diff --git a/README.md b/README.md index 7c06d082..1a1d9fc4 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,7 @@ Internal development can be performed by branching from `gh-pages` to your own f Pages are described by categories. These are stored in a Jekyll collection at [_categories](_categories/). The content that describes each category is defined in a YAML header in a file in that directory. The categories avaiable for reference elsewhere are named as the file or as present in the 'name' field of the YAML header. For example, if you want to create a page with a governance category, you would look in [_categories/governance.md](_categories/governance.md) in the 'name' field and use that value. + ### Creating a page To create a page using the article layout, start by specifying at the very beginning the title, layout, excerpt, and category in the YAML front matter. The title and excerpt will show up in the article's user guide thumbnail and the category tag will be used to sort the article into its corresponding user guide tab. If no category is specified, it will default into the "How-To" tab. @@ -94,6 +95,20 @@ Images can be inserted using either Markdown or HTML, it all depends on your pre ### Inserting code The docs may contain a high level overview of a feature, but should link to the [Python docs](https://python-docs.synapse.org/build/html/index.html) and [synapser](https://r-docs.synapse.org/articles/synapser.html) docs, pointing to the relevant anchor, for code examples. This is to ensure code is validated with the client release cycles. + +### Inserting relative links +A page may link to other pages within the documentation site. To do this, use a `link` Liquid tag to properly render the URL: + +``` +[link text]({{ site.baseurl }}{% link _articles/getting_started.md %}) +``` + +If the link uses an anchor to jump to a specific part of the page, it must go outside the `link` tag: + +``` +[Annotations]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}#adding-annotations) +``` + ## License Distributed under the Eclipse Public License, the same as Clojure. diff --git a/_articles/access_controls.md b/_articles/access_controls.md index b6aab7ff..b38b5fcb 100644 --- a/_articles/access_controls.md +++ b/_articles/access_controls.md @@ -6,7 +6,7 @@ category: governance order: 2 --- -Synapse has two ways to control who can access your content. Sharing Settings determine _who_ can access content, and is akin to individual or group (team) permissions. Conditions for Use determine _how_ data can be used by those users who have been granted access. All content in Synapse has Sharing Settings but not all content has Conditions for Use. See the [Sharing Settings](sharing_settings.md) article for information about those settings - this article covers conditions for use only. +Synapse has two ways to control who can access your content. Sharing Settings determine _who_ can access content, and is akin to individual or group (team) permissions. Conditions for Use determine _how_ data can be used by those users who have been granted access. All content in Synapse has Sharing Settings but not all content has Conditions for Use. See the [Sharing Settings]({{ site.baseurl }}{% link _articles/sharing_settings.md %}) article for information about those settings - this article covers conditions for use only. diff --git a/_articles/accounts_certified_users_and_profile_validation.md b/_articles/accounts_certified_users_and_profile_validation.md index ca4c0582..3e33a496 100644 --- a/_articles/accounts_certified_users_and_profile_validation.md +++ b/_articles/accounts_certified_users_and_profile_validation.md @@ -26,7 +26,7 @@ The table below summarizes the user privileges for each level. ## User Responsibilities -You are solely responsible for your actions on Synapse. You are required to abide by the [Synapse Terms and Conditions of Use](https://s3.amazonaws.com/static.synapse.org/governance/SageBionetworksSynapseTermsandConditionsofUse.pdf?v=4) and all policies and principles described in the [Synapse governance documents](governance.md). We strongly encourage you to familiarize yourself with these documents. Please contact the Synapse Access and Compliance Team () if you have any questions. +You are solely responsible for your actions on Synapse. You are required to abide by the [Synapse Terms and Conditions of Use](https://s3.amazonaws.com/static.synapse.org/governance/SageBionetworksSynapseTermsandConditionsofUse.pdf?v=4) and all policies and principles described in the [Synapse governance documents]({{ site.baseurl }}{% link _articles/governance.md %}). We strongly encourage you to familiarize yourself with these documents. Please contact the Synapse Access and Compliance Team () if you have any questions. {% include important.html content="By using Synapse you consent to all Synapse governance policies and procedures." %} @@ -69,11 +69,11 @@ Go to the settings area of your [Synapse profile homepage](https://www.synapse.o 1. Confirm your user profile is complete including **your full name, current affiliation, and city/country.** 1. Link to your ORCID profile. **Make sure your profile is public and populate it with at least one piece of information about yourself in addition to your name.** -1. Physically sign (in ink), initial, and submit the Synapse [Oath](../assets/other/oath.md) +1. Physically sign (in ink), initial, and submit the Synapse [Oath]({{ site.baseurl }}{% link assets/other/oath.md %}) 1. Submit recent (current within the past month) identity attestation documentation. Acceptable forms of documentation, in English, are: -* A letter from a signing official on letterhead attesting to your identity. _Please note that you can not serve as your own signing official_ ([template here](../assets/other/signing_official_template.md)) OR -* A notarized letter attesting to your identity ([template here](../assets/other/notarized_letter_template.md)) OR +* A letter from a signing official on letterhead attesting to your identity. _Please note that you can not serve as your own signing official_ ([template here]({{ site.baseurl }}{% link assets/other/signing_official_template.md %})) OR +* A notarized letter attesting to your identity ([template here]({{ site.baseurl }}{% link assets/other/notarized_letter_template.md %})) OR * A copy of your professional license (e.g., a photocopy of your medical license) _Please note that a copy of a work or university identification badge is not an accepted form of identity attestation documentation._ @@ -83,7 +83,7 @@ You will receive a notification email when your profile has been validated and a Acceptable forms of documentation, in English, are: -* A letter from a signing official on letterhead attesting to your identity. _Please note that you can not serve as your own signing official_ ([template here](../assets/other/signing_official_template.md)) OR -* A notarized letter attesting to your identity ([template here](../assets/other/notarized_letter_template.md)) OR +* A letter from a signing official on letterhead attesting to your identity. _Please note that you can not serve as your own signing official_ ([template here]({{ site.baseurl }}{% link assets/other/signing_official_template.md %})) OR +* A notarized letter attesting to your identity ([template here]({{ site.baseurl }}{% link assets/other/notarized_letter_template.md %})) OR * A copy of your professional license (e.g., a photocopy of your medical license) _Please note that a copy of a work or university identification badge is not an accepted form of identity attestation documentation._ diff --git a/_articles/annotation_and_query.md b/_articles/annotation_and_query.md index 4fcc22d0..085c9c4f 100644 --- a/_articles/annotation_and_query.md +++ b/_articles/annotation_and_query.md @@ -11,7 +11,7 @@ category: metadata-and-annotations In this case, the annotations you may want to add might look like this: -![Annotation example](../assets/images/annotationsComplete.png) +![Annotation example]({../assets/images/annotationsComplete.png) ## Types of Annotations @@ -24,7 +24,7 @@ Annotations can be one of four types: ## How to Assign Annotations -Annotations may be added when initially uploading a file or at a later date. This can be done using the command line client, the [Python client](https://python-docs.synapse.org/build/html/Views.html#updating-annotations-using-view), the [R client](https://r-docs.synapse.org/articles/views.html#updating-annotations-using-view), or from the web. Using the programmatic clients facilitates batch and automated population of annotations across many files. The web client can be used to bulk update many files using [file views](views.md). +Annotations may be added when initially uploading a file or at a later date. This can be done using the command line client, the [Python client](https://python-docs.synapse.org/build/html/Views.html#updating-annotations-using-view), the [R client](https://r-docs.synapse.org/articles/views.html#updating-annotations-using-view), or from the web. Using the programmatic clients facilitates batch and automated population of annotations across many files. The web client can be used to bulk update many files using [file views]({{ site.baseurl }}{% link _articles/views.md %}). ### Adding Annotations @@ -32,7 +32,7 @@ To add annotations on a single entity through the web client, click the **Annota ![Annotation web location](../assets/images/webAnnotation.png) -To add annotations on multiple files, please refer to our Synapse in Practice article [Managing Custom Metadata at Scale](managing_custom_metadata_at_scale.md) for a tutorial on how to do this efficiently and effectively leveraging [file views](views.md). +To add annotations on multiple files, please refer to our Synapse in Practice article [Managing Custom Metadata at Scale]({{ site.baseurl }}{% link _articles/managing_custom_metadata_at_scale.md %}) for a tutorial on how to do this efficiently and effectively leveraging [file views]({{ site.baseurl }}{% link _articles/views.md %}). ##### Command line @@ -65,7 +65,7 @@ Click **File Tools**, **Annotations** and **Edit** to add, delete, or modify ann ![Annotation editor](../assets/images/annotationsDetail.png) -To add annotations on multiple files, please refer to our Synapse in Practice article [Managing Custom Metadata at Scale](managing_custom_metadata_at_scale.md) for a tutorial on how to do this efficiently and effectively leveraging [file views](views.md). +To add annotations on multiple files, please refer to our Synapse in Practice article [Managing Custom Metadata at Scale]({{ site.baseurl }}{% link _articles/managing_custom_metadata_at_scale.md %}) for a tutorial on how to do this efficiently and effectively leveraging [file views]({{ site.baseurl }}{% link _articles/views.md %}). ##### Command line @@ -133,7 +133,7 @@ SELECT * FROM syn123456 WHERE "id" = 'syn00012' ### Finding Files in a Specific Project -To find all files in a specific Project, create a View in the web client. For example, if you'd like to see all files in a Project, navigate to your project and then the **Tables** tab. From there, click **Tables Tools** and **Add File View**. Click **Add container** and **Enter Synapse Id** to create a tabluar file view that contains every file in the project, which you can now query. Importantly, if you want to later query on annotations, you must select **Add All Annotations**. For a more in-depth look at this feature, please read our articles on [File Views](views.md). +To find all files in a specific Project, create a View in the web client. For example, if you'd like to see all files in a Project, navigate to your project and then the **Tables** tab. From there, click **Tables Tools** and **Add File View**. Click **Add container** and **Enter Synapse Id** to create a tabluar file view that contains every file in the project, which you can now query. Importantly, if you want to later query on annotations, you must select **Add All Annotations**. For a more in-depth look at this feature, please read our articles on [File Views]({{ site.baseurl }}{% link _articles/views.md %}). ### Listing Files in a Specific Folder @@ -213,4 +213,4 @@ SELECT * FROM syn123 where "chemicalStructure" = '4''-chemical' # See Also -[Downloading Data](downloading_data.md), [Tables](tables.md) +[Downloading Data]({{ site.baseurl }}{% link _articles/downloading_data.md %}), [Tables]({{ site.baseurl }}{% link _articles/tables.md %}) diff --git a/_articles/challenge_administration.md b/_articles/challenge_administration.md index dc8be93e..43646fe4 100644 --- a/_articles/challenge_administration.md +++ b/_articles/challenge_administration.md @@ -27,7 +27,7 @@ Maintence of both a **Staging** and **Live** `Project` enables `Wiki` content to {% include important.html content="All edits and changes should be made on the Staging site." %} -For background on how to create and share `Projects`, `Files`, `Folders` and `Wiki` pages, please see our article [Making a Project](making_a_project.md). +For background on how to create and share `Projects`, `Files`, `Folders` and `Wiki` pages, please see our article [Making a Project]({{ site.baseurl }}{% link _articles/making_a_project.md %}). ### Synapse Teams @@ -39,7 +39,7 @@ The command `createchallenge` creates three Synapse `Teams`: * **Challenge pre-registration team** - This `Team` is recommended for when the challenge is under development. It allows participants to join a mailing list to receive notification of challenge launch news. -Please visit this [page](teams.md) to learn more about `Teams`. +Please visit this [page]({{ site.baseurl }}{% link _articles/teams.md %}) to learn more about `Teams`. ### Activating Challenge Configuration @@ -49,7 +49,7 @@ The command `createchallenge` also connects the **challenge participant team** t The challenge data (e.g. training dataset, scoring data...) are uploaded to the **Live** challenge `Project` when it is ready to be shared with participants. -For background on how to create and share `Project`, `Files`, `Folders` and `Wiki` pages, please see our article [Making a Project](making_a_project.md). +For background on how to create and share `Project`, `Files`, `Folders` and `Wiki` pages, please see our article [Making a Project](%{ link _articles/making_a_project.md %}). ### Adding Conditions for Use @@ -57,13 +57,13 @@ Synapse has the ability to apply access restrictions to sensitive data (e.g. hum There are cases where there are no human data concerns and instead a pop-up agreement needs to be presented before the first data download. Contact the **Access and Compliance Team** to set up this agreement. -Please view the [Access Controls page](access_controls.md) to learn how to add conditions for use on data. +Please view the [Access Controls page]({{ site.baseurl }}{% link _articles/access_controls.md %}) to learn how to add conditions for use on data. ### Create an Evaluation Queue for Submissions Challenge participants can submit Synapse Entities (e.g. `File`, `Folder`, `Project`, `Docker`) to evaluation queues. Multiple Evaluation queues can be created to support challenges with more than one question. -Please visit the [Evaluation Queue article](evaluation_queues.md) to learn more about queue configuration. +Please visit the [Evaluation Queue article]({{ site.baseurl }}{% link _articles/evaluation_queues.md %}) to learn more about queue configuration. One of the features of Synapse for DREAM Challenges is the live compilation of submission statistics for all evaluation queues, including total submission count, count per individual/team, count per submission state (scored, invalid) and count per week. You can see the statistics for various challenges [here](https://www.synapse.org/#!Synapse:syn2504723/wiki/65150). In order to activate statistics for your evaluation queues, you must be an administrator of the challenge Project. Each queue needs to be configured to generate the statistics. To do this: @@ -90,4 +90,4 @@ Throughout the challenge, participants will continuously submit to the evaluatio Organizers can create a leaderboard when scores are ready to be revealed to participants. Leaderboards are sorted, paginated, tabular forms that display submission annotations (e.g. scores from the scoring application and other metadata) and update as annotations or scores change. A leaderboard can provide real-time insight into the progress of a challenge. -Learn more about adding leaderboards in the [Evaluation Queue article](evaluation_queues.md). +Learn more about adding leaderboards in the [Evaluation Queue article]({{ site.baseurl }}{% link _articles/evaluation_queues.md %}). diff --git a/_articles/challenge_participation.md b/_articles/challenge_participation.md index ec89a303..f8321c99 100644 --- a/_articles/challenge_participation.md +++ b/_articles/challenge_participation.md @@ -18,10 +18,10 @@ This tutorial will teach you the steps of participating in a challenge. ## Challenge Registration -If you do not have a Synapse account, please go to our [getting started guide](getting_started.md#becoming-a-certified-user) to become a certified Synapse user. +If you do not have a Synapse account, please go to our [getting started guide]({{ site.baseurl}}{% link _articles/getting_started.md %}#becoming-a-certified-user) to become a certified Synapse user. Participants **must** be registered for the challenge if they want to submit and participate. The registration button can be found on the home page or `How to Participate` page for every challenge. In order to be fully registered for any challenge, you must have a Synapse account. In addition, DREAM Challenges require that you: -(1) become a [certified user](getting_started.md#becoming-a-certified-user); +(1) become a [certified user]({{ site.baseurl}}{% link _articles/getting_started.md %}#becoming-a-certified-user); (2) agree to the DREAM Rules of participation, and @@ -29,7 +29,7 @@ Participants **must** be registered for the challenge if they want to submit and ## Join or Create a Team -We encourage you to form a team with other participants for the challenge. You can either join a team or create your own team of collaborators. See instructions on how to form a team [here](teams.md). It is important to note that you **cannot** be on more than one team. Once you have submitted as a team or individual, you will not be able to submit as another team. If you decide to be part of a team, please register your team to the challenge - there will be a place to do this in every challenge wiki. +We encourage you to form a team with other participants for the challenge. You can either join a team or create your own team of collaborators. See instructions on how to form a team [here]({{ site.baseurl }}{% link _articles/teams.md %}). It is important to note that you **cannot** be on more than one team. Once you have submitted as a team or individual, you will not be able to submit as another team. If you decide to be part of a team, please register your team to the challenge - there will be a place to do this in every challenge wiki. ## Accessing Challenge Data @@ -37,11 +37,11 @@ The data stored on the challenge Synapse site can be accessed using the Synapse ## Run your Algorithms and Submit to the Challenge -You can submit to a challenge queue by using the R, Python or web client. All submissions must be first uploaded to Synapse. Follow these [instructions](getting_started.md#project-and-data-management-on-synapse) to learn how to upload to a project. Most challenge queues will be labeled by `challengename-subchallenge#` as a challenge may have different questions that it may want you to answer. Learn more about submitting to [evaluation queues](evaluation_queues.md) +You can submit to a challenge queue by using the R, Python or web client. All submissions must be first uploaded to Synapse. Follow these [instructions]({{ site.baseurl }}{% link _articles/getting_started.md %}) to learn how to upload to a project. Most challenge queues will be labeled by `challengename-subchallenge#` as a challenge may have different questions that it may want you to answer. Learn more about submitting to [evaluation queues]({{ site.baseurl }}{% link _articles/evaluation_queues.md %}) ## Share Ideas and Ask Questions Every challenge has a discussion forum for participants (the `Discussion` tab on the Challenge Project page). The forum is a space for participants to ask any questions and raise ideas. -Instructions on how to use the discussion forum can be found [here](discussion.md) +Instructions on how to use the discussion forum can be found [here]({{ site.baseurl }}{% link _articles/discussion.md %}) diff --git a/_articles/client_configuration.md b/_articles/client_configuration.md index 619ec735..9e26e323 100644 --- a/_articles/client_configuration.md +++ b/_articles/client_configuration.md @@ -33,4 +33,4 @@ From your [Synapse homepage](https://www.synapse.org/), navigate to your user me ## See Also -[Getting Started](getting_started.md), [Custom Storage Locations](custom_storage_location.md), [Downloading Data](downloading_data.md) +[Getting Started]({{ site.baseurl }}{% link _articles/getting_started.md %}), [Custom Storage Locations]({{ site.baseurl }}{% link _articles/custom_storage_location.md %}), [Downloading Data]({{ site.baseurl }}{% link _articles/downloading_data.md %}) diff --git a/_articles/contribute_and_access_controlled_use_data.md b/_articles/contribute_and_access_controlled_use_data.md index 26948154..0b4c571a 100644 --- a/_articles/contribute_and_access_controlled_use_data.md +++ b/_articles/contribute_and_access_controlled_use_data.md @@ -14,7 +14,7 @@ You must be a `Certified User` to contribute data to Synapse. You are responsibl If there are no ethical, legal or regulatory reasons to impose `Conditions for Use`, the data can be used for any lawful research purpose. All human data shared in Synapse, with or without `Conditions for Use`, must be de-identified according to **HIPAA standards** and comply with all applicable privacy laws and regulations. Guidance on de-identification according to HIPAA rules can be found [here](http://www.hhs.gov/ocr/privacy){:target="_blank"}. -`Conditions for Use` can be set at the `Project`, `Folder`, `File` and `Table` level. We recommend grouping `Files` that require the same `Conditions for Use` in a dedicated `Folder` within your `Project`. For more information about setting `Conditions for Use` please see [Access Controls and Data Governance](access_controls.md). +`Conditions for Use` can be set at the `Project`, `Folder`, `File` and `Table` level. We recommend grouping `Files` that require the same `Conditions for Use` in a dedicated `Folder` within your `Project`. For more information about setting `Conditions for Use` please see [Access Controls and Data Governance]({{ site.baseurl }}{% link _articles/access_controls.md %}). @@ -31,7 +31,7 @@ To access `Controlled Use` data you must fulfill the `Conditions for Use` set by ### Bridge Data Synapse houses data collected through research apps. This data is called Bridge data. This data has been donated by thousands of volunteers -from around the world. Bridge data is only accessible to Users with a `Validated Profile`. To learn more see [Synapse User Credentials](accounts_certified_users_and_profile_validation.md#validated-profile). +from around the world. Bridge data is only accessible to Users with a `Validated Profile`. To learn more see [Synapse User Credentials]({{ site.baseurl}}{% link _articles/accounts_certified_users_and_profile_validation.md %}#validated-profile). {% include warning.html content="Controlled and Bridge data may not be redistributed." %} Sharing a Synapse account violates the Synapse Terms of Use. Each user wishing to access `Controlled Data` must individually agree to the `Conditions for Use` to access the data. **Please be mindful when sharing information. Do not send data or metadata via email.** diff --git a/_articles/discussion.md b/_articles/discussion.md index 5eafe78f..f20c677c 100644 --- a/_articles/discussion.md +++ b/_articles/discussion.md @@ -64,4 +64,4 @@ Moderators may also "pin" important threads using the **pin** icon located next # See Also -[Wikis](wikis.md) +[Wikis]({{ site.baseurl }}{% link _articles/wikis.md %}) diff --git a/_articles/downloading_data.md b/_articles/downloading_data.md index a8212aec..c019b1d2 100644 --- a/_articles/downloading_data.md +++ b/_articles/downloading_data.md @@ -86,7 +86,7 @@ entity = syn.get("syn3260973", version=1) entity <- synGet("syn3260973", version=1) ``` -See [versioning](versioning.md) for more details. +See [versioning]({{ site.baseurl }}{% link _articles/versioning.md %}) for more details. ### Links @@ -140,7 +140,7 @@ entity <- synGet("syn00123", downloadLocation="/path/to/folder") ## Finding and Downloading Files -Files can be [annotated](annotation_and_query.md) to facilitate finding them. In order to search the annotations, a [File View](views.md) must be created first. It is possible to query based on any of the annotations attached to the files. +Files can be [annotated]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}) to facilitate finding them. In order to search the annotations, a [File View]({{ site.baseurl }}{% link _articles/views.md %}) must be created first. It is possible to query based on any of the annotations attached to the files. For example, the [PCBC Project](https://www.synapse.org/#!Synapse:syn1773109) has a [table](https://www.synapse.org/#!Synapse:syn7511263) listing sequencing data files that have been annotated. To find all **mRNA fastq** files originating from **CD34+ cells** in the we can query by: @@ -214,7 +214,7 @@ files = synapseutils.syncFromSynapse(syn, 'syn2390898') ### Download Tables -Please view [here](tables.md) to learn how to use `Tables`. +Please view [here]({{ site.baseurl }}{% link _articles/tables.md %}) to learn how to use `Tables`. ### Download Wikis @@ -282,4 +282,4 @@ all_files = syncFromSynapse(entity='syn123', path='/path/to/myFolder') # See Also -[Versioning](versioning.md), [Tables](tables.md), [Wikis](wikis.md), [File Views](views.md), [Annotations and Queries](annotation_and_query.md) +[Versioning]({{ site.baseurl }}{% link _articles/versioning.md %}), [Tables]({{ site.baseurl }}{% link _articles/tables.md %}), [Wikis]({{ site.baseurl }}{% link _articles/wikis.md %}), [File Views]({{ site.baseurl }}{% link _articles/views.md %}), [Annotations and Queries]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}) diff --git a/_articles/edit_wiki_order.md b/_articles/edit_wiki_order.md index 2837085e..83723e05 100644 --- a/_articles/edit_wiki_order.md +++ b/_articles/edit_wiki_order.md @@ -21,4 +21,4 @@ If you want to create new pages within an existing hierarchy rather than moving ## See Also -[Wikis](wikis.md) +[Wikis]({{ site.baseurl }}{% link _articles/wikis.md %}) diff --git a/_articles/evaluation_queues.md b/_articles/evaluation_queues.md index 54c626b4..09c4541e 100644 --- a/_articles/evaluation_queues.md +++ b/_articles/evaluation_queues.md @@ -10,7 +10,7 @@ An Evaluation queue allows for people to submit Synapse `Files`, `Docker` images ## Create an Evaluation Queue -To create a queue, you must first create a Synapse `Project`. To create a Synapse Project, follow the instructions on the [Project and Data Management](getting_started.md#making-and-managing-projects-in-synapse) page. An Evaluation queue can take several parameters that you can use to customize your preferences. The minimum requirements to create a queue are: +To create a queue, you must first create a Synapse `Project`. To create a Synapse Project, follow the instructions on the [Project and Data Management]({{ site.baseurl}}{% link _articles/getting_started.md %}#making-and-managing-projects-in-synapse) page. An Evaluation queue can take several parameters that you can use to customize your preferences. The minimum requirements to create a queue are: * name – Unique name of the evaluation * description – A short description of the evaluation @@ -216,4 +216,4 @@ If you are happy with your leaderboard configurations, save both the configurati # See Also -To learn how to create a Wiki page, please visit [the Wikis article](wikis.md). +To learn how to create a Wiki page, please visit [the Wikis article]({{ site.baseurl }}{% link _articles/wikis.md %}). diff --git a/_articles/faq.md b/_articles/faq.md index da4d91b5..486268d3 100644 --- a/_articles/faq.md +++ b/_articles/faq.md @@ -20,11 +20,11 @@ Synapse allows researchers to share and describe data, analyses, and other conte #### No, seriously what does Synapse do? -For a comprehensive introduction to Synapse see our [Getting Started guide](getting_started.md). +For a comprehensive introduction to Synapse see our [Getting Started guide]({{ site.baseurl }}{% link _articles/getting_started.md %}). #### How much does it cost to use Synapse? -We allow groups to get started for free by subsidizing relatively moderate amounts of internal Synapse cloud storage (e.g. 10s of GB). If your needs will exceed this limit we suggest contacting [SynapseInfo@sagebase.org](mailto:SynapseInfo@sagebase.org) for other solutions, including the ability for groups to host their own content either in cloud storage, proxied from [local file servers](custom_storage_location.md) or as external links. +We allow groups to get started for free by subsidizing relatively moderate amounts of internal Synapse cloud storage (e.g. 10s of GB). If your needs will exceed this limit we suggest contacting [SynapseInfo@sagebase.org](mailto:SynapseInfo@sagebase.org) for other solutions, including the ability for groups to host their own content either in cloud storage, proxied from [local file servers]({{ site.baseurl }}{% link _articles/custom_storage_location.md %}) or as external links. #### How is Synapse funded? @@ -44,7 +44,7 @@ Anyone age 13 or older may use Synapse. We have highlighted a series of [researc #### What are the Synapse Terms of Use? -The [Terms and Conditions of Use](https://s3.amazonaws.com/static.synapse.org/governance/SageBionetworksSynapseTermsandConditionsofUse.pdf?v=4) fully describes the governance terms and conditions of Synapse. In order to register on Synapse, you must review and agree to the terms of the Synapse Awareness and Ethics Pledge. For more information see the complete Synapse [Governance policies](governance.md). +The [Terms and Conditions of Use](https://s3.amazonaws.com/static.synapse.org/governance/SageBionetworksSynapseTermsandConditionsofUse.pdf?v=4) fully describes the governance terms and conditions of Synapse. In order to register on Synapse, you must review and agree to the terms of the Synapse Awareness and Ethics Pledge. For more information see the complete Synapse [Governance policies]({{ site.baseurl }}{% link _articles/governance.md %}). #### Is Synapse open source? @@ -56,7 +56,7 @@ Yes, Synapse is built on top of a RESTful service that is automatically [documen #### How do I set up my own instance of Synapse? -Synapse was developed with the philosophy to encourage collaboration across institutional boundaries and is therefore provided as “Software As A Service” with a single instance used by all users. This makes it easy both to discover new content and share with new collaborators. We do support private project spaces where content sharing is controlled by the individual user. In addition, Synapse has the ability to reference resources that are stored elsewhere. This allows Synapse to store metadata about the content such as annotations, descriptive wiki pages and provenance but not the actual data. Currently Synapse has specific support for files stored at URLs, on SFTP servers, on AWS S3 and arbitrary file servers (see: [Custom Storage Locations](custom_storage_location.md)). +Synapse was developed with the philosophy to encourage collaboration across institutional boundaries and is therefore provided as “Software As A Service” with a single instance used by all users. This makes it easy both to discover new content and share with new collaborators. We do support private project spaces where content sharing is controlled by the individual user. In addition, Synapse has the ability to reference resources that are stored elsewhere. This allows Synapse to store metadata about the content such as annotations, descriptive wiki pages and provenance but not the actual data. Currently Synapse has specific support for files stored at URLs, on SFTP servers, on AWS S3 and arbitrary file servers (see: [Custom Storage Locations]({{ site.baseurl }}{% link _articles/custom_storage_location.md %})). #### What do I do if I find a bug? @@ -64,14 +64,14 @@ You may browse open issues or file a bug through our [Jira](https://sagebionetwo #### How do I get started? -Whether you are looking to access content or use Synapse to track your own work, start by [registering](https://www.synapse.org/#!RegisterAccount:0) for a Synapse user account. Before uploading files, you will need to take a short [certification quiz](https://www.synapse.org/#!Quiz:Certification) that demonstrates your understanding of the ethical considerations in sharing data and the manner in which data is managed and shared in Synapse. See the [Getting Started guide](getting_started.md) for tips on how to access data, create your own project, and share content with others. +Whether you are looking to access content or use Synapse to track your own work, start by [registering](https://www.synapse.org/#!RegisterAccount:0) for a Synapse user account. Before uploading files, you will need to take a short [certification quiz](https://www.synapse.org/#!Quiz:Certification) that demonstrates your understanding of the ethical considerations in sharing data and the manner in which data is managed and shared in Synapse. See the [Getting Started guide]({{ site.baseurl }}{% link _articles/getting_started.md %}) for tips on how to access data, create your own project, and share content with others. # Accessing Content #### My colleague put some content in Synapse. How do I find it? This will depend if the content is public or private. If private, you will need to make sure your colleague has shared this content with you. Shared content is visible from your “Dashboard page” under the tab “Shared directly with me”. If you favorite the content (using the yellow star) it will appear under your list of favorites visible from the top of any Synapse page or on your [Profile](https://www.synapse.org/#!Profile:v/projects/favorites). -All public data is queryable. For more information see [help on querying](annotation_and_query.md) or from the “Search” box in the top right corner of any Synapse page. +All public data is queryable. For more information see [help on querying]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}) or from the “Search” box in the top right corner of any Synapse page. #### I have heard Synapse hosts several public datasets. How do I find them? @@ -79,7 +79,7 @@ Synapse hosts multiple research communities that generate data which is released #### What does a Synapse account let me do than I can’t do without it? -You can browse public content in Synapse without registering. However, without an account you cannot add new content to Synapse, nor can you upload or download `Files` or `Tables`. With an account you can create `Projects` and `Wikis`, download `Open Data` and request access to `Controlled Data`. Further, an account lets you collaborate with other Synapse users and create user teams. For more information see the [User Credentials](accounts_certified_users_and_profile_validation.md) page. +You can browse public content in Synapse without registering. However, without an account you cannot add new content to Synapse, nor can you upload or download `Files` or `Tables`. With an account you can create `Projects` and `Wikis`, download `Open Data` and request access to `Controlled Data`. Further, an account lets you collaborate with other Synapse users and create user teams. For more information see the [User Credentials]({{ site.baseurl }}{% link _articles/accounts_certified_users_and_profile_validation.md %}) page. #### What is a validated profile? @@ -89,11 +89,11 @@ Validating your profile is a process where your identity is established through #### I have my research results - How can Synapse help me share them? -Synapse makes it easy to share files of any sort, with whomever you choose whether a small group of collaborators or the general public. You may share raw data, summarized data, analysis results, or anything in between. We recommend using [Getting started with Synapse guide](getting_started.md) for more details on how to upload and manage content. +Synapse makes it easy to share files of any sort, with whomever you choose whether a small group of collaborators or the general public. You may share raw data, summarized data, analysis results, or anything in between. We recommend using [Getting started with Synapse guide]({{ site.baseurl }}{% link _articles/getting_started.md %}) for more details on how to upload and manage content. #### Why do I have to be a certified user to upload content? -User certification ensures that you understand your responsibilities for sharing data through Synapse, especially data derived from human participants. These responsibilities include making sure that data derived from human participants is de-identified and that all applicable privacy laws and regulations are observed. See the [How to contribute data](contribute_and_access_controlled_use_data.md) for more information. +User certification ensures that you understand your responsibilities for sharing data through Synapse, especially data derived from human participants. These responsibilities include making sure that data derived from human participants is de-identified and that all applicable privacy laws and regulations are observed. See the [How to contribute data]({{ site.baseurl }}{% link _articles/contribute_and_access_controlled_use_data.md %}) for more information. #### How do I get certified? @@ -101,11 +101,11 @@ To become a certified user, you will need to pass a brief [quiz](https://www.syn #### Is everything I share on Synapse public? -No. Use `Sharing settings` to control who can see the content you create. By default, `Projects` and their content are visible only to the user who created it. By using the Synapse `Sharing settings`, you have the ability to grant other Synapse users, Synapse teams, or the public access to your Project content. You can learn more here: [Sharing Settings and Conditions for Use](access_controls.md). +No. Use `Sharing settings` to control who can see the content you create. By default, `Projects` and their content are visible only to the user who created it. By using the Synapse `Sharing settings`, you have the ability to grant other Synapse users, Synapse teams, or the public access to your Project content. You can learn more here: [Sharing Settings and Conditions for Use]({{ site.baseurl }}{% link _articles/access_controls.md %}). #### Can I store sensitive information about human subjects in Synapse? -Yes. Synapse has an IRB-approved data governance procedure that employs `Conditions for Use` to allow for the sharing of sensitive data in a controlled manner. You can learn more by reading our [Sharing Settings and Conditions for Use](access_controls.md) documentation and [Governance documentation](governance.md). If you have questions or would like assistance in applying `Conditions of Use` to your data, please contact the Synapse Access and Compliance Team at [act@sagebase.org](mailto:act@sagebase.org). +Yes. Synapse has an IRB-approved data governance procedure that employs `Conditions for Use` to allow for the sharing of sensitive data in a controlled manner. You can learn more by reading our [Sharing Settings and Conditions for Use]({{ site.baseurl}}{% link _articles/access_controls.md %}) documentation and [Governance documentation]({{ site.baseurl }}{% link _articles/governance.md %}). If you have questions or would like assistance in applying `Conditions of Use` to your data, please contact the Synapse Access and Compliance Team at [act@sagebase.org](mailto:act@sagebase.org). #### How do I know the content I put in Synapse will be secure? What security measures does Synapse have? @@ -113,4 +113,4 @@ Synapse stores content in Amazon Web Services, which provides a layer of securit #### Where are my files stored? -By default, Synapse stores files in Amazon Simple Storage Services (S3). However it is possible to set up Synapse to store files in different locations such as your local SFTP server. For files stored outside of S3, Synapse can be used to organize, manage, and access files through the use of Synapse annotations to store file-specific metadata. (see: [Custom Storage Locations](custom_storage_location.md)) +By default, Synapse stores files in Amazon Simple Storage Services (S3). However it is possible to set up Synapse to store files in different locations such as your local SFTP server. For files stored outside of S3, Synapse can be used to organize, manage, and access files through the use of Synapse annotations to store file-specific metadata. (see: [Custom Storage Locations]({{ site.baseurl }}{% link _articles/custom_storage_location.md %})) diff --git a/_articles/files_and_versioning.md b/_articles/files_and_versioning.md index 074bbbce..e4ad5bd9 100644 --- a/_articles/files_and_versioning.md +++ b/_articles/files_and_versioning.md @@ -17,9 +17,9 @@ category: managing-data } -Synapse `Files` can be created by uploading or linking to digital files on the web. They are accessible to anyone who has [access](access_controls.md), can be annotated with custom metadata, can be embedded into Synapse `Wiki` pages, and can be associated with a [DOI](doi.md). `Files` carry the Conditions for Use of the Synapse `Folder` they are placed in, plus any additional specific Conditions for Use they have on their own. +Synapse `Files` can be created by uploading or linking to digital files on the web. They are accessible to anyone who has [access]({{ site.baseurl }}{% link _articles/access_controls.md %}), can be annotated with custom metadata, can be embedded into Synapse `Wiki` pages, and can be associated with a [DOI]({{ site.baseurl }}{% link _articles/doi.md %}). `Files` carry the Conditions for Use of the Synapse `Folder` they are placed in, plus any additional specific Conditions for Use they have on their own. -By default, `Files` uploaded to Synapse are stored in 'Synapse Storage', which is freely available to you. `Files` can also be stored on your own Amazon S3 bucket (see [Custom Storage Locations](custom_storage_location.md)) or other custom locations. Furthermore, if you don't want to upload a file (it has external restrictions on sharing, is really large, for example) you can also link to the file. In this way, the file will be accessible through the Synapse clients when you are on the computer that the file is stored, but can be annotated, queried, and documented with a Wiki through Synapse. Lastly, you can provide web-accessible links as Synapse files, which will redirect to that location. All of the same Synapse `File` features are available are available on external links as well. +By default, `Files` uploaded to Synapse are stored in 'Synapse Storage', which is freely available to you. `Files` can also be stored on your own Amazon S3 bucket (see [Custom Storage Locations]({{ site.baseurl }}{% link _articles/custom_storage_location.md %})) or other custom locations. Furthermore, if you don't want to upload a file (it has external restrictions on sharing, is really large, for example) you can also link to the file. In this way, the file will be accessible through the Synapse clients when you are on the computer that the file is stored, but can be annotated, queried, and documented with a Wiki through Synapse. Lastly, you can provide web-accessible links as Synapse files, which will redirect to that location. All of the same Synapse `File` features are available are available on external links as well. Synapse `Files` (as well as `Folders` and `Projects`) are identified by a unique identifier called a Synapse ID. It takes the form `syn12345678`. This identifier can be used to refer to a specific file on the web and through the clients. @@ -63,7 +63,7 @@ file <- synStore(file) ## Moving a File -All Synapse clients offer a way to move files and folders. Please note that [File Views](views.md) and [sync manifests](uploading_in_bulk.md) **cannot** be used to move files. +All Synapse clients offer a way to move files and folders. Please note that [File Views]({{ site.baseurl }}{% link _articles/views.md %}) and [sync manifests]({{ site.baseurl }}{% link _articles/uploading_in_bulk.md %}) **cannot** be used to move files. The command line client has a sub-command `mv` which can be used to move files and folders. The Python client provides the [syn.move](https://python-docs.synapse.org/build/html/Client.html#synapseclient.Synapse.move) command, and the R client has [synMove()](https://r-docs.synapse.org/reference/synMove.html). @@ -229,7 +229,7 @@ Any change to a `File` will automatically update its version. If this isn't the ##### Web -Please refer to the [Annotations and Queries](annotation_and_query.md) article for instructions on adding/editing annotations via the web client. +Please refer to the [Annotations and Queries]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}) article for instructions on adding/editing annotations via the web client. ##### Command line @@ -261,7 +261,7 @@ annotations <- synSetAnnotations(file, annotations=list(fileType = "bam", assay **Setting provenance without changing version** ##### Web -Please refer to the [Provenance](provenance.md) article for instructions on adding/editing annotations via the web client. +Please refer to the [Provenance]({{ site.baseurl }}{% link _articles/provenance.md %}) article for instructions on adding/editing annotations via the web client. ##### Command line @@ -348,4 +348,4 @@ Some files in Synapse are supported with previews to allow users to peek at the ## See Also -[Provenance](provenance.md), [Annotations and Queries](annotation_and_query.md), [Downloading Data](downloading_data.md) +[Provenance]({{ site.baseurl }}{% link _articles/provenance.md %}), [Annotations and Queries]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}), [Downloading Data]({{ site.baseurl }}{% link _articles/downloading_data.md %}) diff --git a/_articles/forms.md b/_articles/forms.md index 144d5777..50a0b797 100644 --- a/_articles/forms.md +++ b/_articles/forms.md @@ -15,7 +15,7 @@ With Forms, you can: ## Creating a Table -In order to use Forms, you'll need to first create a `Table`. Read more about creating tables here: [Tables](tables.md) +In order to use Forms, you'll need to first create a `Table`. Read more about creating tables here: [Tables]({{ site.baseurl }}{% link _articles/tables.md %}) ## Activating and Deactivating 'Alpha' Mode @@ -41,8 +41,8 @@ The form is also responsive, so it will render on both large and small screens. ## Allowing Others to Contribute -Entering data into a `Form` is equivalent to editing the data in a `Table`, so users who wish to add data using the form will need to have "Edit" permissions on the Table. See [Sharing Settings](access_controls.md) for more information on controlling who can edit your Table. +Entering data into a `Form` is equivalent to editing the data in a `Table`, so users who wish to add data using the form will need to have "Edit" permissions on the Table. See [Sharing Settings]({{ site.baseurl }}{% link _articles/access_controls.md %}) for more information on controlling who can edit your Table. ## See Also -[Tables](tables.md), [Wikis](wikis.md), [Sharing Settings](access_controls.md) +[Tables]({{ site.baseurl }}{% link _articles/tables.md %}), [Wikis]({{ site.baseurl }}{% link _articles/wikis.md %}), [Sharing Settings]({{ site.baseurl }}{% link _articles/access_controls.md %}) diff --git a/_articles/getting_started.md b/_articles/getting_started.md index 4d4acc65..1f46b664 100644 --- a/_articles/getting_started.md +++ b/_articles/getting_started.md @@ -40,7 +40,7 @@ To create a new Project: Your Projects [dashboard](https://www.synapse.org/#!Profile:v/projects) stores your collection of Projects. -Read about [Projects](making_a_project.md) in the User Guide. +Read about [Projects]({{ site.baseurl }}{% link _articles/making_a_project.md %}) in the User Guide. ## Synapse IDs diff --git a/_articles/getting_started_clients.md b/_articles/getting_started_clients.md index bda44002..e5daf1fc 100644 --- a/_articles/getting_started_clients.md +++ b/_articles/getting_started_clients.md @@ -12,7 +12,7 @@ The API clients provide a way to use Synapse programmatically. This page shows y * Python * R -To manage stored login credentials, visit the [Client Configuration page](client_configuration.md). +To manage stored login credentials, visit the [Client Configuration page]({{ site.baseurl }}{% link _articles/client_configuration.md %}). ## Command Line diff --git a/_articles/links.md b/_articles/links.md index bc30640b..6eeec70a 100644 --- a/_articles/links.md +++ b/_articles/links.md @@ -65,4 +65,4 @@ linkEnt <- synStore(linkEnt) ### See Also -[Annotations and Queries](annotation_and_query.md), [Downloading Data](downloading_data.md), [Files and Versioning](versioning.md) +[Annotations and Queries]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}), [Downloading Data]({{ site.baseurl }}{% link _articles/downloading_data.md %}), [Files and Versioning]({{ site.baseurl }}{% link _articles/versioning.md %}) diff --git a/_articles/making_a_project.md b/_articles/making_a_project.md index caf6ada5..104bfa21 100644 --- a/_articles/making_a_project.md +++ b/_articles/making_a_project.md @@ -8,7 +8,7 @@ order: 2 `Projects` in Synapse are "containers" that groups relevant content and people together. Researchers using Synapse can work in private or collaborate in groups. Some users share their research across large consortia. Projects support the following: -* **Organize Your Work**: With Synapse you can organize the parts in your workflow (data, code, etc) into a hierarchy like a file system. With the tabs across the top of each project, you can easily navigate to your [Wikis](wikis.md), [Files and Folders](files_and_versioning.md), SQL-based [Tables](tables.md), and even conduct conversations using [Discussion Forums](discussion.md). +* **Organize Your Work**: With Synapse you can organize the parts in your workflow (data, code, etc) into a hierarchy like a file system. With the tabs across the top of each project, you can easily navigate to your [Wikis]({{ site.baseurl }}{% link _articles/wikis.md %}), [Files and Folders]({{ site.baseurl }}{% link _articles/files_and_versioning.md %}), SQL-based [Tables]({{ site.baseurl }}{% link _articles/tables.md %}), and even conduct conversations using [Discussion Forums]({{ site.baseurl }}{% link _articles/discussion.md %}). * **Store Data, Code, and Results**: You can upload your data, code, and results to Synapse, or store a reference to their location in your local computer system or on the web. Everything can be stored as Files, hosted by Synapse, in your own external cloud storage, or using [Docker Containers](http://docs.synapse.org/articles/docker.html). diff --git a/_articles/managing_custom_metadata_at_scale.md b/_articles/managing_custom_metadata_at_scale.md index 2c69b71b..87bd2425 100644 --- a/_articles/managing_custom_metadata_at_scale.md +++ b/_articles/managing_custom_metadata_at_scale.md @@ -5,7 +5,7 @@ excerpt: Update Annotations in bulk using File Views and programmatic clients. category: metadata-and-annotations --- -This vignette will combine concepts from [Annotations and Queries](annotation_and_query.md), [Views](views.md), [Uploading and Downloading Data in Bulk](uploading_in_bulk.md) in order to **create a manifest** `velociraptor_manifest.txt`, **upload** 100 files and **edit** annotations on these files using the Synapse clients. +This vignette will combine concepts from [Annotations and Queries]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}), [Views]({{ site.baseurl }}{% link _articles/views.md %}), [Uploading and Downloading Data in Bulk]({{ site.baseurl }}{% link _articles/uploading_in_bulk.md %}) in order to **create a manifest** `velociraptor_manifest.txt`, **upload** 100 files and **edit** annotations on these files using the Synapse clients. ## Annotation dictionaries @@ -32,7 +32,7 @@ Here it is in a visual example: | /local/path/to/velociraptor_b.fastq | syn123 | blue_1 | wholeGenomeSeq | Velociraptor mongoliensis | HoodDNASequencer | female | fastq | | /local/path/to/velociraptor_d.fastq | syn123 | delta_1 | wholeGenomeSeq | Velociraptor mongoliensis | HoodDNASequencer | female | fastq | -See **Creating a Manifest** in [Uploading and Downloading Data in Bulk](uploading_in_bulk.md#Creating-a-Manifest) for additional details. +See **Creating a Manifest** in [Uploading and Downloading Data in Bulk]({{ site.baseurl }}{% link _articles/uploading_in_bulk.md %}#Creating-a-Manifest) for additional details. **Save** this file in a tab-delimited format called `velociraptor_manifest.tsv`. @@ -45,7 +45,7 @@ And ta-da! Your files have been uploaded! ## Create a File View (Web) -Since the files have been uploaded with annotations, a file [View](views.md) allows users to query, facet, and bulk manipulate the files and metadata. +Since the files have been uploaded with annotations, a file [View]({{ site.baseurl }}{% link _articles/views.md %}) allows users to query, facet, and bulk manipulate the files and metadata. To create your File View: diff --git a/_articles/managing_teams_for_groups_and_projects.md b/_articles/managing_teams_for_groups_and_projects.md index 1464d723..b381b474 100644 --- a/_articles/managing_teams_for_groups_and_projects.md +++ b/_articles/managing_teams_for_groups_and_projects.md @@ -7,7 +7,7 @@ category: collaboration-and-communication ## Creating Permissions Models for Synapse Projects -Synapse supports several different kinds of project permissions. These are described in more detail as "sharing settings" in the article on [access controls](access_controls.md#sharing-settings). Additionally, Synapse supports setting "local sharing settings" that allow you to make your project public while keeping some folders, files, or tables private. To do this, you would use local sharing settings. Permissions and sharing settings within Synapse are otherwise hierarchical; that is, if you set permissions on a project, everything within that project inherits those permissions until local sharing settings have been created. +Synapse supports several different kinds of project permissions. These are described in more detail as "sharing settings" in the article on [access controls]({{ site.baseurl }}{% link _articles/access_controls.md %}#sharing-settings). Additionally, Synapse supports setting "local sharing settings" that allow you to make your project public while keeping some folders, files, or tables private. To do this, you would use local sharing settings. Permissions and sharing settings within Synapse are otherwise hierarchical; that is, if you set permissions on a project, everything within that project inherits those permissions until local sharing settings have been created. When thinking through the process of creating a permissions model for your project, consider the following questions: @@ -20,7 +20,7 @@ When thinking through the process of creating a permissions model for your proje ## Using Teams for Permissions -Teams are groups of Synapse users; learn more about [managing teams here](teams.md). If you are working with a group of users, and you want to allow some users to view or download data, while other users should be in charge of managing the project or adding new data, you should consider using teams to grant users permission. For example, you can create a "project administrators" group and grant that team permission to administer the project. Then, when you need to modify permissions on the project, you can add or remove people from the team rather than modifying the sharing settings on the project. This is especially useful if you have more than one project that the same group of people will be working across; using teams for permissions can help prevent administrative errors like forgetting to remove someone from a project if they leave your collaboration. +Teams are groups of Synapse users; learn more about [managing teams here]({{ site.baseurl }}{% link _articles/teams.md %}). If you are working with a group of users, and you want to allow some users to view or download data, while other users should be in charge of managing the project or adding new data, you should consider using teams to grant users permission. For example, you can create a "project administrators" group and grant that team permission to administer the project. Then, when you need to modify permissions on the project, you can add or remove people from the team rather than modifying the sharing settings on the project. This is especially useful if you have more than one project that the same group of people will be working across; using teams for permissions can help prevent administrative errors like forgetting to remove someone from a project if they leave your collaboration. ## Recommended Team Types @@ -38,7 +38,7 @@ The folder with then be shared only with the specific user groups that the entir # Triaging Project Permissions Using Views -Sometimes local sharing settings are accidentally created, and once created, they can be somewhat tricky to detect. One quick way to triage your project permissions is by using a [view](views.md) with a scope set to a single project, or across multiple projects with similar permissions models. The field that you will be using below is called +Sometimes local sharing settings are accidentally created, and once created, they can be somewhat tricky to detect. One quick way to triage your project permissions is by using a [view]({{ site.baseurl }}{% link _articles/views.md %}) with a scope set to a single project, or across multiple projects with similar permissions models. The field that you will be using below is called "benefactorId" -- this is the unique set of permissions assigned to groups of things. When you first create a project, the project itself is the "benefactor" of permissions, and there is only one benefactor ID for all the things in the project. As soon as you create your first set of local sharing settings, there are now two benefactors; the project is still providing the permissions for most the content, but whatever you have set local sharing settings on (say, a folder) now is the benefactor for anything inside it; it's the new benefactor of permissions for that sub-hierarchy, and everything inside will share the same, new benefactorId. diff --git a/_articles/provenance.md b/_articles/provenance.md index c9acfcf9..db6dc182 100644 --- a/_articles/provenance.md +++ b/_articles/provenance.md @@ -250,4 +250,4 @@ finalList <- lapply(finalList, function(x) synStore(x, activity=act)) ### See Also -[Files and Versioning](versioning.md), [Annotations and Queries](annotation_and_query.md) +[Files and Versioning]({{ site.baseurl }}{% link _articles/versioning.md %}), [Annotations and Queries]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}) diff --git a/_articles/sharing_settings.md b/_articles/sharing_settings.md index b577182f..4b3390a6 100644 --- a/_articles/sharing_settings.md +++ b/_articles/sharing_settings.md @@ -56,7 +56,7 @@ Administrator permissions allows a Synapse user to change the sharing settings a To adjust the sharing settings on a project, click the `Project Settings` button. This will open a window listing the Synapse users who have access to the `Project` and their roles. When you create a new `Project` you are the only Synapse user listed in this window, because projects are private by default, and your access level will be `Administrator`. -Use the `Add People` feature to add collaborators individually or to add a [team of collaborators](teams.md). +Use the `Add People` feature to add collaborators individually or to add a [team of collaborators]({{ site.baseurl }}{% link _articles/teams.md %}). diff --git a/_articles/tables.md b/_articles/tables.md index 591b3d6c..864a0a51 100644 --- a/_articles/tables.md +++ b/_articles/tables.md @@ -220,4 +220,4 @@ Finally, query the table and download the album cover files. Clicking on any fil # See Also -[Annotations and Queries](annotation_and_query.md), [Downloading Data](downloading_data.md), [Files and Versioning](files_and_versioning.md) +[Annotations and Queries]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}), [Downloading Data]({{ site.baseurl }}{% link _articles/downloading_data.md %}), [Files and Versioning]({{ site.baseurl }}{% link _articles/files_and_versioning.md %}) diff --git a/_articles/teams.md b/_articles/teams.md index 62130c74..15c06186 100644 --- a/_articles/teams.md +++ b/_articles/teams.md @@ -83,4 +83,4 @@ When participating in a Challenge, you may submit solutions as an individual or ### See Also -[Wikis](wikis.md), [Files and Versioning](versioning.md), [Sharing Settings](access_controls.md) +[Wikis]({{ site.baseurl }}{% link _articles/wikis.md %}), [Files and Versioning]({{ site.baseurl }}{% link _articles/versioning.md %}), [Sharing Settings]({{ site.baseurl }}{% link _articles/access_controls.md %}) diff --git a/_articles/uploading_in_bulk.md b/_articles/uploading_in_bulk.md index 865f50f9..997c348d 100644 --- a/_articles/uploading_in_bulk.md +++ b/_articles/uploading_in_bulk.md @@ -5,7 +5,7 @@ excerpt: Learn how to upload and download data in bulk using a manifest file and category: managing-data --- -Working with a large number of files on the web can be tedious, especially if you want to download, upload, or set [annotations](annotation_and_query.md) and [provenance](provenance.md). The command line, Python client and R client have convenience functions for bulk upload and download. Uploading require a tab delimited *manifest* where each file to be uploaded and, optionally, annotations to be applied, are specified as a row in the file. Downloading in bulk requires identifying a container (`Folder`, `Project`, `Table`, or `View`) that contains the files of interest. In this article we will cover how to: +Working with a large number of files on the web can be tedious, especially if you want to download, upload, or set [annotations]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}) and [provenance]({{ site.baseurl }}{% link _articles/provenance.md %}). The command line, Python client and R client have convenience functions for bulk upload and download. Uploading require a tab delimited *manifest* where each file to be uploaded and, optionally, annotations to be applied, are specified as a row in the file. Downloading in bulk requires identifying a container (`Folder`, `Project`, `Table`, or `View`) that contains the files of interest. In this article we will cover how to: * create a manifest * upload the files in bulk @@ -59,7 +59,7 @@ Files can be downloaded in bulk using the `syncFromSynapse` function. This funct ## Editing in Bulk -You can edit files in bulk by changing the values in the manifest and pushing it up to Synapse using the `syncToSynapse` function. The manifest allows you to modify everything: file path, provenance, annotations, and versions. However, if only annotations are being updated, we recommend using our [File Views](views.md) feature. +You can edit files in bulk by changing the values in the manifest and pushing it up to Synapse using the `syncToSynapse` function. The manifest allows you to modify everything: file path, provenance, annotations, and versions. However, if only annotations are being updated, we recommend using our [File Views]({{ site.baseurl }}{% link _articles/views.md %}) feature. Please note that you cannot move things with a manifest. If the parentId is changed, it will create a copy and the file will exist in two different locations. @@ -67,4 +67,4 @@ Please note that you cannot move things with a manifest. If the parentId is chan # See Also -[Downloading Data](downloading_data.md), [Provenance](provenance.md), [Annotations and Queries](annotation_and_query.md), [File Views](views.md), [Files and Versioning](files_and_versioning.md) +[Downloading Data]({{ site.baseurl }}{% link _articles/downloading_data.md %}), [Provenance]({{ site.baseurl }}{% link _articles/provenance.md %}), [Annotations and Queries]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}), [File Views]({{ site.baseurl }}{% link _articles/views.md %}), [Files and Versioning]({{ site.baseurl }}{% link _articles/files_and_versioning.md %}) diff --git a/_articles/user_profiles.md b/_articles/user_profiles.md index c02927cf..d5575dba 100644 --- a/_articles/user_profiles.md +++ b/_articles/user_profiles.md @@ -9,7 +9,7 @@ Anyone can browse public content on the Synapse web site, but in order to downlo Register -Certain actions in Synapse require additional steps, such as Certification or Validation. Explore our [accounts, certification and profile validation](accounts_certified_users_and_profile_validation.md) page to find out more information on the different levels of users. +Certain actions in Synapse require additional steps, such as Certification or Validation. Explore our [accounts, certification and profile validation]({{ site.baseurl }}{% link _articles/accounts_certified_users_and_profile_validation.md %}) page to find out more information on the different levels of users. ## Managing Your Profile @@ -54,4 +54,4 @@ Please contact us to deactivate your Synapse account. # See Also -[Accounts, Certification and Profile Validation](accounts_certified_users_and_profile_validation.md), [Discussion](discussion.md) +[Accounts, Certification and Profile Validation]({{ site.baseurl }}{% link _articles/accounts_certified_users_and_profile_validation.md %}), [Discussion]({{ site.baseurl }}{% link _articles/discussion.md %}) diff --git a/_articles/using_tabular_data_in_wikis.md b/_articles/using_tabular_data_in_wikis.md index e9f7852e..dc43e490 100644 --- a/_articles/using_tabular_data_in_wikis.md +++ b/_articles/using_tabular_data_in_wikis.md @@ -9,11 +9,11 @@ category: managing-data `Wiki` widgets are tools to support narrative content. Embedded `Wiki` `Tables` can enable quick access to `Files` of highest importance and orient users to the resources contained in a collaborative project. `Wiki` `Tables` accept queries of existing `Tables` or `File Views`, providing a strategy to restrict scope and focus content. -More information on related concepts is available on the [Tables](tables.md), [Making a Project](making_a_project.md), [Views](views.md) and [Wikis](wikis.md) pages. +More information on related concepts is available on the [Tables]({{ site.baseurl }}{% link _articles/tables.md %}), [Making a Project]({{ site.baseurl }}{% link _articles/making_a_project.md %}), [Views]({{ site.baseurl }}{% link _articles/views.md %}) and [Wikis]({{ site.baseurl }}{% link _articles/wikis.md %}) pages. ## Start with a File View or Table -The [Views](views.md) page provides steps to list `Files` and `Folders` within `Views` and `Tables`. This will be the content embedded in the `Wiki`. +The [Views]({{ site.baseurl }}{% link _articles/views.md %}) page provides steps to list `Files` and `Folders` within `Views` and `Tables`. This will be the content embedded in the `Wiki`. ## Focus Scope diff --git a/_articles/views.md b/_articles/views.md index 816197d9..7e041cbd 100644 --- a/_articles/views.md +++ b/_articles/views.md @@ -5,7 +5,7 @@ excerpt: Use project and file views to query across multiple projects and folder category: managing-data --- -A view is a type of Synapse [Table](tables.md) that queries across metadata ([Annotations](annotation_and_query.md)) for particular items (currently: projects or files) with a particular "scope". A `File View` lists all `Files` or `Tables` within one or more `Folders` or `Projects`. A `Project View` lists all `Projects` you've added to the view. Views can: +A view is a type of Synapse [Table]({{ site.baseurl }}{% link _articles/tables.md %}) that queries across metadata ([Annotations]({{ site.baseurl }}{% link _articles/annotation_and_query.md %})) for particular items (currently: projects or files) with a particular "scope". A `File View` lists all `Files` or `Tables` within one or more `Folders` or `Projects`. A `Project View` lists all `Projects` you've added to the view. Views can: * Allow `Projects`, `Files`, and `Tables` to be easily searched and queried * Allow view/editing metadata attributes in bulk @@ -32,7 +32,7 @@ Note that it may take a few moments for the updated View to rebuild as it querie ## Query a View -A view can be queried exactly the same as any other `Table` in Synapse. Please see [Tables](tables.md) for more examples. See the [Using Simple Search](views.md#using-simple-search) and [Using Advanced Search](views.md#using-advanced-search) sections below. +A view can be queried exactly the same as any other `Table` in Synapse. Please see [Tables]({{ site.baseurl }}{% link _articles/tables.md %}) for more examples. See the [Using Simple Search]({{ site.baseurl }}{% link _articles/views.md %}#using-simple-search) and [Using Advanced Search]({{ site.baseurl }}{% link _articles/views.md %}#using-advanced-search) sections below. For example, to query for everything in `syn123`: @@ -56,7 +56,7 @@ query <- synTableQuery('SELECT * FROM syn123') ## Update Annotations in Bulk -Views can be used to update annotations in bulk. To add new annotations, see the [Annotations](annotation_and_query.md#adding-annotations) article. To update other metadata in bulk, such as provenance, see the [Bulk Processing](uploading_in_bulk.md) article. +Views can be used to update annotations in bulk. To add new annotations, see the [Annotations]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}#adding-annotations) article. To update other metadata in bulk, such as provenance, see the [Bulk Processing]({{ site.baseurl }}{% link _articles/uploading_in_bulk.md %}) article. For example, if you would like to use the Python client to update the annotation `dogSays`:`bark` to `dogSays`:`woof` in every file in a `File View` with the synId syn456, you can do: @@ -88,7 +88,7 @@ In advanced search, you can use a SQL-like query to search for items in that vie ## Insert a View into a Wiki -Views can also be placed inside a [`Wiki`](wikis.md) once they have been created. You can embed the entire view or a subset of a query on it. +Views can also be placed inside a [`Wiki`]({{ site.baseurl }}{% link _articles/wikis.md %}) once they have been created. You can embed the entire view or a subset of a query on it. To insert a file view with a synId of `syn8146547`: @@ -102,4 +102,4 @@ Save the query and the edits to the `Wiki` to embed the view. # See Also -[Annotations and Queries](annotation_and_query.md), [Tables](tables.md), [Wikis](wikis.md) +[Annotations and Queries]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}), [Tables]({{ site.baseurl }}{% link _articles/tables.md %}), [Wikis]({{ site.baseurl }}{% link _articles/wikis.md %}) diff --git a/_articles/wikis.md b/_articles/wikis.md index 1f194050..a2fa742f 100644 --- a/_articles/wikis.md +++ b/_articles/wikis.md @@ -96,9 +96,9 @@ See the 'Insert' list for the following widgets to customize your Wiki design. | **Table: Query on a Synapse `Table`**
Provides a Query for any Synapse Table and displays the information in the Wiki. | | | **Query on `Files`/`Folders`**
Provides a Query based an annotations (need link) added to Files and Folders. Columns in the Query table can be renamed and ordered through the 'Add Column Renderer' | | | **Button Link**
Insert a button that links to content within Synapse or elsewhere. **Tip:** buttons can be colored purple by adding `'&highlight=true'` to the end of the widget markdown || -| **Join Team Button**
Provide a button for people to join Synapse [Teams](teams.md) | | +| **Join Team Button**
Provide a button for people to join Synapse [Teams]({{ site.baseurl }}{% link _articles/teams.md %}) | | | **Team Badge**
Creates a link to the `Team` profile | | -| **Genome Browser**
You can add a [Biodalliance genome browser](http://www.biodalliance.org) using tracks from files uploaded to Synapse or from external sources. Choose between Human or Mouse and adjust your tracks for height and color. See the Biodalliance Setup page for [more information](genome_browser.md) | | +| **Genome Browser**
You can add a [Biodalliance genome browser](http://www.biodalliance.org) using tracks from files uploaded to Synapse or from external sources. Choose between Human or Mouse and adjust your tracks for height and color. See the Biodalliance Setup page for [more information]({{ site.baseurl }}{% link _articles/genome_browser.md %}) | | | **Video**
Video, Vimeo Video, and YouTube Video insert a video from various sources. | | ## Tagging Synapse Users @@ -113,4 +113,4 @@ See the Synapse Data Use Procedure document for [details](https://s3.amazonaws.c ## See Also -[Discussion](discussion.md) +[Discussion]({{ site.baseurl }}{% link _articles/discussion.md %})