SeqFeature +These files connect the GDC API to JBrowse by creating a set of features based on an API call. + +## js/View +The top level contains files that create the various dialog boxes that appear in the menu bar. These allow for the dynamic generation of tracks. + +### Export +These files define export types for mutation, gene, and CNV tracks. + +### Track +These files extend the track dropdown options to include things like shareable links and view filters. This is also where overrides for the format of the feature dialogs are. \ No newline at end of file diff --git a/images/GDC-cnv-gain.png b/docs/images/GDC-cnv-gain.png similarity index 100% rename from images/GDC-cnv-gain.png rename to docs/images/GDC-cnv-gain.png diff --git a/images/GDC-genes-protein-coding.png b/docs/images/GDC-genes-protein-coding.png similarity index 100% rename from images/GDC-genes-protein-coding.png rename to docs/images/GDC-genes-protein-coding.png diff --git a/images/GDC-mutations-base-g.png b/docs/images/GDC-mutations-base-g.png similarity index 100% rename from images/GDC-mutations-base-g.png rename to docs/images/GDC-mutations-base-g.png diff --git a/images/GDC-portal-explore.png b/docs/images/GDC-portal-explore.png similarity index 100% rename from images/GDC-portal-explore.png rename to docs/images/GDC-portal-explore.png diff --git a/images/GDC-primary-sites.png b/docs/images/GDC-primary-sites.png similarity index 100% rename from images/GDC-primary-sites.png rename to docs/images/GDC-primary-sites.png diff --git a/images/GDC-project-browser.png b/docs/images/GDC-project-browser.png similarity index 100% rename from images/GDC-project-browser.png rename to docs/images/GDC-project-browser.png diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..6880afc --- /dev/null +++ b/docs/index.md @@ -0,0 +1,27 @@ +--- +layout: default +title: Home +nav_order: 1 +description: "GDC Viewer is a JBrowse plugin for creating tracks using data from the GDC portal." +permalink: / +--- + +# GDC JBrowse Plugin +{: .fs-9 } +A plugin for [JBrowse](https://jbrowse.org/) for viewing [GDC](https://gdc.cancer.gov/) data. +{: .fs-6 .fw-300 } +--- + +# Overview +This plugin provides the ability to create mutation, gene, and CNV tracks on JBrowse based on complex query filters. These filters are the same as those used in the GDC API. For example, you could create a track of all mutations found in gliomas that have a high VEP score. + +[See the tracks page]({{ site.baseurl }}{% link tracks.md %}) for some examples of what this plugin is capable of. + +# Features +* Create Mutation, Gene and CNV tracks with rich metadata +* Used faceted search similar to that found on the GDC Portal to create complex filters +* Share your tracks with others +* Export your tracks to common formats like BED, GFF3 and CSV + +# Contributing +For any bugs, issues, or feature recommendations please create an issue or PR through GitHub. \ No newline at end of file diff --git a/docs/install.md b/docs/install.md new file mode 100644 index 0000000..12c6c2c --- /dev/null +++ b/docs/install.md @@ -0,0 +1,58 @@ +--- +layout: default +title: Installation +nav_order: 2 +--- + +# Installation and Setup +## 1. Install JBrowse +Follow JBrowse readme for [quick setup.](https://github.com/GMOD/jbrowse/#install-jbrowse-from-github-for-developers) + +## 2. Install Plugin +See [JBrowse - Installing Plugins](https://jbrowse.org/docs/plugins.html) for a general approach to installing plugins. + +For installing gdc-viewer plugin: +1. Copy the gdc-viewer folder into the JBrowse `plugins` directory. +2. Add 'gdc-viewer' to the array of plugins in the `jbrowse_conf.json`. + +## 3. Install Reference Sequence Data +Now setup the reference sequence used. GDC requires the GRCh38 Human reference files. + +Download the GRCh38 `.fa` and `.fa.fai` files online (ex. http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch38/). Then put the following in `./data/tracks.conf` (note files may be named something else). + +``` +refSeqs=GRCh38.genome.fa.fai + +[tracks.refseqs] +urlTemplate=GRCh38.genome.fa +``` + +## 4. Adding new tracks +We have some basic example tracks in `data/tracks.conf`. You can also add new tracks by using the GDC dialog accessible within JBrowse. + +## 5. Run JBrowse +You'll have to run the following commands: + +``` +./setup.sh +utils/jb_run.js -p 3000 +``` + +JBrowse should now be running with the GDC Plugin working! + +# JBrowse configuration +## Faceted Track Selector +Add the following to your jbrowse.conf to use the faceted track selector. +``` +[trackSelector] +type = Faceted +displayColumns = + + label + + key + + datatype + + case + + project + + primarySite +``` + +Note that this will only show preloaded tracks as well as tracks you have added using the various dialogs. It does not dynamically create tracks based on what is available from the GDC. \ No newline at end of file diff --git a/docs/testing.md b/docs/testing.md new file mode 100644 index 0000000..211ea1e --- /dev/null +++ b/docs/testing.md @@ -0,0 +1,14 @@ +--- +layout: default +title: Testing +nav_order: 5 +--- +# Automated testing +Cypress.io is used for testing this plugin. The following steps show how to run the tests locally. +1. Install JBrowse but don't install chromosome files. +2. Download Chr 1 fasta from `http://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz`. There should be the fasta index file in `cypress/data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.fai`. Put these files into `jbrowse/data/`. +3. Install Cypress.io with `npm install`. +4. Place `cypress/data/tracks.conf` into your `jbrowse/data/` directory. Make sure no other tracks are present. +5. Run `npx cypress open` or `npx cypress run` or `npm run e2e` + +**Note** while some tests have mocked endpoints, not all endpoints are mocked. This could lead to breakage of tests in the future. \ No newline at end of file diff --git a/docs/tracks.md b/docs/tracks.md new file mode 100644 index 0000000..487a81f --- /dev/null +++ b/docs/tracks.md @@ -0,0 +1,179 @@ +--- +layout: default +title: Tracks +nav_order: 3 +--- + +# Tracks +{: .no_toc } + +Create Mutation (SSM), Gene, and CNV tracks using a dynamic track generator +{: .fs-6 .fw-300 } + +## Table of contents +{: .no_toc .text-delta } + +1. TOC +{:toc} + +# Filters +All tracks support filters as they are defined in the [GDC API Documentation](https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-query). + +Note that filters should have the filter type prepended to the front. Ex. Case filters use `cases.`, Mutation filters use `ssms.`, and Gene filters use `genes.`. GraphQL is used to retrieve results, so if the filters work there, they work with these Store classes. + +The following shows a filter for cases by ethnicity: +``` +{ + "op":"in", + "content":{ + "field":"cases.demographic.ethnicity", + "value":[ + "hispanic or latino" + ] + } +} +``` + +You can view/edit the filters associated with a track by clicking the down arrow for the track menu and selecting `View Applied Filters`. Be careful, there are currently no checks to see if the filters are valid before applying them. + +# Available Track Types + +## Genes +A simple view of all of the genes seen across all cases. + +You can view case specific genes by setting the `case` field. Multiple cases are supported by using commas. + +You can apply filters to the track too, in the same format as GDC. The below example only shows Genes whose biotype is not 'protein_coding'. + +``` +{ + "op":"!=", + "content":{ + "field":"genes.biotype", + "value":"protein_coding" + } +} +``` + +To put it in the track config you may want to minimize it as such: +``` +filters={"op":"!=","content":{"field":"genes.biotype","value":"protein_coding"}} +``` + +Example Track: +``` +[tracks.GDC_Genes] +storeClass=gdc-viewer/Store/SeqFeature/Genes +type=JBrowse/View/Track/GeneTrack +key=GDC Genes +metadata.datatype=Gene +filters={"op":"!=","content":{"field":"genes.biotype","value":"protein_coding"}} +``` + +![GDC Genes](images/GDC-genes-protein-coding.png) + +### Extra notes +{: .no_toc } +You can set the max number of genes to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear. + +## Mutations (SSMs) +A simple view of all of the simple somatic mutations seen across all cases. + +You can view case specific mutations by setting the `case` field. Multiple cases are supported by using commas. + +You can apply filters to the track too, in the same format as GDC. The below example only shows mutations whose reference allele is 'G'. +``` +{ + "op":"=", + "content":{ + "field":"ssms.reference_allele", + "value":"G" + } +} +``` + +To put it in the track config you may want to minimize it as such: +``` +filters={"op":"=","content":{"field":"ssms.reference_allele","value":"G"}} +``` + +Example Track: +``` +[tracks.GDC_SSM] +storeClass=gdc-viewer/Store/SeqFeature/SimpleSomaticMutations +type=gdc-viewer/View/Track/SSMVariants +key=GDC SSM +metadata.datatype=SSM +filters={"op":"=","content":{"field":"ssms.reference_allele","value":"G"}} +``` + +![GDC SSMs](images/GDC-mutations-base-g.png) + +### Extra notes +{: .no_toc } +You can set the max number of mutations to return with the `size` field (per panel). It defaults to 100. The smaller the number, the faster the results will appear. + +## CNVs +A simple view of all of the CNVs seen across all cases. + +You can view case specific CNVs by setting the `case` field. Multiple cases are supported by using commas. + +You can apply filters to the track too, in the same format as GDC. The below example only shows CNVs that are 'Gains'. +``` +{ + "op":"=", + "content":{ + "field":"cnv_change", + "value":[ + "Gain" + ] + } +} +``` + +To put it in the track config you may want to minimize it as such: +``` +filters={"op":"=","content":{"field":"cnv_change","value":["Gain"]}} +``` + +Example Track: +``` +[tracks.GDC_CNV] +storeClass=gdc-viewer/Store/SeqFeature/CNVs +type=gdc-viewer/View/Track/CNVTrack +key=GDC CNV +metadata.datatype=CNV + +``` + +![GDC CNVs](images/GDC-cnv-gain.png) + +### Extra notes +{: .no_toc } +You can set the max number of CNVs to return with the `size` field (per panel). It defaults to 500. The smaller the number, the faster the results will appear. + +# Dynamic Track Generation +## Explore cases, genes and mutations +This dialog is similar to the Exploration section of the GDC data portal. As you apply facets on the left-hand side, updated results will be shown on the right side. You can create case specific Mutation, Gene, and CNV tracks, along with GDC-wide Mutation, Gene and CNV tracks. + +You can optionally apply the current facets to the track itself when you add a track. For example, say you have applied the facet VEP impact of high. On the `Mutations` tab there is the option to add all mutations from the GDC or add all filtered mutations from the GDC. The first option will create a track with all mutations present on the GDC portal (no filtering). The second option will create a track with only mutations that have a VEP impact of high. As you can see, this becomes very powerful when you combine multiple facets. + +![GDC Portal](images/GDC-portal-explore.png) + +## Explore Projects +This dialog shows the projects present on the GDC Data Portal. You can add Mutation, Gene, and CNV tracks for each project. + +![GDC projects](images/GDC-project-browser.png) + +## Explore Primary Sites +This dialog shows the primary sites present on the GDC Data Portal. You can add Mutation, Gene, and CNV tracks for each primary site. + +![GDC primary sites](images/GDC-primary-sites.png) + +# Export Types +The following export types are supported by both GDC Genes and Mutations. To export, select `Save track data` in the track dropdown. Note that not all track information is carried over to the exported file. +* BED +* GFF3 +* Sequin Table +* CSV +* Track Config \ No newline at end of file diff --git a/gdc-viewer/js/Model/GeneFeature.js b/gdc-viewer/js/Model/GeneFeature.js index 98edab1..82011d2 100644 --- a/gdc-viewer/js/Model/GeneFeature.js +++ b/gdc-viewer/js/Model/GeneFeature.js @@ -2,43 +2,12 @@ * Simple implementation of a Gene feature object. */ define([ - 'JBrowse/Util' + 'JBrowse/Model/SimpleFeature', + 'dojo/_base/declare' ], - function( Util ) { + function( SimpleFeature, declare ) { -var counter = 0; - -var GeneFeature = Util.fastDeclare({ - -/** - * @param args.data {Object} key-value data, must include 'start' and 'end' - * @param args.parent {Feature} optional parent feature - * @param args.id {String} optional unique identifier. can also be in data.uniqueID. - * - * Note: args.data.subfeatures can be an array of these same args, - * which will be inflated to more instances of this class. - */ -constructor: function( args ) { - args = args || {}; - this.data = args.data || {}; - this._parent = args.parent; - this._uniqueID = args.id || this.data.uniqueID || ( - this._parent ? this._parent.id()+'_'+(counter++) : 'GeneFeature_'+(counter++) - ); - - // inflate any subfeatures that are not already feature objects - var subfeatures; - if(( subfeatures = this.data.subfeatures )) { - for( var i = 0; i < subfeatures.length; i++ ) { - if( typeof subfeatures[i].get != 'function' ) { - subfeatures[i] = new GeneFeature( - { data: subfeatures[i], - parent: this - }); - } - } - } -}, +return declare(SimpleFeature, { projects: undefined, @@ -50,41 +19,26 @@ get: function(name) { var thisB = this; if (name == 'projects') { var geneId = this.data[name.toLowerCase()]; - var bodyValProjects = { - query: `query projectData( $count: Int ) { projectsViewer: viewer { projects { hits(first: $count) { edges { node { primary_site disease_type project_id id } } } } } }`, + + var bodyValProjectsTable = { + query: `query ProjectTable( $caseAggsFilters: FiltersArgument $ssmTested: FiltersArgument $cnvGain: FiltersArgument $cnvLoss: FiltersArgument $cnvTested: FiltersArgument $projectCount: Int ) { viewer { explore { cases { gain: aggregations(filters: $cnvGain) { project__project_id { buckets { doc_count key } } } loss: aggregations(filters: $cnvLoss) { project__project_id { buckets { doc_count key } } } cnvTotal: aggregations(filters: $cnvTested) { project__project_id { buckets { doc_count key } } } filtered: aggregations(filters: $caseAggsFilters) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } projects { hits(first: $projectCount) { edges { node { primary_site disease_type project_id id } } } } }`, variables: { - "count": 100 + "caseAggsFilters": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } }, { "op": "NOT", "content": { "field": "cases.gene.ssm.observation.observation_id", "value": "MISSING" } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] }, + "ssmTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } } ] }, + "cnvGain": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Gain" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] }, + "cnvLoss": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Loss" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] }, + "cnvTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } } ] }, + "projectCount": 100 } } - fetch('https://api.gdc.cancer.gov/v0/graphql/gene-projects', { + fetch('https://api.gdc.cancer.gov/v0/graphql/projectsTable', { method: 'post', headers: { 'X-Requested-With': null }, - body: JSON.stringify(bodyValProjects) - }).then(function(response) { - return(response.json()); - }).then(function(response) { - thisB.projects = response.data.projectsViewer.projects.hits.edges; - var bodyValProjectsTable = { - query: `query ProjectTable( $caseAggsFilters: FiltersArgument $ssmTested: FiltersArgument $cnvGain: FiltersArgument $cnvLoss: FiltersArgument $cnvTested: FiltersArgument $cnvTestedByGene: FiltersArgument $cnvAll: FiltersArgument $ssmFilters: FiltersArgument ) { viewer { explore { ssms { hits(first: 0, filters: $ssmFilters) { total } } cases { cnvAll: hits(filters: $cnvAll) { total } cnvTestedByGene: hits(filters: $cnvTestedByGene) { total } gain: aggregations(filters: $cnvGain) { project__project_id { buckets { doc_count key } } } loss: aggregations(filters: $cnvLoss) { project__project_id { buckets { doc_count key } } } cnvTotal: aggregations(filters: $cnvTested) { project__project_id { buckets { doc_count key } } } filtered: aggregations(filters: $caseAggsFilters) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } }`, - variables: { - "caseAggsFilters": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } }, { "op": "NOT", "content": { "field": "cases.gene.ssm.observation.observation_id", "value": "MISSING" } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] }, - "ssmTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } } ] }, - "cnvGain": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Gain" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] }, - "cnvLoss": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Loss" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] }, - "cnvTested": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } } ] }, - "cnvTestedByGene": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] }, - "cnvAll": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "cnv" ] } }, { "op": "in", "content": { "field": "cnvs.cnv_change", "value": [ "Gain", "Loss" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] }, - "ssmFilters": { "op": "and", "content": [ { "op": "in", "content": { "field": "cases.available_variation_data", "value": [ "ssm" ] } }, { "op": "in", "content": { "field": "genes.gene_id", "value": [ geneId ] } } ] } - } - } - return fetch('https://api.gdc.cancer.gov/v0/graphql/projectsTable', { - method: 'post', - headers: { 'X-Requested-With': null }, - body: JSON.stringify(bodyValProjectsTable) - }) + body: JSON.stringify(bodyValProjectsTable) }).then(function(response) { return(response.json()); }).then(function(response) { + thisB.projects = response.data.projects.hits.edges; document.getElementsByClassName('value projects')[0].innerHTML = thisB.createProjectTable(response); }).catch(function(err) { document.getElementsByClassName('value projects')[0].innerHTML = 'Error creating projects table'; @@ -106,7 +60,7 @@ createProjectTable: function(response) { Project Disease Type Site - # SSM Affected Cases + # Mutation Affected Cases # CNV Gains # CNV Losses @@ -178,58 +132,8 @@ getValueWithPercentage: function(numerator, denominator) { findProjectByKey: function(projects, key) { var project = projects.find(project => project.key === key); return project ? project.doc_count : 0; -}, - -/** - * Set an item of data. - */ -set: function( name, val ) { - this.data[ name ] = val; -}, - -/** - * Get an array listing which data keys are present in this feature. - */ -tags: function() { - var t = []; - var d = this.data; - for( var k in d ) { - if( d.hasOwnProperty( k ) ) - t.push( k ); - } - return t; -}, - -/** - * Get the unique ID of this feature. - */ -id: function( newid ) { - if( newid ) - this._uniqueID = newid; - return this._uniqueID; -}, - -/** - * Get this feature's parent feature, or undefined if none. - */ -parent: function() { - return this._parent; -}, - -/** - * Get an array of child features, or undefined if none. - */ -children: function() { - return this.get('subfeatures'); -}, - -toJSON: function() { - const d = Object.assign({},this) - delete d._parent - return d } }); -return GeneFeature; }); \ No newline at end of file diff --git a/gdc-viewer/js/Model/SSMFeature.js b/gdc-viewer/js/Model/SSMFeature.js index d9d4700..af04f03 100644 --- a/gdc-viewer/js/Model/SSMFeature.js +++ b/gdc-viewer/js/Model/SSMFeature.js @@ -2,43 +2,12 @@ * Simple implementation of an SSM feature object. */ define([ - 'JBrowse/Util' + 'JBrowse/Model/SimpleFeature', + 'dojo/_base/declare' ], - function( Util ) { + function( SimpleFeature, declare ) { -var counter = 0; - -var SSMFeature = Util.fastDeclare({ - -/** - * @param args.data {Object} key-value data, must include 'start' and 'end' - * @param args.parent {Feature} optional parent feature - * @param args.id {String} optional unique identifier. can also be in data.uniqueID. - * - * Note: args.data.subfeatures can be an array of these same args, - * which will be inflated to more instances of this class. - */ -constructor: function( args ) { - args = args || {}; - this.data = args.data || {}; - this._parent = args.parent; - this._uniqueID = args.id || this.data.uniqueID || ( - this._parent ? this._parent.id()+'_'+(counter++) : 'SSMFeature_'+(counter++) - ); - - // inflate any subfeatures that are not already feature objects - var subfeatures; - if(( subfeatures = this.data.subfeatures )) { - for( var i = 0; i < subfeatures.length; i++ ) { - if( typeof subfeatures[i].get != 'function' ) { - subfeatures[i] = new SSMFeature( - { data: subfeatures[i], - parent: this - }); - } - } - } -}, +return declare(SimpleFeature, { projects: undefined, @@ -50,35 +19,23 @@ get: function(name) { var thisB = this; if (name == 'projects') { var mutationId = this.data[name.toLowerCase()]; - var bodyValProjects = { - query: `query projectData( $count: Int ) { projectsViewer: viewer { projects { hits(first: $count) { edges { node { primary_site disease_type project_id id } } } } } }`, + + var bodyValProjectsTable = { + query: `query projectsTable($ssmTested: FiltersArgument, $caseAggsFilter: FiltersArgument, $projectCount: Int) { viewer { explore { cases { filtered: aggregations(filters: $caseAggsFilter) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } projects { hits(first: $projectCount) { edges { node { primary_site disease_type project_id id } } } } }`, variables: { - "count": 100 + "ssmTested": { "op":"and", "content":[ { "op":"in", "content":{ "field":"cases.available_variation_data", "value":[ "ssm" ] } } ] } , + "caseAggsFilter": { "op":"and", "content":[ { "op":"in", "content":{ "field":"ssms.ssm_id", "value":[ mutationId ] } }, { "op":"in", "content":{ "field":"cases.available_variation_data", "value":[ "ssm" ] } } ] }, + "projectCount": 100 } } - fetch('https://api.gdc.cancer.gov/v0/graphql/ssm-projects', { + fetch('https://api.gdc.cancer.gov/v0/graphql/projectsTable', { method: 'post', headers: { 'X-Requested-With': null }, - body: JSON.stringify(bodyValProjects) - }).then(function(response) { - return(response.json()); - }).then(function(response) { - thisB.projects = response.data.projectsViewer.projects.hits.edges; - var bodyValProjectsTable = { - query: `query projectsTable($ssmTested: FiltersArgument, $caseAggsFilter: FiltersArgument) { viewer { explore { cases { filtered: aggregations(filters: $caseAggsFilter) { project__project_id { buckets { doc_count key } } } total: aggregations(filters: $ssmTested) { project__project_id { buckets { doc_count key } } } } } } }`, - variables: { - "ssmTested": { "op":"and", "content":[ { "op":"in", "content":{ "field":"cases.available_variation_data", "value":[ "ssm" ] } } ] } , - "caseAggsFilter": { "op":"and", "content":[ { "op":"in", "content":{ "field":"ssms.ssm_id", "value":[ mutationId ] } }, { "op":"in", "content":{ "field":"cases.available_variation_data", "value":[ "ssm" ] } } ] } - } - } - return fetch('https://api.gdc.cancer.gov/v0/graphql/projectsTable', { - method: 'post', - headers: { 'X-Requested-With': null }, - body: JSON.stringify(bodyValProjectsTable) - }) + body: JSON.stringify(bodyValProjectsTable) }).then(function(response) { return(response.json()); }).then(function(response) { + thisB.projects = response.data.projects.hits.edges; document.getElementsByClassName('value projects')[0].innerHTML = thisB.createProjectTable(response); }).catch(function(err) { document.getElementsByClassName('value projects')[0].innerHTML = 'Error creating projects table'; @@ -100,7 +57,7 @@ createProjectTable: function(response) { Project Disease Type Site - # SSM Affected Cases + # Mutation Affected Cases `; @@ -168,58 +125,8 @@ getValueWithPercentage: function(numerator, denominator) { findProjectByKey: function(projects, key) { var project = projects.find(project => project.key === key); return project ? project.doc_count : 0; -}, - -/** - * Set an item of data. - */ -set: function( name, val ) { - this.data[ name ] = val; -}, - -/** - * Get an array listing which data keys are present in this feature. - */ -tags: function() { - var t = []; - var d = this.data; - for( var k in d ) { - if( d.hasOwnProperty( k ) ) - t.push( k ); - } - return t; -}, - -/** - * Get the unique ID of this feature. - */ -id: function( newid ) { - if( newid ) - this._uniqueID = newid; - return this._uniqueID; -}, - -/** - * Get this feature's parent feature, or undefined if none. - */ -parent: function() { - return this._parent; -}, - -/** - * Get an array of child features, or undefined if none. - */ -children: function() { - return this.get('subfeatures'); -}, - -toJSON: function() { - const d = Object.assign({},this) - delete d._parent - return d } }); -return SSMFeature; }); \ No newline at end of file diff --git a/gdc-viewer/js/Store/SeqFeature/CNVs.js b/gdc-viewer/js/Store/SeqFeature/CNVs.js index 6b3972a..87d3ba9 100644 --- a/gdc-viewer/js/Store/SeqFeature/CNVs.js +++ b/gdc-viewer/js/Store/SeqFeature/CNVs.js @@ -43,7 +43,7 @@ function( */ createQuery: function(ref, start, end) { var thisB = this; - var cnvQuery = `query cnvResults($filters: FiltersArgument) { explore { cnvs { hits(filters: $filters) { total edges { node { id cnv_id start_position end_position chromosome ncbi_build cnv_change } } } } } } `; + var cnvQuery = `query cnvResults($filters: FiltersArgument $size: Int $offset: Int) { explore { cnvs { hits(first: $size, offset: $offset, filters: $filters) { total edges { node { id cnv_id start_position end_position chromosome ncbi_build cnv_change } } } } } } `; var combinedFilters = thisB.getFilterQuery(ref, start, end); var bodyVal = { @@ -60,7 +60,7 @@ function( /** * Get the features to be displayed - * @param {object} query + * @param {object} query Query object * @param {function} featureCallback * @param {function} finishCallback * @param {function} errorCallback @@ -102,7 +102,7 @@ function( /** * Creates a CNV feature with the given gene object - * @param {object} cnv + * @param {object} cnv CNV object returned by GDC API * @param {function} featureCallback */ createCNVFeature: function(cnv, featureCallback) { @@ -128,7 +128,7 @@ function( var thisB = this; var locationFilter = {"op":"and","content":[{"op":">=","content":{"field":"cnvs.start_position","value":start}},{"op":"<=","content":{"field":"cnvs.end_position","value":end}},{"op":"=","content":{"field":"cnvs.chromosome","value":[chr]}}]}; if (thisB.case) { - var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case}}; + var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case.split(',')}}; locationFilter.content.push(caseFilter); } return(locationFilter); diff --git a/gdc-viewer/js/Store/SeqFeature/Genes.js b/gdc-viewer/js/Store/SeqFeature/Genes.js index 146ca01..1fd21a9 100644 --- a/gdc-viewer/js/Store/SeqFeature/Genes.js +++ b/gdc-viewer/js/Store/SeqFeature/Genes.js @@ -75,12 +75,14 @@ function( 'strand': thisB.prettyText(gene.gene_strand), 'type': 'Gene', 'gene description': thisB.prettyText(gene.description), + 'chromosome': gene.gene_chromosome, 'about': { 'biotype': thisB.prettyText(gene.biotype), 'gene name': thisB.prettyText(gene.name), 'id': thisB.prettyText(gene.gene_id), 'symbol': thisB.prettyText(gene.symbol), - 'synonyms': thisB.prettyText(gene.synonyms) + 'synonyms': thisB.prettyText(gene.synonyms), + 'strand': thisB.prettyText(gene.gene_strand) }, 'references': { 'ncbi gene': thisB.createLinkWithId(NCBI_LINK, gene.external_db_ids.entrez_gene), @@ -151,7 +153,7 @@ function( var thisB = this; var locationFilter = {"op":"and","content":[{"op":">=","content":{"field":"genes.gene_start","value":start}},{"op":"<=","content":{"field":"genes.gene_end","value":end}},{"op":"=","content":{"field":"genes.gene_chromosome","value":[chr]}}]}; if (thisB.case) { - var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case}}; + var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case.split(',')}}; locationFilter.content.push(caseFilter); } return(locationFilter); diff --git a/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js b/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js index 7625801..5c3d99f 100644 --- a/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js +++ b/gdc-viewer/js/Store/SeqFeature/SimpleSomaticMutations.js @@ -147,6 +147,7 @@ function( 'end': thisB.prettyText(mutation.end_position), 'type': 'Simple Somatic Mutation', 'projects': mutation.ssm_id, + 'chromosome': mutation.chromosome, 'about': { 'subtype': thisB.prettyText(mutation.mutation_subtype), 'dna change': thisB.prettyText(mutation.genomic_dna_change), @@ -171,7 +172,7 @@ function( */ createQuery: function(ref, start, end) { var thisB = this; - var ssmQuery = `query ssmResultsTableQuery( $ssmsTable_size: Int $ssmsTable_offset: Int $ssmsTable_filters: FiltersArgument $score: String $sort: [Sort] ) { viewer { explore { ssms { hits(first: $ssmsTable_size, offset: $ssmsTable_offset, filters: $ssmsTable_filters, score: $score, sort: $sort) { total edges { node { id start_position end_position mutation_type cosmic_id reference_allele ncbi_build score genomic_dna_change mutation_subtype ssm_id consequence { hits { edges { node { transcript { is_canonical annotation { vep_impact polyphen_impact polyphen_score sift_score sift_impact hgvsc } consequence_type gene { gene_id symbol gene_strand } aa_change transcript_id } id } } } } } } } } } } }`; + var ssmQuery = `query ssmResultsTableQuery( $ssmsTable_size: Int $ssmsTable_offset: Int $ssmsTable_filters: FiltersArgument $score: String $sort: [Sort] ) { viewer { explore { ssms { hits(first: $ssmsTable_size, offset: $ssmsTable_offset, filters: $ssmsTable_filters, score: $score, sort: $sort) { total edges { node { id start_position end_position mutation_type cosmic_id reference_allele ncbi_build score genomic_dna_change mutation_subtype ssm_id chromosome consequence { hits { edges { node { transcript { is_canonical annotation { vep_impact polyphen_impact polyphen_score sift_score sift_impact hgvsc } consequence_type gene { gene_id symbol gene_strand } aa_change transcript_id } id } } } } } } } } } } }`; var combinedFilters = thisB.getFilterQuery(ref, start, end); var bodyVal = { @@ -243,7 +244,7 @@ function( var thisB = this; var locationFilter = {"op":"and","content":[{"op":">=","content":{"field":"ssms.start_position","value":start}},{"op":"<=","content":{"field":"ssms.end_position","value":end}},{"op":"=","content":{"field":"ssms.chromosome","value":['chr'+chr]}}]}; if (thisB.case) { - var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case}}; + var caseFilter = {"op":"in","content":{"field": "cases.case_id","value": thisB.case.split(',')}}; locationFilter.content.push(caseFilter); } return(locationFilter); diff --git a/gdc-viewer/js/View/BaseGDCDialog.js b/gdc-viewer/js/View/BaseGDCDialog.js index 9740878..5138a05 100644 --- a/gdc-viewer/js/View/BaseGDCDialog.js +++ b/gdc-viewer/js/View/BaseGDCDialog.js @@ -1,5 +1,5 @@ /** - * A base class for GDC dialogs + * A base class for GDC dialogs, including common functions and variables */ define([ 'dojo/_base/declare', diff --git a/gdc-viewer/js/View/Export/CSV.js b/gdc-viewer/js/View/Export/CSV.js index 33ae771..52ba1f4 100644 --- a/gdc-viewer/js/View/Export/CSV.js +++ b/gdc-viewer/js/View/Export/CSV.js @@ -18,12 +18,12 @@ return declare( ExportBase, 'type', 'start', 'end', - 'strand', - 'id' + 'chromosome' ], // The extended header for genes geneHeader: [ + 'strand', 'gene name', 'biotype', 'symbol', @@ -51,21 +51,24 @@ return declare( ExportBase, */ _printHeader: function() { this.fullHeader = [] - if (this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/Genes') { - this.fullHeader = this.geneHeader - } else if (this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/SimpleSomaticMutations') { - this.fullHeader = this.ssmHeader - } else if (this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/CNVs') { - this.fullHeader = this.cnvHeader + if (this.store.config.type === 'gdc-viewer/Store/SeqFeature/Genes' || this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/Genes') { + this.fullHeader = [...this.geneHeader]; + } else if (this.store.config.type === 'gdc-viewer/Store/SeqFeature/SimpleSomaticMutations' || this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/SimpleSomaticMutations') { + this.fullHeader = [...this.ssmHeader]; + } else if (this.store.config.type === 'gdc-viewer/Store/SeqFeature/CNVs' || this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/CNVs') { + this.fullHeader = [...this.cnvHeader]; } var headerString - if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs') { - headerString = (this.defaultHeader.concat(this.fullHeader)).join(',') + '\n' + if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs' && this.store.config.type !== 'gdc-viewer/Store/SeqFeature/CNVs') { + headerString = (this.defaultHeader.concat(this.fullHeader)).join(',') } else { - headerString = this.cnvHeader.join(',') + '\n' + headerString = this.cnvHeader.join(',') } - this.print(headerString) + if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs' && this.store.config.type !== 'gdc-viewer/Store/SeqFeature/CNVs') { + this.print('id,') + } + this.print(headerString + '\n') }, /** @@ -75,10 +78,12 @@ return declare( ExportBase, formatFeature: function( feature ) { var featureArray = [] + var about = feature.get('about') + // SSM and Gene features have the extra about section - if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs') { + if (this.store.config.storeClass !== 'gdc-viewer/Store/SeqFeature/CNVs' && this.store.config.type !== 'gdc-viewer/Store/SeqFeature/CNVs') { + featureArray.push(about['id']) this.defaultHeader.forEach(field => featureArray.push(feature.get(field))) - var about = feature.get('about') this.fullHeader.forEach(field => { if (field === 'synonyms') { if (about[field]) { diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js index 1e9a936..26bd7f9 100644 --- a/gdc-viewer/js/View/GDCDialog.js +++ b/gdc-viewer/js/View/GDCDialog.js @@ -386,10 +386,10 @@ function ( * @return {number} */ compareTermElements: function(a, b) { - if (a.key < b.key) - return -1; - if (a.key > b.key) + if (a.count < b.count) return 1; + if (a.count > b.count) + return -1; return 0; }, @@ -449,33 +449,36 @@ function ( } dom.empty(thisB.mutationResultsTab.containerNode); + var ssmExplanation = dom.create('div', { innerHTML: "Add mutation tracks for all mutations available on the GDC portal. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.mutationResultsTab.containerNode); + // Buttons for SSMs var ssmMenu = new Menu({ style: "display: none;"}); var menuItemSSMFiltered = new MenuItem({ - label: "Filtered SSMs form GDC", + label: "Filtered Mutations", iconClass: "dijitIconNewTask", onClick: function() { thisB.addTrack('SimpleSomaticMutations', undefined, undefined, combinedFilters, 'gdc-viewer/View/Track/SSMTrack'); - alert("Adding track with all SSMs from the GDC, with current filters applied"); + alert("Adding track with all Mutations from the GDC, with current filters applied"); } }); ssmMenu.addChild(menuItemSSMFiltered); ssmMenu.startup(); var buttonAllSSMs = new ComboButton({ - label: "All SSMs from GDC", + label: "All Mutations", iconClass: "dijitIconNewTask", dropDown: ssmMenu, onClick: function() { thisB.addTrack('SimpleSomaticMutations', undefined, undefined, undefined, 'gdc-viewer/View/Track/SSMTrack'); - alert("Add track with all SSMs from the GDC"); + alert("Add track with all Mutations from the GDC"); } }); buttonAllSSMs.placeAt(thisB.mutationResultsTab.containerNode); buttonAllSSMs.startup(); - thisB.addTooltipToButton(menuItemSSMFiltered, "Add track with all SSMs from the GDC, with current filters applied"); - thisB.addTooltipToButton(buttonAllSSMs, "Add track with all SSMs from the GDC"); + thisB.addTooltipToButton(menuItemSSMFiltered, "Add track with all Mutations from the GDC, with current filters applied"); + thisB.addTooltipToButton(buttonAllSSMs, "Add track with all Mutations from the GDC"); + // Determine information for pagination and results var totalSSMs = response.data.viewer.explore.ssms.hits.total; var startResultCount = ((thisB.mutationPage - 1) * thisB.pageSize); if (totalSSMs > 0) { @@ -560,10 +563,12 @@ function ( combinedFilters = JSON.parse(combinedFilters); } + var geneExplanation = dom.create('div', { innerHTML: "Add gene and CNV tracks for all genes available on the GDC portal. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.geneResultsTab.containerNode); + // Buttons for Genes var geneMenu = new Menu({ style: "display: none;"}); var menuItemGeneFiltered = new MenuItem({ - label: "Filtered Genes from GDC", + label: "Filtered Genes", iconClass: "dijitIconNewTask", onClick: function() { thisB.addTrack('Genes', undefined, undefined, combinedFilters, 'gdc-viewer/View/Track/GeneTrack'); @@ -574,7 +579,7 @@ function ( geneMenu.startup(); var buttonAllGenes = new ComboButton({ - label: "All Genes from GDC", + label: "All Genes", iconClass: "dijitIconNewTask", dropDown: geneMenu, style: "padding-right: 8px;", @@ -591,7 +596,7 @@ function ( // Buttons for CNVs var cnvMenu = new Menu({ style: "display: none;"}); var menuItemCnvFiltered = new MenuItem({ - label: "Filtered CNVs from GDC", + label: "Filtered CNVs", iconClass: "dijitIconNewTask", onClick: function() { thisB.addTrack('CNVs', undefined, undefined, combinedFilters, 'gdc-viewer/View/Track/CNVTrack'); @@ -602,7 +607,7 @@ function ( cnvMenu.startup(); var buttonAllCnvs = new ComboButton({ - label: "All CNVs from GDC", + label: "All CNVs", iconClass: "dijitIconNewTask", dropDown: cnvMenu, onClick: function() { @@ -615,6 +620,7 @@ function ( thisB.addTooltipToButton(menuItemCnvFiltered, "Add track with all CNVs from the GDC, with current filters applied"); thisB.addTooltipToButton(buttonAllCnvs, "Add track with all CNVs from the GDC"); + // Determine information for pagination and results var totalGenes = response.data.genesTableViewer.explore.genes.hits.total; var startResultCount = ((thisB.genePage - 1) * thisB.pageSize); if (totalGenes > 0) { @@ -678,6 +684,7 @@ function ( }).then(function(response) { dom.empty(thisB.caseResultsTab.containerNode); + // Determine information for pagination and results var totalCases = response.data.exploreCasesTableViewer.explore.cases.hits.total; var startResultCount = ((thisB.casePage - 1) * thisB.pageSize); if (totalCases > 0) { @@ -685,8 +692,9 @@ function ( } var endResultCount = thisB.casePage * thisB.pageSize <= totalCases ? thisB.casePage * thisB.pageSize : totalCases; + var casesExplanation = dom.create('div', { innerHTML: "Add mutation, gene, and CNV tracks for a given case. Optionally apply the selected filters when adding tracks.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px;" }, thisB.caseResultsTab.containerNode); var resultsInfo = dom.create('div', { innerHTML: "Showing " + startResultCount.toLocaleString() + " to " + endResultCount.toLocaleString() + " of " + totalCases.toLocaleString() }, thisB.caseResultsTab.containerNode); - thisB.createDonorsTable(response, thisB.caseResultsTab.containerNode); + thisB.createCasesTable(response, thisB.caseResultsTab.containerNode); thisB.createPaginationButtons(thisB.caseResultsTab.containerNode, totalCases / thisB.pageSize, 'case', thisB.casePage); }).catch(function(err) { console.log(err); @@ -699,7 +707,7 @@ function ( * @param {object} response the response from the GDC graphQL query * @param {object} location dom element to place the table */ - createDonorsTable: function(response, location) { + createCasesTable: function(response, location) { var thisB = this; var table = `
`; var tableNode = dom.toDom(table); @@ -710,7 +718,7 @@ function ( Primary Site Gender Genes - SSMs + Mutations CNVs `; @@ -744,7 +752,7 @@ function ( // Gene Buttons var geneMenu = new Menu({ style: "display: none;"}); var menuItemGeneFiltered = new MenuItem({ - label: "Filtered Genes for Donor", + label: "Filtered Genes", iconClass: "dijitIconNewTask", onClick: (function(hit, combinedFilters) { return function() { @@ -757,7 +765,7 @@ function ( geneMenu.startup(); var buttonAllGenes = new ComboButton({ - label: "All Genes for Donor", + label: "All Genes", iconClass: "dijitIconNewTask", dropDown: geneMenu, onClick: (function(hit) { @@ -769,8 +777,8 @@ function ( }); buttonAllGenes.placeAt(geneButtonNode); buttonAllGenes.startup(); - thisB.addTooltipToButton(menuItemGeneFiltered, "Add track with all genes for the given donor, with current filters applied"); - thisB.addTooltipToButton(buttonAllGenes, "Add track with all genes for the given donor"); + thisB.addTooltipToButton(menuItemGeneFiltered, "Add track with all genes for the given case, with current filters applied"); + thisB.addTooltipToButton(buttonAllGenes, "Add track with all genes for the given case"); // Place buttons in table dom.place(geneButtonNode, caseRowContentNode); @@ -781,7 +789,7 @@ function ( // SSM Buttons var ssmMenu = new Menu({ style: "display: none;"}); var menuItemSsmFiltered = new MenuItem({ - label: "Filtered SSMs for Donor", + label: "Filtered Mutations", iconClass: "dijitIconNewTask", onClick: (function(hit, combinedFilters) { return function() { @@ -794,7 +802,7 @@ function ( ssmMenu.startup(); var buttonAllSsms = new ComboButton({ - label: "All SSMs for Donor", + label: "All Mutations", iconClass: "dijitIconNewTask", dropDown: ssmMenu, onClick: (function(hit) { @@ -806,8 +814,8 @@ function ( }); buttonAllSsms.placeAt(ssmButtonNode); buttonAllSsms.startup(); - thisB.addTooltipToButton(menuItemSsmFiltered, "Add track with all SSMs for the given donor, with current filters applied"); - thisB.addTooltipToButton(buttonAllSsms, "Add track with all SSMS for the given donor"); + thisB.addTooltipToButton(menuItemSsmFiltered, "Add track with all Mutations for the given case, with current filters applied"); + thisB.addTooltipToButton(buttonAllSsms, "Add track with all Mutations for the given case"); // Place buttons in table dom.place(ssmButtonNode, caseRowContentNode); @@ -818,7 +826,7 @@ function ( // CNV Buttons var cnvMenu = new Menu({ style: "display: none;"}); var menuItemCnvFiltered = new MenuItem({ - label: "Filtered CNVs for Donor", + label: "Filtered CNVs", iconClass: "dijitIconNewTask", onClick: (function(hit, combinedFilters) { return function() { @@ -831,7 +839,7 @@ function ( cnvMenu.startup(); var buttonAllCnvs = new ComboButton({ - label: "All CNVs for Donor", + label: "All CNVs", iconClass: "dijitIconNewTask", dropDown: cnvMenu, onClick: (function(hit) { @@ -843,8 +851,8 @@ function ( }); buttonAllCnvs.placeAt(cnvButtonNode); buttonAllCnvs.startup(); - thisB.addTooltipToButton(menuItemCnvFiltered, "Add track with all CNVs for the given donor, with current filters applied"); - thisB.addTooltipToButton(buttonAllCnvs, "Add track with all CNVs for the given donor"); + thisB.addTooltipToButton(menuItemCnvFiltered, "Add track with all CNVs for the given case, with current filters applied"); + thisB.addTooltipToButton(buttonAllCnvs, "Add track with all CNVs for the given case"); // Place buttons in table dom.place(cnvButtonNode, caseRowContentNode); @@ -888,8 +896,8 @@ function ( Symbol Name - # SSM Affected Cases in Cohort - # SSM Affected Cases Across the GDC + # Mutation Affected Cases in Cohort + # Mutation Affected Cases Across the GDC # CNV Gain # CNV Loss Is Cancer Gene Census diff --git a/gdc-viewer/js/View/GDCPrimarySitesDialog.js b/gdc-viewer/js/View/GDCPrimarySitesDialog.js index 3915971..55b0581 100644 --- a/gdc-viewer/js/View/GDCPrimarySitesDialog.js +++ b/gdc-viewer/js/View/GDCPrimarySitesDialog.js @@ -54,6 +54,7 @@ function ( var thisB = this; var headerSection = dom.create('div', { style: "margin-bottom: 5px;" }, thisB.dialogContainer); var aboutMessage = dom.create('h1', { innerHTML: "View primary sites available on the GDC Data Portal" }, headerSection); + var pageExplanation = dom.create('div', { innerHTML: "Add mutation, gene and CNV tracks for all cases across the GDC, filtered by primary site.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; margin-top:5px;" }, headerSection); }, /** @@ -143,19 +144,19 @@ function ( var geneMenu = new Menu({ style: "display: none;"}); var menuItemSSM = new MenuItem({ - label: "SSMs for Primary Site", + label: "All Mutations", iconClass: "dijitIconNewTask", onClick: (function(hit) { return function() { thisB.addTrack('SimpleSomaticMutations', hit.key, 'gdc-viewer/View/Track/SSMTrack'); - alert("Adding SSM track for primary site " + hit.key); + alert("Adding Mutation track for primary site " + hit.key); } })(hit) }); geneMenu.addChild(menuItemSSM); var menuItemGene = new MenuItem({ - label: "Genes for Primary Site", + label: "All Genes", iconClass: "dijitIconNewTask", onClick: (function(hit) { return function() { @@ -167,7 +168,7 @@ function ( geneMenu.addChild(menuItemGene); var menuItemCNV = new MenuItem({ - label: "CNVs for Primary Site", + label: "All CNVs", iconClass: "dijitIconNewTask", onClick: (function(hit) { return function() { @@ -191,7 +192,7 @@ function ( // Add tooltips thisB.addTooltipToButton(menuItemGene, "Add track with all genes for the given primary site"); thisB.addTooltipToButton(menuItemCNV, "Add track with all CNVs for the given primary site"); - thisB.addTooltipToButton(menuItemSSM, "Add track with all SSMs for the given primary site"); + thisB.addTooltipToButton(menuItemSSM, "Add track with all Mutations for the given primary site"); // Place buttons in table dom.place(projectButtonNode, projectRowContentNode); diff --git a/gdc-viewer/js/View/GDCProjectDialog.js b/gdc-viewer/js/View/GDCProjectDialog.js index f7efdd2..509f874 100644 --- a/gdc-viewer/js/View/GDCProjectDialog.js +++ b/gdc-viewer/js/View/GDCProjectDialog.js @@ -54,6 +54,7 @@ function ( var thisB = this; var headerSection = dom.create('div', { style: "margin-bottom: 5px;" }, thisB.dialogContainer); var aboutMessage = dom.create('h1', { innerHTML: "View projects available on the GDC Data Portal" }, headerSection); + var pageExplanation = dom.create('div', { innerHTML: "Add mutation, gene and CNV tracks for all cases across the GDC, filtered by project.", style: "font-size: 14px; margin-bottom: 5px; padding: 5px; margin-top:5px;" }, headerSection); }, /** @@ -165,7 +166,7 @@ function ( var geneMenu = new Menu({ style: "display: none;"}); var menuItemSSM = new MenuItem({ - label: "SSMs for Project", + label: "All Mutations", iconClass: "dijitIconNewTask", onClick: (function(hit) { return function() { @@ -177,7 +178,7 @@ function ( geneMenu.addChild(menuItemSSM); var menuItemGene = new MenuItem({ - label: "Genes for Project", + label: "All Genes", iconClass: "dijitIconNewTask", onClick: (function(hit) { return function() { @@ -189,7 +190,7 @@ function ( geneMenu.addChild(menuItemGene); var menuItemCNV = new MenuItem({ - label: "CNVs for Project", + label: "All CNVs", iconClass: "dijitIconNewTask", onClick: (function(hit) { return function() { @@ -213,7 +214,7 @@ function ( // Add tooltips thisB.addTooltipToButton(menuItemGene, "Add track with all genes for the given project"); thisB.addTooltipToButton(menuItemCNV, "Add track with all CNVs for the given project"); - thisB.addTooltipToButton(menuItemSSM, "Add track with all SSMs for the given project"); + thisB.addTooltipToButton(menuItemSSM, "Add track with all Mutations for the given project"); // Place buttons in table dom.place(projectButtonNode, projectRowContentNode); diff --git a/gdc-viewer/js/View/Track/BaseTrack.js b/gdc-viewer/js/View/Track/BaseTrack.js index 3ad73d0..21e18fd 100644 --- a/gdc-viewer/js/View/Track/BaseTrack.js +++ b/gdc-viewer/js/View/Track/BaseTrack.js @@ -26,6 +26,9 @@ define( ); }, + /** + * Override the available export types + */ _exportFormats: function() { return [ {name: 'gdc-viewer/View/Export/GFF3', label: 'GFF3', fileExt: 'gff3'}, diff --git a/gdc-viewer/js/View/Track/CNVTrack.js b/gdc-viewer/js/View/Track/CNVTrack.js index e07b30d..ff9d407 100644 --- a/gdc-viewer/js/View/Track/CNVTrack.js +++ b/gdc-viewer/js/View/Track/CNVTrack.js @@ -28,6 +28,9 @@ define( ); }, + /** + * Override the available export types + */ _exportFormats: function() { return [ {name: 'GFF3', label: 'GFF3', fileExt: 'gff3'}, diff --git a/gdc-viewer/js/View/Track/CommonTrack.js b/gdc-viewer/js/View/Track/CommonTrack.js index 1ecba25..3e5e891 100644 --- a/gdc-viewer/js/View/Track/CommonTrack.js +++ b/gdc-viewer/js/View/Track/CommonTrack.js @@ -19,6 +19,9 @@ define( ValidationTextArea) { return declare(null, { + /** + * Adds additional track menu options + */ _trackMenuOptions: function () { var options = this.inherited(arguments); options.push({ type: 'dijit/MenuSeparator' } ); @@ -45,20 +48,21 @@ define( var track = this; var details = domConstruct.create('div', { className: 'detail', style: 'display: flex; flex-direction: column; align-items: center; justify-content: center;' }); - var headerString = '

Track Filters

'; + // Create header text + var headerString = '

View and Update Filters Applied To The Current Track

'; var headerElement = domConstruct.toDom(headerString); domConstruct.place(headerElement, details); - // Create help text - var helpString = 'The following filters have been applied to the track. You can update the filters here, though no validation is done on the input.'; + // Create filter help text + var helpString = 'The following filters have been applied to the track. You can update the filters here, though only basic validation is done on the input.'; var helpElement = domConstruct.toDom(helpString); domConstruct.place(helpElement, details); - var filterString = '

Filters

'; + var filterString = '

Filters

Filters narrow down the features displayed on the track. We use the same format as the GDC GraphQL API.
'; var filterElement = domConstruct.toDom(filterString); domConstruct.place(filterElement, details); - // Get filtered text + // Display filtered text var filteredText = JSON.stringify(track.store.filters, null, 2) var textArea = new ValidationTextArea({ @@ -79,7 +83,8 @@ define( } }).placeAt(details); - var caseString = '

Case UUID

'; + // Display cases + var caseString = '

Case UUIDs

Comma separated unique identifiers for the case, expressed as UUIDs.
'; var caseElement = domConstruct.toDom(caseString); domConstruct.place(caseElement, details); @@ -87,12 +92,13 @@ define( value: track.store.config.case, style: "width: 80%", id: "caseTextBox", - regExp: "^[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}$", + regExp: "^[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}(,[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})*$", invalidMessage: "Invalid Case UUID - Must be version 4 UUID", trim: true }).placeAt(details); - var sizeHeader = '

Size

'; + // Display size + var sizeHeader = '

Size

This is the maximum number of results to return per panel.
'; var sizeElement = domConstruct.toDom(sizeHeader); domConstruct.place(sizeElement, details); @@ -100,12 +106,13 @@ define( value: track.store.size, style: "width: 80%", id: "sizeTextBox", - constraints: { min: 1, max: 1000, places: 0 }, + constraints: { min: 1, max: 2000, places: 0 }, smallDelta: 10 }).placeAt(details); + // Add button to update the track with changed content var updateTrackButton = new Button({ - label: 'Apply New Filters', + label: 'Apply Filters', iconClass: 'dijitIconSave', onClick: function() { const trackString = document.getElementById("filterTextArea").value; @@ -125,6 +132,7 @@ define( } }).placeAt(details); + // Change listeners for text boxes caseIdTextBox.on('change', function(e) { updateTrackButton.set('disabled', !caseIdTextBox.validate() || !sizeTextBox.validate() || !textArea.validate()) }); @@ -171,14 +179,14 @@ define( var shareableLink = window.location.protocol + "//" + window.location.host + window.location.pathname + '?' + params.toString(); // Create help text - var helpString = 'Use the following link to share the selected track at the current location.'; + var helpString = 'Use the following link to share the selected track at the current location.'; var helpElement = domConstruct.toDom(helpString); domConstruct.place(helpElement, details); // Create text area with shareable link var textArea = domConstruct.create( 'textarea',{ - rows: 10, + rows: 3, value: shareableLink, style: "width: 80%", readOnly: true @@ -192,5 +200,5 @@ define( return details; } }); - } + } ); \ No newline at end of file diff --git a/gdc-viewer/js/View/Track/GeneTrack.js b/gdc-viewer/js/View/Track/GeneTrack.js index c4ec13e..a33e42e 100644 --- a/gdc-viewer/js/View/Track/GeneTrack.js +++ b/gdc-viewer/js/View/Track/GeneTrack.js @@ -12,7 +12,13 @@ define( domConstruct, BaseTrack) { return declare(BaseTrack, { - + /** + * Override the additional details shown in the dialogs + * @param {*} track + * @param {*} f + * @param {*} featDiv + * @param {*} container + */ _renderAdditionalTagsDetail: function( track, f, featDiv, container ) { var atElement = domConstruct.create( 'div', diff --git a/gdc-viewer/js/View/Track/SSMTrack.js b/gdc-viewer/js/View/Track/SSMTrack.js index 9d777a1..d1b2313 100644 --- a/gdc-viewer/js/View/Track/SSMTrack.js +++ b/gdc-viewer/js/View/Track/SSMTrack.js @@ -12,7 +12,13 @@ define( domConstruct, BaseTrack) { return declare(BaseTrack, { - + /** + * Override the additional details shown in the dialogs + * @param {*} track + * @param {*} f + * @param {*} featDiv + * @param {*} container + */ _renderAdditionalTagsDetail: function( track, f, featDiv, container ) { var atElement = domConstruct.create( 'div', diff --git a/gdc-viewer/js/View/Track/ValidationTextArea.js b/gdc-viewer/js/View/Track/ValidationTextArea.js index 9c3dde3..7127d31 100644 --- a/gdc-viewer/js/View/Track/ValidationTextArea.js +++ b/gdc-viewer/js/View/Track/ValidationTextArea.js @@ -1,3 +1,6 @@ +/** + * Extends SimpleTextArea to support the validation features of the ValidationTextBox + */ define( [ "dojo/_base/declare", diff --git a/gdc-viewer/js/main.js b/gdc-viewer/js/main.js index 01ef9d5..9fe0321 100644 --- a/gdc-viewer/js/main.js +++ b/gdc-viewer/js/main.js @@ -28,13 +28,13 @@ return declare( JBrowsePlugin, })); this.browser.addGlobalMenuItem('gdc', new MenuItem( { - label: 'Explore Projects', + label: 'Explore projects', iconClass: "dijitIconSearch", onClick: lang.hitch(this, 'createGDCProject') })); this.browser.addGlobalMenuItem('gdc', new MenuItem( { - label: 'Explore Primary Sites', + label: 'Explore primary sites', iconClass: "dijitIconSearch", onClick: lang.hitch(this, 'createGDCPrimarySites') }));