Merge pull request #19 from neurostuff/18-update-docs

feat: added to docs

docs/guide/Project/Curation.md

@@ -5,7 +5,7 @@ sidebar_position: 0
 
 # Curation
 
-_Curation_ is the first step in creating a meta-analysis, and begins by _searching_ for and _importing_ studies into the project. Next, you will _review_ studies for inclusion based on their relevancy to your research question. This involves **excluding** irrelevant studies, and **including** relevant ones.
+_Curation_ is the first step in creating a meta-analysis, and begins by _searching_ for and _importing_ studies into the project. You will then _review_ those studies for inclusion based on their relevancy to your research question. This involves **excluding** irrelevant studies, and **including** relevant ones.
 
 At the end of the process, you will be ready to create a [**Studyset**](/compose-docs/guide/glossary#studyset) of related studies that are amenable for neuroimaging meta-analysis
 

docs/guide/Project/Extraction.md

@@ -1,54 +1,89 @@
 ---
 title: Extraction
-sidebar_position: 0
+sidebar_position: 1
 ---
 
 # Extraction
 
-Extraction is the second step in creating a meta-analysis. It involves taking the 
-new [**Studyset**](/compose-docs/guide/glossary#studyset) creates in the curation step and extracting relevant information from studies, such as [**annotations**](/compose-docs/guide/glossary#annotation), 
+Extraction is the second step in creating a meta-analysis. It involves taking the
+new [**Studyset**](/compose-docs/guide/glossary#studyset) creates in the curation step and extracting relevant information from studies, such as [**annotations**](/compose-docs/guide/glossary#annotation),
 and peak activation coordinates, or [**points**](/compose-docs/guide/glossary#point).
 
 ## Getting Started
-After the curation phase is complete, the user is redirected to the extraction phase. You can also access the Extraction phase through the main project page. 
 
-Here, the extraction phase starts when 
-a wizard that pops up and guides the user through the process of initializing the extraction phase. On top of creating the 
+After the curation phase is complete, the user is redirected to the extraction phase. You can also access the Extraction phase through the main project page.
+
+Here, the extraction phase starts when
+a wizard that pops up and guides the user through the process of initializing the extraction phase. On top of creating the
 initial [**annotation columns**](./Extraction#annotations), this wizard also guides the user through the
 process of [**ingestion** ](./Extraction#ingestion) of the curated studies to create a new [**studyset**](../glossary#studyset).
 
 ## Ingestion
 
-Ingestion describes the process of taking the studies from the curation phase and inserting them into the database one by one. 
+Ingestion describes the process of taking the studies from the curation phase and inserting them into the database one by one.
 
-For each study, neurosynth-compose searches the neurostore database and checks to see if a matching study exists. If a match 
+For each study, neurosynth-compose searches the neurostore database and checks to see if a matching study exists. If a match
 does not exist, then a new study is created and the user must go to the paper to fill out the relevant details.
-If one or more matches are found, the user has the option of either ignoring the existing options and creating a new study anyway, or selecting 
-one of the existing matches.
-
-**Selecting an existing study is recommended as opposed to creating a new study from scratch. By selecting an existing neurostore study, you 
-are leveraging neurostore's automatic extraction. As the coordinates have already been extracted for you, this will save you a lot of time and effort 
-during the extraction process.** 
+If one or more matches are found, neurosynth-compose will choose the most recently updated one by default. The user can later go in and switch to a different version if the one selected is not the ony they wanted.
 
 :::info Why ingestion?
-During the curation phase, studies are actually not inserted into the database. A vast majority of the studies that 
-are imported into the curation phase are excluded during the curation process. Inserting these studies into the database would clutter 
-it and create a lot of empty entries which don't have coordinates and might not even be used. By waiting until we have our finalized 
+During the curation phase, studies are actually not inserted into the database. A vast majority of the studies that
+are imported into the curation phase are excluded during the curation process. Inserting these studies into the database would clutter
+it and create a lot of empty entries which don't have coordinates and might not even be used. By waiting until we have our finalized
 included subset of studies, we reduce the number of empty, useless studies in the database.
 :::
 
+## Extraction Table
+
+![Extraction Table](/guide/extraction_table.png)
+
+Once ingestion is complete, the user is shown a table listing the studies within the studyset. The extraction step involves iteratively reviewing each study to make sure they contain information amenable to a meta-analysis.
+Studies in the extraction phase are filtered and categorized to help better organize and facilitate the process. Initially, all studies
+start as **Unreviewed**. The user can then decide to mark them as **Save For Later** if they want to revisit the study, or **Completed**.
+
+If the study does not have any already extracted coordinates, then the user should go and find the original paper and manually search for the coordinates to add to the study.
+
+If the study has automatically extracted coordinates, then the user only has to validate that these coordinates are satisfactory.
+
+The table provides functionality for filtering amongst various columns as well as sorting. To start editing a study, click on one of the table rows.
+
 ## Annotations
 
+![Annotations Table](/guide/annotation_spreadsheet.png)
+
+[Annotations](../glossary#annotation) are a way to assign data to each [**analysis**](../glossary#analysis) within the studyset. Annotation values can be later used to filter out analyses to include within a meta-analysis.
+
+In the extraction page, click the "Annotations" button on the top right. Annotations are represented with a spreadsheet like interface, where the row headers are the respective studies and their analyses, and the column headers are the properties for
+each of those study analyses. Each cell in the spreadsheet repreesnts the value for a given property of a study's analysis.
+
+By default, all annotations will start with a column **included** which will be set to true. This column can be modified if needed.
+
 ## Study Editing
 
-Studies in the extraction phase are filtered and categorized to help better organize and facilitate the process. Initially, all studies 
-start as **Uncategorized**. The user can then decide to mark them as **Save For Later** if they want to revisit the study, or **Completed**.
+![Study Editing](/guide/study_edit.png)
+
+Clicking on a study in the extraction table will lead you to the study editing page. This page allows you to edit study coordinates, add new analyses to the study, as well as modify the study name, authors, PMID, DOI, etc.
+If you would like to update the annotation values just for the given study, you can do so utilizing the study annotations table.
+
+## Syncing Between Curation and Extraction
 
+![Out of Sync](/guide/out_of_sync.png)
 
-### Read Only Studies
+In an ideal meta-analysis process, once the curation phase is completed then it is not touched again. However, this is not always possible in the real world.
 
-### Study Annotations
+If the curation phase is modified (for example if a study previously marked as "included" was excluded, or an additional study that was previously excluded was changed to "included") then the extraction phase
+no longer represents the output of the curation phase. In a situation like this, we need to resynchronize these two so that the extraction phase is aligned again. When neurosynth-compose encounters a mismatch
+between the two phases, a banner will pop up prompting the user to synchronize the extraction phase with the new curation phase updates.
 
-### Study Edit Interface
+Successfully resynchronizing the two phases will cause the banner to go away.
 
-## Syncing Between Curation and Extraction
+## Completion
+
+The extraction phase is considered complete and the user is prompted to move on when all studies have been marked as complete. Once this step is complete, it is then time to specify the configurations for your meta-analysis.
+When all studies are marked as completed, a button should appear prompting the user to continue the meta-analysis process.
+
+:::info
+If you would like to skip the extraction step, then you can go back to the project page and click the button: "Mark all as complete" underneath the extraction section.
+
+![Mark all as complete](/guide/mark_all_as_complete.png)
+:::

docs/guide/Running/index.mdx → docs/guide/Project/Running.md

@@ -1,6 +1,6 @@
 ---
 title: Running Analyses
-sidebar_position: 2
+sidebar_position: 3
 ---
 
 # Running Analyses
@@ -9,7 +9,7 @@ You have a several options for running the analysis. In all cases, you will need
 
 ![Meta-analysis run](/tutorial/ma_run.png)
 
-Under the hood, analyses are managed by the [nsc-runner](https://github.com/neurostuff/nsc-runner) Python package, and executed by the [NiMARE](https://nimare.readthedocs.io/en/stable/) (Neuroimaging Meta-Analysis Research Environment) Python package. 
+Under the hood, analyses are managed by the [nsc-runner](https://github.com/neurostuff/nsc-runner) Python package, and executed by the [NiMARE](https://nimare.readthedocs.io/en/stable/) (Neuroimaging Meta-Analysis Research Environment) Python package.
 
 ## Google Colab
 
@@ -18,21 +18,21 @@ Under the hood, analyses are managed by the [nsc-runner](https://github.com/neur
 The easiest way to run an analysis is to use the [Google Colab](https://colab.research.google.com/) notebook linked above.
 
 The provided notebook runs entirely in the cloud, and does not require any local installation of software.
-To use simply paste your analysis ID into the first cell (`META_ID`), and using the Toolbar selet (Runtime -> Run All) 
+To use simply paste your analysis ID into the first cell (`META_ID`), and using the Toolbar selet (Runtime -> Run All)
 or the keyboard shortcut (Ctrl or ⌘ + F9) to run the notebook.
 
 ![Colab notebook](/guide/nsc_colab_notebook.png)
 
 The notebook will install all required software, run the analysis, and upload the results to Neurosynth Compose.
-Once the analysis is complete, you can use the notebook to explore the results using the interative report, download an archive 
+Once the analysis is complete, you can use the notebook to explore the results using the interative report, download an archive
 of the results, or browse the results in the Neurosynth Compose web interface, in the Meta-Analysis section of your Project.
 
 :::tip
 The Colab notebook has limited and varying freely available resources, and may not be able to run large analyses.
 If your analysis fails, try running it again, or using one of the other methods below.
 :::
 
-## Docker 
+## Docker
 
 The easiest way to run analyses locally is to use the `nsc-runner` [Docker](https://www.docker.com/) image provided by Neurosynth Compose.
 
@@ -72,7 +72,7 @@ where `<version>` is the version of `nsc-runner` that you want to download. If y
 
 You can see the tags available for download on [GitHub](https://github.com/neurostuff/compose-runner/pkgs/container/nsc-runner)
 
-## Manually prepared environment using pip 
+## Manually prepared environment using pip
 
 :::warning
 Manually installing `nsc-runner` may be difficult due to complex dependencies in the SciPy stack, or fMRI-specific tooling. Proceed only if you know what you’re doing.

docs/guide/Project/Specification.md

@@ -0,0 +1,8 @@
+---
+title: Specification
+sidebar_position: 2
+---
+
+## Work in progress!
+
+We're still working on completing the documentation for this. Please check back later.

docs/guide/Project/index.mdx

@@ -173,4 +173,4 @@ This error indicates that neurosynth-compose tried to extract the author data fr
 You can open a specific project by logging in, navigating to the
 [My Projects](https://compose.neurosynth.org/projects) page, and selecting a project you've created.
 
-When you view a project for the first time, you'll notice that you'll default to the "Edit Project" tab. Another tab, "View Meta-Analyses", will become visible when you have completed both the curation and extraction phases.
+When you view a project for the first time, you'll notice that you'll default to the "Project" tab. Another tab, "Meta-Analyses", will become visible when you have completed both the curation and extraction phases.