From 85e1722160e138c1f1698e93381a8fd26c83f367 Mon Sep 17 00:00:00 2001 From: Alexis Varsava Date: Thu, 9 May 2024 15:31:31 -0400 Subject: [PATCH 1/4] typo and grammar scrub --- CONTRIBUTING.md | 2 +- docs/actnow.md | 4 ++-- docs/algebraicguide.md | 2 +- docs/ask-your-doctor.md | 2 +- docs/builtin.md | 2 +- docs/compiler-hacking.md | 4 ++-- docs/faq.md | 8 +++---- docs/glossary.md | 8 +++---- docs/guided-meditations.md | 10 ++++---- docs/implementation.md | 14 +++++------ docs/index.md | 2 +- docs/input-formats.md | 2 +- docs/installation.md | 2 +- docs/language.md | 24 +++++++++---------- docs/olive-complex-cookbook.md | 4 ++-- docs/ops-guide.md | 4 ++-- docs/optionalguide.md | 2 +- docs/tutorial.md | 8 +++---- .../oicr/gsi/shesmu/jira/JiraConnection.java | 4 ++-- .../pinery/barcodes/BarcodeGrouper.java | 2 +- .../on/oicr/gsi/shesmu/vidarr/RunState.java | 2 +- .../plugin/cache/InvalidatableRecord.java | 2 +- .../plugin/cache/LabelledKeyValueCache.java | 2 +- .../plugin/filter/ActionFilterBuilder.java | 2 +- .../shesmu/plugin/functions/ShesmuMethod.java | 2 +- .../plugin/grouper/GrouperDefinition.java | 8 +++---- .../shesmu/plugin/input/JsonInputSource.java | 2 +- .../plugin/input/VariableDefinition.java | 2 +- .../refill/CustomRefillerParameter.java | 2 +- .../plugin/types/GenericTypeGuarantee.java | 4 ++-- .../oicr/gsi/shesmu/plugin/types/Imyhat.java | 2 +- .../shesmu/plugin/types/ImyhatConsumer.java | 2 +- shesmu-server-ui/src/actionfilters.ts | 4 ++-- shesmu-server-ui/src/alert.ts | 2 +- shesmu-server-ui/src/definitions.ts | 4 ++-- shesmu-server-ui/src/histogram.ts | 2 +- shesmu-server-ui/src/html.ts | 6 ++--- shesmu-server-ui/src/io.ts | 4 ++-- shesmu-server-ui/src/simulation.ts | 6 ++--- shesmu-server-ui/src/stats.ts | 4 ++-- .../gsi/shesmu/compiler/BaseOliveBuilder.java | 4 ++-- .../gsi/shesmu/compiler/BinaryOperation.java | 2 +- .../oicr/gsi/shesmu/compiler/CollectNode.java | 4 ++-- .../compiler/CollectNodeConcatenate.java | 12 +++++----- .../on/oicr/gsi/shesmu/compiler/Compiler.java | 6 ++--- .../shesmu/compiler/EcmaScriptRenderer.java | 2 +- .../gsi/shesmu/compiler/ExpressionNode.java | 4 ++-- .../compiler/ExpressionNodeVariable.java | 2 +- .../compiler/ExpressionNodeWdlPair.java | 2 +- .../compiler/GroupNodeOptionalUnpack.java | 2 +- .../compiler/OliveClauseNodeRequire.java | 2 +- .../oicr/gsi/shesmu/compiler/ProgramNode.java | 4 ++-- .../on/oicr/gsi/shesmu/compiler/Target.java | 4 ++-- .../definitions/ActionDefinition.java | 2 +- .../definitions/ConstantDefinition.java | 2 +- .../definitions/SignatureDefinition.java | 4 ++-- .../gsi/shesmu/core/StandardDefinitions.java | 4 ++-- .../gsi/shesmu/runtime/ActionGenerator.java | 2 +- .../gsi/shesmu/runtime/CompiledGenerator.java | 2 +- .../gsi/shesmu/runtime/RuntimeSupport.java | 2 +- .../shesmu/server/BaseHotloadingCompiler.java | 2 +- .../shesmu/server/BaseSimulateRequest.java | 2 +- .../oicr/gsi/shesmu/server/StaticActions.java | 2 +- .../shesmu/server/plugins/PluginManager.java | 5 ++-- .../ca/on/oicr/gsi/shesmu/swagger.json | 4 ++-- 65 files changed, 129 insertions(+), 128 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3f9d59364..7dfa2d327 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -46,7 +46,7 @@ We have several types of automated testing: Please make sure to add or update the relevant tests for your changes. Testing plugins is difficult because they are often mostly integration code that has to -communicate with a external services. We accept any level of testing on plugins +communicate with external services. We accept any level of testing on plugins as long as it is fast and delegate any plugin bugs to plugin authors. ## Commits diff --git a/docs/actnow.md b/docs/actnow.md index c061f04ba..c612ad5b4 100644 --- a/docs/actnow.md +++ b/docs/actnow.md @@ -1,5 +1,5 @@ # Static Actions -While Shesmu is mostly about the olives, it _does_ runs actions and it can be +While Shesmu is mostly about the olives, it _does_ run actions and it can be convenient to do that directly. These can be actions generated manually or using the olive simulator. @@ -15,7 +15,7 @@ _Actions_ page can find all actions from that file. Files can contain different kinds of actions. -The actions in the file are fixed. If they need to be updated in anyway, the +The actions in the file are fixed. If they need to be updated in any way, the file can be replaced or edited to include new actions, but Shesmu will never modify the file. diff --git a/docs/algebraicguide.md b/docs/algebraicguide.md index cbea34d6f..ea1fe39f1 100644 --- a/docs/algebraicguide.md +++ b/docs/algebraicguide.md @@ -25,7 +25,7 @@ Languages that use algebraic data types, including Scala and Rust, typically att Elsewhere in the Rust program, `Foo::Something(some_string)` can be used to create a new value. For Shesmu, the same approach is taken where the different -members in a algebraic type have names to help sort them out. +members in an algebraic type have names to help sort them out. In many languages, including Java, types have a particular name that defines them. For instance, if we create these two classes: diff --git a/docs/ask-your-doctor.md b/docs/ask-your-doctor.md index 565044f10..74a7bf846 100644 --- a/docs/ask-your-doctor.md +++ b/docs/ask-your-doctor.md @@ -45,7 +45,7 @@ previously run. Although action was _run a workflow_ in our original conception, it has expanded beyond that. We have action that include _Open a JIRA ticket_. If this -action is rerun, it doesn't always open a new ticket; it checks that JIRA has a +action is rerun, it doesn't always open a new ticket; it checks that JIRA has an open ticket that matches certain criteria. Similarly, _run a workflow_ doesn't necessarily run a workflow; it checks the metadatabase to check if a workflow with matching parameters has been run. diff --git a/docs/builtin.md b/docs/builtin.md index 016151b1d..3c8aead03 100644 --- a/docs/builtin.md +++ b/docs/builtin.md @@ -20,7 +20,7 @@ These functions are available on any instance: - `std::date::to_seconds`: get the number of seconds since the UNIX epoch for this date. - `std::float::is_infinite`: check if a floating-point number is infinite. - `std::float::is_nan`: check if a floating-point number is not-a-number. -- `std::float::parse` Convert a string containing digits and a decimal point into an float. +- `std::float::parse` Convert a string containing digits and a decimal point into a float. - `std::integer::parse` Convert a string containing digits into an integer. - `std::json::array_from_dict`: convert a dictionary to an array of arrays. If a dictionary has strings for keys, it will normally be encoded as a JSON object. For other key types, it will be encoded as a JSON array of two element arrays. This function forces conversion of a dictionary with string keys to the array-of-arrays JSON encoding. Shesmu will be able to convert either back to dictionary. - `std::json::object`: create a JSON object from fields. diff --git a/docs/compiler-hacking.md b/docs/compiler-hacking.md index fb2acea49..4ad1d2ab1 100644 --- a/docs/compiler-hacking.md +++ b/docs/compiler-hacking.md @@ -1,4 +1,4 @@ -# Understanding the Shemsu compiler +# Understanding the Shesmu compiler This is a guide to understanding the Shesmu olive compiler. This is meant to explain the core components that get the language to Java bytecode. @@ -290,7 +290,7 @@ This is the end of the example olive bytecode. ## Olive Design and Lambdas Every clause in an olive generates additional calls to methods in Java's -`Stream` or methods in Shemu's `RuntimeSupport` to manipulate the stream. Those +`Stream` or methods in Shesmu's `RuntimeSupport` to manipulate the stream. Those methods take parameters: some of which are simple values; others are method references/lambdas. diff --git a/docs/faq.md b/docs/faq.md index c0ece2119..b5dbb2499 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -4,10 +4,10 @@ This is intended for olive developers and operators. ## It's gone haywire!!! On the main status page, hit the _STOP ALL ACTIONS_ button. Also, that's not a question. -## I don't see the alert on Shemu's Alerts page. What gives? +## I don't see the alert on Shesmu's Alerts page. What gives? Shesmu, like most of other programs, feeds data into [Prometheus](https://prometheus.io/docs/introduction/overview/) and Prometheus sends alerts to AlertManager when the application is behaving badly. Shesmu also has `Alert` olives that create alerts about data in the system and send these directly to AlertManager. Only these data alerts will be displayed on the Shesmu _Alerts_ page. -## What going on with these actions? +## What is going on with these actions? Go to the Shesmu instance of interest, click on the _Actions_ tab. Here, you can find all the actions the server is trying to perform. If you click on the Stats button, you'll get some tables about the actions: - counts for each action state (failed, succeeded, ...) @@ -32,7 +32,7 @@ If you've changed the olive/LIMS/run blacklist/whatever to exclude this action, Have at look at the _Last Generated_ by an _Olive_ age. If this is over 2 hours, you can be very confident the olive is no longer creating this action ## I changed my olive but the actions are the same. What gives? -Every time an olive runs, all the actions are generated and go into Shemu's scheduler. When the olive runs again, it regenerates all those actions and Shesmu needs to decide if two actions are the same. Actions get to decide if two actiosn are equivalent and that may not include all parameters. If you look at the actions, it will list the olives that generated and you will see two version of the same source file. +Every time an olive runs, all the actions are generated and go into Shesmu's scheduler. When the olive runs again, it regenerates all those actions and Shesmu needs to decide if two actions are the same. Actions get to decide if two actions are equivalent and that may not include all parameters. If you look at the actions, it will list the olives that generated and you will see two version of the same source file. To get Shesmu to replace the actions, purge the old ones (either individually or in bulk). This will cause the new action to be in the scheduler. @@ -61,4 +61,4 @@ No worries, this isn't much harder: You can click almost any cell header or value and then use the buttons at the bottom to act on the subset of actions. Use the _Add Filter_ button to slice and dice the actions displayed. ## Can I see how some data is propagating through this olive? -Not quite, but if go to the _Olives_ page and select the olive, click _Edit in Simulator_ to have the source code for that file show up in the simulation dashboard. Add a _Where_ or _Dump_ clauses to filter the data of interest and simulate it to see what's going on. +Not quite, but you can go to the _Olives_ page and select the olive, and click _Edit in Simulator_ to have the source code for that file show up in the simulation dashboard. Add a _Where_ or _Dump_ clauses to filter the data of interest and simulate it to see what's going on. diff --git a/docs/glossary.md b/docs/glossary.md index ef433c89a..1ac1f4d8a 100644 --- a/docs/glossary.md +++ b/docs/glossary.md @@ -54,7 +54,7 @@ strings, or converted into tuples. The data that is available to olives. This data is effectively tabular even though it is never really encoded that way. Each record/row gets processed by an olive where each column is available as a variable. Columns cannot be -missing/null. Missing entires need to either be substituted with dummy values +missing/null. Missing entries need to either be substituted with dummy values or optional values. If the schema is ragged, it can be expressed as a JSON value. @@ -65,7 +65,7 @@ design to choice to prevent _matched_ lists where the indices mean something. Create a list of tuples in this case. ## Object -Shemu's objects are not like Java's object. They are more like JSON objects or +Shesmu's objects are not like Java's object. They are more like JSON objects or tuples with property names instead of indices. ## Olive @@ -100,7 +100,7 @@ an entire table in a database. ## Search A filter with a name that allows the UI to quickly select an interesting set of -actions. The can be used for debugging or as dashboards. +actions. They can be used for debugging or as dashboards. ## Signature A fingerprint (hash or value) derived from the values of variables read by an olive. @@ -113,7 +113,7 @@ should be rerun. The input format determines which variables should make it into the signature and which should be excluded. ## Throttler -A method to stop actions from running. Since Shesmu may be talking to may +A method to stop actions from running. Since Shesmu may be talking to many systems at once, throttlers provide a way to take some of those systems down for maintenance or limit Shesmu's traffic to them during an overload. Actions and olives check for permission to run from the throttlers and will quit early diff --git a/docs/guided-meditations.md b/docs/guided-meditations.md index e4b634ba5..5f4b5bb8e 100644 --- a/docs/guided-meditations.md +++ b/docs/guided-meditations.md @@ -88,7 +88,7 @@ Invert the value of _X_ (_i.e._, if _X_ is true, then false) - `[` _L_ `] = *` Check that an alert has a label _L_ associated with it. If it is present with -any value, including the empty string, the it will match. _L_ may be a valid +any value, including the empty string, then it will match. _L_ may be a valid Shesmu identifier, any string quoted, or an expression surrounded by `{}`. - `[` _L_ `] =` _V_ @@ -99,7 +99,7 @@ surrounded by `{}`. - `[` _L_ `] ~ /`_pattern_`/` Check that an alert has a label _L_ and its value matches the regular expression _pattern_ . If it is present with any value, including the empty -string, the it will match. _L_ may be a valid +string, then it will match. _L_ may be a valid Shesmu identifier, any string quoted, or an expression surrounded by `{}`. - `LIVE` @@ -219,9 +219,9 @@ Allows the user to choose between several options. _step_ is a list of displays - `Form` _entry1_[`,` _entry2_ ...] `Then` _step_ Allows collecting information from the user and then proceed to the next step with that information available. _step_ is a list of displays followed by -another step. For details on the form entires, see the next section. +another step. For details on the form entries, see the next section. -#### Form Entires +#### Form Entries To collect data from the user, a form entry will display a prompt that is stored in a variable. - _name_ `=` _type_ `With Label` _labelexpr_ @@ -406,7 +406,7 @@ following: ### Define and Go-to It can be useful to reuse steps in different contents. At the beginning of a -file, a reuable step can be defined: +file, a reusable step can be defined: - `Define` _name_ `(` _type1_ _name1_`,` ... `)` _step_ `;` diff --git a/docs/implementation.md b/docs/implementation.md index 4c2e05db1..6cc32b6b3 100644 --- a/docs/implementation.md +++ b/docs/implementation.md @@ -122,7 +122,7 @@ type safe. To create a new source format: 1. Create a class, _V_, that will hold all the data for a “row” in the incoming data. It must be a class and not an interface. 1. Create a parameterless method in _V_ for every variable to be exposed. The -method names must be valid Shemsu names (lowercase with underscores) and +method names must be valid Shesmu names (lowercase with underscores) and decorated with [`@ShesmuVariable`](javadoc/ca.on.oicr.gsi.shesmu/ca/on/oicr/gsi/shesmu/plugin/input/ShesmuVariable.html) annotations with the correct type descriptor. All methods must return @@ -188,7 +188,7 @@ of these can be fixed (the same across all rows) or dynamic (a function that takes an input row as a parameter). There are a number of overrides and super-constructors to handle different numbers of input and output variables. The exact configuration will depend on what information the grouper requires. -It maybe easiest to implement the grouper and see what information is necessary +It may be easiest to implement the grouper and see what information is necessary and then work backward to the grouper definition. 1. Create a class _G_ that implements @@ -262,7 +262,7 @@ All plugin integration is provided by: A number of plugin features can be added to the `PluginFileType` or the `PluginFile`. Anything placed in the `PluginFileType` will be a global -defintion. When Shesmu administrator creates configuration file, Shesmu will +definition. When Shesmu administrator creates configuration file, Shesmu will spawn an instance of `PluginFile` to read that file. Any annotated methods attached the `PluginFile` will be created per-instance. The name of the configuration file will be included in the definition if it is created @@ -327,8 +327,8 @@ be provided using a Shesmu type descriptor in the `type` parameter of the annotation to any parameters. The `@ShesmuParameter` annotation can also provide help text. -The name can be provided two ways: from the name of the method itself or fro -the `name` parameter of `@ShemsuMethod` annotation. If the name is associated +The name can be provided two ways: from the name of the method itself or from +the `name` parameter of `@ShesmuMethod` annotation. If the name is associated with a `PluginFile` class, it must contain a `$` which will be replaced with the name of the file. For instance, if the name of the method is `$_items` and the file name is `foo.bar`, then the constant or variable will be available to @@ -336,7 +336,7 @@ olives as `foo_items`. The `@ShesmuMethod` annotation also has a `description` property that will be shown in the definition page. In the description, `{instance}` and `{file}` -will be replace with the instance name and configuration file path, +will be replaced with the instance name and configuration file path, respectively. #### Using the Definer @@ -533,7 +533,7 @@ will provide it with the functions it requires to manipulate that type. To deliver a database to olives using `PluginFileType` or `PluginFile`: -1. Create a static method in `PluginFileType` or a virtual method in `PluginFile`, parameterized by ``, that return _F_``. The returned type is used to discover parameters, so it must the be the correct subtype. +1. Create a static method in `PluginFileType` or a virtual method in `PluginFile`, parameterized by ``, that return _F_``. The returned type is used to discover parameters, so it must be the correct subtype. 1. Annotate this method with [`@ShesmuRefill`](javadoc/ca.on.oicr.gsi.shesmu/ca/on/oicr/gsi/shesmu/plugin/refill/ShesmuRefill.html). 1. Name this method with a Shesmu-compatible name or set the `name` property in the annotation. diff --git a/docs/index.md b/docs/index.md index fe9bfc0d4..611e11269 100644 --- a/docs/index.md +++ b/docs/index.md @@ -85,7 +85,7 @@ Once a plugin is configured, it can provide: - input formats: the data that olives can draw on using the `Input` declaration at the start of a file, or in `Join` or `LeftJoin` clauses - signers: special variables that are computed based on the current row being processed in the olive - source linker: once a Shesmu server is deployed, it can be useful to have links from the Shesmu dashboard to the original `.shesmu` sources, especially when they are stored in git or the like. A source linker knows how to convert a path on the local file system into a URL. -- throttlers: when Shesmu has actions to perform, it will perform them as as quickly as possible. It may be useful to throttle Shesmu based on external criteria. +- throttlers: when Shesmu has actions to perform, it will perform them as quickly as possible. It may be useful to throttle Shesmu based on external criteria. To view what olives may use, from the main Shesmu status page, use the `Definition` menu to view the available resources including documentation and diff --git a/docs/input-formats.md b/docs/input-formats.md index ba5ef212b..c6d488c41 100644 --- a/docs/input-formats.md +++ b/docs/input-formats.md @@ -1,5 +1,5 @@ # Configuring Input Formats -A _input format_ is the type of data that Shesmu olives process--that is, the +An _input format_ is the type of data that Shesmu olives process--that is, the variables that are available to Shesmu programs. The actual data comes from a matching _input data repository_ and many repositories can provide the same format. diff --git a/docs/installation.md b/docs/installation.md index 63bcfd168..8771da2cb 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -105,7 +105,7 @@ On a Linux server, create a systemd configuration in `/lib/systemd/system/shesmu [Install] WantedBy=multi-user.target -If your Shesmu server cannot determine it's own URL (it attempts to use the +If your Shesmu server cannot determine its own URL (it attempts to use the FQDN of the local system), in the `[Unit]` section, add: Environment=LOCAL_URL=http://shesmu.myinstitute.org:8081/ diff --git a/docs/language.md b/docs/language.md index a96d55214..df1a295b2 100644 --- a/docs/language.md +++ b/docs/language.md @@ -146,7 +146,7 @@ Terminals determine what an olive will do. - `Run` _action_ _tags_ `With` _param1_ `=` _expr1_[`,` _param2_ `=` _expr2_[`,` ...]]`;` Creates action to be scheduled and run. _action_ determines which action will -be run what what parameters are available. Optional parameters can be +be run and what parameters are available. Optional parameters can be conditionally assigned: _param_ `=` _expr_ `If` _condition_ @@ -186,7 +186,7 @@ this action. - `Tags` _expr_ Adds the elements in the result of _expr_, which must be a list of strings, to -the tags associated with this actions. +the tags associated with this action. ## Clauses An olive can have many clauses that filter and reshape the data. All clauses @@ -273,7 +273,7 @@ and outer key lists. Consider a situation where a process outputs several files and another process ingests a subset of them; a `IntersectionJoin` could be used to find output process that used some of the input. -If an set-to-single value join is required, use `IntersectionJoin` and put the +If a set-to-single value join is required, use `IntersectionJoin` and put the single element in a list. This reshapes the data. @@ -314,7 +314,7 @@ process outputs several files and another process ingests a subset of them; a `LeftIntersectionJoin` could be used to find output process that used some of the input. -If an set-to-single value join is required, use `LeftIntersectionJoin` and put +If a set-to-single value join is required, use `LeftIntersectionJoin` and put the single element in a list. This reshapes the data. @@ -523,7 +523,7 @@ _testexpr_ must be boolean and both _trueexpr_ and _falseexpr_ must have the sam Performs a conditional compilation. The _tests_ are a comma-separated list of constant names or `Function` + function names. If all of these items are defined, _trueexpr_ is used; otherwise, _falseexpr_ is used. It's important to -note that, unlike `If`, this is a compile time decisions. Therefore, _trueexpr_ +note that, unlike `If`, this is a compile-time decision. Therefore, _trueexpr_ and _falseexpr_ don't have to return the same type and the unused path can depend on constants and functions that are not defined. @@ -666,7 +666,7 @@ End - _expr_ `As` _type_ Convert a value to or from JSON. If _type_ is `json`, then the result from -_expr_ will be convert to JSON in the Shesmu-standard way. If _type_ is any +_expr_ will be converted to JSON in the Shesmu-standard way. If _type_ is any other type, then _expr_ must be a `json` value and it will be converted from JSON to the matching Shesmu type. Since the conversion from JSON to Shesmu cannot be guaranteed, it will return an optional of _type_. To create a JSON @@ -1054,7 +1054,7 @@ Instead of _field_` = `_expr_, a `...`_expr_ can be used and this will copy all the elements in _expr_, which must be an object. If some fields are to be excluded, use the form: `...`_expr_ `Without` _field1_ _field2_ ... -A field can also be created from a variable of the same name by placing the a +A field can also be created from a variable of the same name by placing the name after a `;`. For example `{ a = 1; b }` is short hand for `{ a = 1, b = b }`. Named fields can be ommited if there are none (_i.e._, `{; b, c}` is the short hand for `{b = b, c = c}`). If a gang is used here, this will create all @@ -1094,7 +1094,7 @@ Specified a new string literal. A string may contain the following special items - `\\t` for a tab character - `\\n` for a new line character -- `\\{` for a open brace character +- `\\{` for an open brace character - `{`_expr_`}` for a string interpolation; the expression must be a string, integer, or date - `{`_expr_`:`_n_`}` for a zero-padded integer string interpolation; the expression must be an integer and _n_ is the number of digits to pad to - `{@`_name_`}` interpolate a name from a gang; the variables in the gang must be strings and integers @@ -1239,7 +1239,7 @@ Returns the number of items in the list. Returns the first _expr_ in the list or an empty optional if no items are present. -Since this returns optional, it maybe useful to chain with `Default`. +Since this returns optional, it may be useful to chain with `Default`. For details on optional values, see [the Mandatory Guide to Optional Values](optionalguide.md). @@ -1274,7 +1274,7 @@ Finds the minimum or maximum item in a list, based on the _sortexpr_, which must be an integer or date. If the list is empty, an empty optional is returned. -Since this returns optional, it maybe useful to chain with `Default`. +Since this returns optional, it may be useful to chain with `Default`. For details on optional values, see [the Mandatory Guide to Optional Values](optionalguide.md). @@ -1319,7 +1319,7 @@ must return an integer or a floating-point number. #### Table - `Table` _name_ `=` _value_`,` ... `With` _format_ -This collects items into a table and formats that table as a string. This can be useful for creating HTML or Markdown tables for inserting into JIRA. The _name_, which must evaluate to a string, will the be name of the column, and _value_, which must also produce a string, will be the contents of that column for every item. The _format_ determines how the text is laid out. It is an object with the following properties: +This collects items into a table and formats that table as a string. This can be useful for creating HTML or Markdown tables for inserting into JIRA. The _name_, which must evaluate to a string, will be the name of the column, and _value_, which must also produce a string, will be the contents of that column for every item. The _format_ determines how the text is laid out. It is an object with the following properties: - `data_start`: the leader for each row - `data_separator`: the text to place in between inner columns @@ -1369,7 +1369,7 @@ Evaluates all _expr_ for each item in the list and returns it if all are the sam If they are different or there are no items, an empty optional is returned. -Since this returns optional, it maybe useful to chain with `Default`. +Since this returns optional, it may be useful to chain with `Default`. For details on optional values, see [the Mandatory Guide to Optional Values](optionalguide.md). diff --git a/docs/olive-complex-cookbook.md b/docs/olive-complex-cookbook.md index c85183fef..38d4ea0b1 100644 --- a/docs/olive-complex-cookbook.md +++ b/docs/olive-complex-cookbook.md @@ -5,7 +5,7 @@ ideas with a dissection of why. ## Selection of Multiple Output The goal here is to select the "best" output from a workflow. Older versions of -the workflow produced one file in a unhelpful format. The new one produces two +the workflow produced one file in an unhelpful format. The new one produces two files: a useful format and the historic unhelpful one. The goal is to pick the best format for newest run of this workflow. @@ -262,7 +262,7 @@ This code takes each mask and does a `Flatten` on it. The mapping between old input masks is usually 1:1, but in the case where `Y`_n_ maps to `Y1N*`, it is 1:2, so the `Flatten` will allow collecting the two. Again, this uses a `Switch` on a tuple. The tuple is the mask type (`Y`, `I`, `N`) and the ordinal -(the number of this type appears in the sequence. So, `{"Y", 0}` is the first +(the number of this type) appears in the sequence. So, `{"Y", 0}` is the first read, `{"I", 0}` is the first index, `{"I", 1}` is the second index, and `{"Y", 1}` is the second read. This assumes a relatively normal read structure for the sequencer. If other reads or indices were common, it might make sense to have diff --git a/docs/ops-guide.md b/docs/ops-guide.md index a078fa426..73d9f71ed 100644 --- a/docs/ops-guide.md +++ b/docs/ops-guide.md @@ -50,7 +50,7 @@ instance: ![Histogram showing changed data](ops-histo-orphan.png) -In this histogram there are a number of actions that haven not been generated +In this histogram there are a number of actions that have not been generated by an olive recently. This likely means that the input data changed and these actions are now orphans and may be candidates to be purged. The larger the gap between now and the last time they were generated, the more likely it is that @@ -343,7 +343,7 @@ The Vidarr actions also generates some useful tags: - `vidarr-workflow:`_name_[`/`_version_`]: The workflow that this action will run, both with and without the version. - `vidarr-state:`[`active`|`attempt`|`conflict`|`dead`|`finished`|`missing`]: - The action uses a state machine while its communicating with Vidarr. This is + The action uses a state machine while it's communicating with Vidarr. This is the current state of that machine. - `vidarr-attempt:`_count_`: The number of times this workflow run has been attempted. diff --git a/docs/optionalguide.md b/docs/optionalguide.md index aebd1ad33..44ce3ab75 100644 --- a/docs/optionalguide.md +++ b/docs/optionalguide.md @@ -143,7 +143,7 @@ to notify the outside world appropriately. Sometimes, part of an olive needs to manipulate an optional value. That part may not be the best or easiest place to do a lowering, so it is desirable to simply manipulate the value, if there is one. This is where the `?` operator comes in. -For example, : +For example: `x? + 3` diff --git a/docs/tutorial.md b/docs/tutorial.md index 1d1701b21..dca9e0669 100644 --- a/docs/tutorial.md +++ b/docs/tutorial.md @@ -182,7 +182,7 @@ The grouping shown so far requires that the groups being produced are known ahead of time. In some situations, it isn't possible to know exactly which items belong in which groups until all the data is available. For these situations, _groupers_ are available that can do complex subgrouping. The groupers are -plugins, so the groupers available can be seen on the running Shemsu server. +plugins, so the groupers available can be seen on the running Shesmu server. The `always_include` grouper can put a row into every subgroup. Suppose a validation should be run for every workflow with the validation method @@ -756,7 +756,7 @@ Since this is very confusing, as a general rule: one star a time. ## Variables Gangs When grouping, it can be useful for have predefined sets of variables to use in -a `By` clause for any given input format. A input format can define a _gang_ that +a `By` clause for any given input format. An input format can define a _gang_ that defines a short-hand name of a set of variables to used in grouping together. The gang can then be used in the `By` of either a `Group` or `Pick` operation: @@ -792,7 +792,7 @@ it is possible to redefine the gangs in a nonsensical way. ## Identifiers All identifier is Shesmu, including olive definitions, function names, action -names, and variables must begin with a lowercase letter a-z, followed by an +names, and variables must begin with a lowercase letter a-z, followed by any number of underscores, lowercase letters a-z, and decimal digits. Olive definitions, function names, action names, and variables exist in different @@ -812,7 +812,7 @@ or: ### Signature and Signable Variables Since Shesmu is designed to create repeatable actions, it's useful to know what data was read to create this data. If an input format has a unique ID for every -record, the some values may be immutable for that ID, but other values may be +record, then some values may be immutable for that ID, but other values may be (externally) changed. For instance, suppose there is a record of what was placed on a sequencer. A user may have incorrectly entered what kit was used to prepare this sample; if so, changing it might need to trigger a new action in diff --git a/plugin-jira/src/main/java/ca/on/oicr/gsi/shesmu/jira/JiraConnection.java b/plugin-jira/src/main/java/ca/on/oicr/gsi/shesmu/jira/JiraConnection.java index 6253e35c1..cddb46c75 100644 --- a/plugin-jira/src/main/java/ca/on/oicr/gsi/shesmu/jira/JiraConnection.java +++ b/plugin-jira/src/main/java/ca/on/oicr/gsi/shesmu/jira/JiraConnection.java @@ -112,8 +112,8 @@ Pair process( static final ObjectMapper MAPPER = new ObjectMapper(); /** - * JIRA uses an Atlassian Document specification that is needlessly complicated for Shemu's needs, - * so we don't bother to understand the schema. + * JIRA uses an Atlassian Document specification that is needlessly complicated for Shesmu's + * needs, so we don't bother to understand the schema. * * @param jsonNode the node to dissect * @return any text found diff --git a/plugin-pinery/src/main/java/ca/on/oicr/gsi/shesmu/pinery/barcodes/BarcodeGrouper.java b/plugin-pinery/src/main/java/ca/on/oicr/gsi/shesmu/pinery/barcodes/BarcodeGrouper.java index 51f346c0f..bda793c67 100644 --- a/plugin-pinery/src/main/java/ca/on/oicr/gsi/shesmu/pinery/barcodes/BarcodeGrouper.java +++ b/plugin-pinery/src/main/java/ca/on/oicr/gsi/shesmu/pinery/barcodes/BarcodeGrouper.java @@ -71,7 +71,7 @@ public Stream> group(List inputs) { final BasesMask newMask = BarcodeAndBasesMask.calculateBasesMask(barcode, basesMasks.get(0)); if (newMask == null) { - // If we've got an mess of a mask, (╯°□°)╯︵ ┻━┻ + // If we've got a mess of a mask, (╯°□°)╯︵ ┻━┻ gauge.set(1); return Stream.empty(); } diff --git a/plugin-vidarr/src/main/java/ca/on/oicr/gsi/shesmu/vidarr/RunState.java b/plugin-vidarr/src/main/java/ca/on/oicr/gsi/shesmu/vidarr/RunState.java index 1ea79a56a..3b41b7fbd 100644 --- a/plugin-vidarr/src/main/java/ca/on/oicr/gsi/shesmu/vidarr/RunState.java +++ b/plugin-vidarr/src/main/java/ca/on/oicr/gsi/shesmu/vidarr/RunState.java @@ -14,7 +14,7 @@ import java.util.stream.Stream; /** - * As Shesmu communicates with Vidarr, the action needs to track whats going on. This class is + * As Shesmu communicates with Vidarr, the action needs to track what's going on. This class is * designed as a state machine where each implementation can determine what to do and returns a next * state. */ diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/cache/InvalidatableRecord.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/cache/InvalidatableRecord.java index 5dfb3b56d..05d0d8086 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/cache/InvalidatableRecord.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/cache/InvalidatableRecord.java @@ -9,7 +9,7 @@ public class InvalidatableRecord implements Record> { /** * Build a new cache record type that checks when a record is valid and does a clean up when the - * item is being replace + * item is being replaced * * @param isValid the predicate to check if the cached value is still valid * @param destructor the clean up procedure diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/cache/LabelledKeyValueCache.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/cache/LabelledKeyValueCache.java index 44ff2e4fd..cae9ef1a1 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/cache/LabelledKeyValueCache.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/cache/LabelledKeyValueCache.java @@ -165,7 +165,7 @@ public final Iterator>> iterator() { return records.entrySet().iterator(); } - /** The the fixed label associated with the specified key */ + /** The fixed label associated with the specified key */ protected abstract L label(K key); @Override diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/filter/ActionFilterBuilder.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/filter/ActionFilterBuilder.java index ad27c5322..b485550e7 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/filter/ActionFilterBuilder.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/filter/ActionFilterBuilder.java @@ -208,7 +208,7 @@ public ActionFilter type(Stream types) { * *

The results include a precedence of the result. This can be discarded if used directly. If * more concatenation is required, it can be used to determine if parentheses are necessary. - * Terminal expressions are 0, unary prefixes are 1, logical conjunction is 2, logical disjuncion + * Terminal expressions are 0, unary prefixes are 1, logical conjunction is 2, logical disjunction * is 3. */ ActionFilterBuilder, ActionState, String, Instant, Long> QUERY = diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/functions/ShesmuMethod.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/functions/ShesmuMethod.java index 32a98eed6..51bb6492d 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/functions/ShesmuMethod.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/functions/ShesmuMethod.java @@ -9,7 +9,7 @@ import java.lang.annotation.Target; /** - * Make this method available to Shesmu olives as a function or a constant (if it take no + * Make this method available to Shesmu olives as a function or a constant (if it takes no * arguments). * *

This must be on static method in a subclass of {@link PluginFileType} or a virtual method on a diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/grouper/GrouperDefinition.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/grouper/GrouperDefinition.java index 4b5eafe8b..2960d5275 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/grouper/GrouperDefinition.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/grouper/GrouperDefinition.java @@ -96,7 +96,7 @@ public static CallSite bootstrap(MethodHandles.Lookup lookup, String name, Metho * information back to the olive * @param factory a function that creates a new grouper * @param the type of the input rows; this is controlled by Shesmu - * @param the type of the ouput rows; this is controlled by Shesmu + * @param the type of the output rows; this is controlled by Shesmu * @param the type of the grouping operation * @param the type of the grouped collector */ @@ -150,7 +150,7 @@ public static CallSite bootstrap(MethodHandles.Lookup lookup, String name, Metho * information back to the olive * @param factory a function that creates a new grouper * @param the type of the input rows; this is controlled by Shesmu - * @param the type of the ouput rows; this is controlled by Shesmu + * @param the type of the output rows; this is controlled by Shesmu * @param the type of the grouping operation * @param the type of the argument to the grouping operation * @param the type of the grouped collector @@ -185,7 +185,7 @@ public , T, S, C> GrouperDefinition( * information back to the olive * @param factory a function that creates a new grouper * @param the type of the input rows; this is controlled by Shesmu - * @param the type of the ouput rows; this is controlled by Shesmu + * @param the type of the output rows; this is controlled by Shesmu * @param the type of the grouping operation * @param the type of the first argument to the grouping operation * @param the type of the second argument to the grouping operation @@ -227,7 +227,7 @@ public , T, S, U, C> GrouperDefinition( * information back to the olive * @param factory a function that creates a new grouper * @param the type of the input rows; this is controlled by Shesmu - * @param the type of the ouput rows; this is controlled by Shesmu + * @param the type of the output rows; this is controlled by Shesmu * @param the type of the grouping operation * @param the type of the first argument to the grouping operation * @param the type of the second argument to the grouping operation diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/input/JsonInputSource.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/input/JsonInputSource.java index 9662cdd09..c38125a99 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/input/JsonInputSource.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/input/JsonInputSource.java @@ -8,7 +8,7 @@ /** * Provide data as a stream of JSON data * - *

Shesmu will automatically use the standard streaming JSON unmarhsalling protocol to simplify + *

Shesmu will automatically use the standard streaming JSON unmarshalling protocol to simplify * data extraction */ public interface JsonInputSource { diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/input/VariableDefinition.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/input/VariableDefinition.java index 0b92aa68a..79ff7f56c 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/input/VariableDefinition.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/input/VariableDefinition.java @@ -8,6 +8,6 @@ * * @param type the Shesmu type for this variable * @param signable whether this variable should be included in signatures - * @param gangs the gangs in this variables is part of + * @param gangs the gangs that this variable is part of */ public record VariableDefinition(Imyhat type, boolean signable, List gangs) {} diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/refill/CustomRefillerParameter.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/refill/CustomRefillerParameter.java index 1c88ef1b0..dd5c5be52 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/refill/CustomRefillerParameter.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/refill/CustomRefillerParameter.java @@ -21,7 +21,7 @@ public abstract class CustomRefillerParameter { * * @param name the name of the parameter * @param store a callback to install the transformer function into the refiller object - * @param type the type being consume from Shesmu + * @param type the type being consumed from Shesmu * @param the type of the refiller * @param the type of the input row * @param the type of the value from the olive diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/GenericTypeGuarantee.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/GenericTypeGuarantee.java index c8eb54b87..7197ab3fa 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/GenericTypeGuarantee.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/GenericTypeGuarantee.java @@ -301,7 +301,7 @@ public R unpack(Object object) { * @param first the type of the first element in the tuple * @param second the type of the second element in the tuple * @param third the type of the third element in the tuple - * @param the type of value after convertion to a Java type + * @param the type of value after conversion to a Java type * @param the type of the first element of the tuple * @param the type of the second element of the tuple * @param the type of the third element of the tuple @@ -358,7 +358,7 @@ public R unpack(Object object) { * @param second the type of the second element in the tuple * @param third the type of the third element in the tuple * @param fourth the type of the third element in the tuple - * @param the type of value after convertion to a Java type + * @param the type of value after conversion to a Java type * @param the type of the first element of the tuple * @param the type of the second element of the tuple * @param the type of the fourth element of the tuple diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/Imyhat.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/Imyhat.java index 066bb4a7d..baa3a848a 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/Imyhat.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/Imyhat.java @@ -1932,7 +1932,7 @@ public static TupleImyhat tuple(Imyhat... types) { public abstract R apply(ImyhatFunction dispatcher, Object value); /** - * Transform this Shemsu type into a another representation + * Transform this Shesmu type into another representation * * @param transformer the converter for each type */ diff --git a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/ImyhatConsumer.java b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/ImyhatConsumer.java index 5f7114d6b..41020dc23 100644 --- a/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/ImyhatConsumer.java +++ b/shesmu-pluginapi/src/main/java/ca/on/oicr/gsi/shesmu/plugin/types/ImyhatConsumer.java @@ -9,7 +9,7 @@ import java.util.stream.Stream; /** - * Cpllect a value based on the provided information + * Collect a value based on the provided information * *

In some cases, a Shesmu value may be passed to Java as {@link Object} and an accompanying * {@link Imyhat}. diff --git a/shesmu-server-ui/src/actionfilters.ts b/shesmu-server-ui/src/actionfilters.ts index fbc252dc0..85d41e7db 100644 --- a/shesmu-server-ui/src/actionfilters.ts +++ b/shesmu-server-ui/src/actionfilters.ts @@ -258,7 +258,7 @@ interface BasicText { matchCase: boolean; } /** - * Standard definitions to handle all the time manipulation gracefull + * Standard definitions to handle all the time manipulation gracefully */ interface BasicQueryTimeAccessor { rangeType: TimeRangeType; @@ -628,7 +628,7 @@ function addFilterDialog( true, "Entries like ", mono("foo.shesmu"), - " will match any action produced by any olive from that file. Entires like ", + " will match any action produced by any olive from that file. Entries like ", mono("foo.shesmu:5"), " and ", mono("foo.shesmu:5:3"), diff --git a/shesmu-server-ui/src/alert.ts b/shesmu-server-ui/src/alert.ts index c5d3271ef..d760a2101 100644 --- a/shesmu-server-ui/src/alert.ts +++ b/shesmu-server-ui/src/alert.ts @@ -74,7 +74,7 @@ export interface AlertFilterEq { type: "eq"; } /** - * An alert filter that checks for a certain lael to be present. + * An alert filter that checks for a certain label to be present. */ export interface AlertFilterHas { label: string; diff --git a/shesmu-server-ui/src/definitions.ts b/shesmu-server-ui/src/definitions.ts index ca5ef8c57..5168d88d0 100644 --- a/shesmu-server-ui/src/definitions.ts +++ b/shesmu-server-ui/src/definitions.ts @@ -36,13 +36,13 @@ import * as valueParser from "./parser.js"; import { combineModels, commonPathPrefix, mapModel } from "./util.js"; export type Definition = - | ActionDefintion + | ActionDefinition | ConstantDefinition | FunctionDefinition | OliveDefinition | RefillerDefinition | SignatureDefinition; -export interface ActionDefintion { +export interface ActionDefinition { kind: "action"; name: string; description: string; diff --git a/shesmu-server-ui/src/histogram.ts b/shesmu-server-ui/src/histogram.ts index 89fd18699..3ae238212 100644 --- a/shesmu-server-ui/src/histogram.ts +++ b/shesmu-server-ui/src/histogram.ts @@ -25,7 +25,7 @@ export interface HistogramRow { */ selectionDisplay(start: number, end: number): string; /** - * A callback inidcating that the user has selected this range of the histogram. + * A callback inidicating that the user has selected this range of the histogram. * * It is guaranteed that start will be less than end. */ diff --git a/shesmu-server-ui/src/html.ts b/shesmu-server-ui/src/html.ts index d98e92ada..8bff5cd48 100644 --- a/shesmu-server-ui/src/html.ts +++ b/shesmu-server-ui/src/html.ts @@ -1578,7 +1578,7 @@ export interface TableCell { */ export interface TreePath { /** - * The "real" value associated with this segement. It will be used for comparisons against other leaves, but not displayed to the user. + * The "real" value associated with this segment. It will be used for comparisons against other leaves, but not displayed to the user. */ value: string; /** @@ -2941,7 +2941,7 @@ export function inputTextArea( } /** - * A UI element that tiggers a regular update + * A UI element that triggers a regular update * * It keeps a counter and updates the counter every time it is triggered. If * the UI element is removed, the model will no longer be updated. @@ -4247,7 +4247,7 @@ export function tableRow( /** * Create a tabbed area with multiple panes * - * @param tabs each tab to display; each tabe has a name, contents, and an optional Ctrl-F handler. One tab may be marked as selected to be active by default + * @param tabs each tab to display; each tab has a name, contents, and an optional Ctrl-F handler. One tab may be marked as selected to be active by default */ export function tabs(...tabs: Tab[]): UIElement { return tabsModel(0, ...tabs).ui; diff --git a/shesmu-server-ui/src/io.ts b/shesmu-server-ui/src/io.ts index f6b2db5c2..ac6c8affd 100644 --- a/shesmu-server-ui/src/io.ts +++ b/shesmu-server-ui/src/io.ts @@ -63,7 +63,7 @@ export interface MutableServerInfo { /** * These are the request types for all the endpoints where JSON requests can be made to the server * - * Null entires are GET requests; all others are treated as POST requests + * Null entries are GET requests; all others are treated as POST requests */ export interface ShesmuRequestType { "action-ids": ActionFilter[]; @@ -184,7 +184,7 @@ export function fetchAsPromise< } /** - * Create a model that acccepts an array and can store it for later iteration + * Create a model that accepts an array and can store it for later iteration */ export function iterableModel(): StatefulModel & Iterable { let state: T[] = []; diff --git a/shesmu-server-ui/src/simulation.ts b/shesmu-server-ui/src/simulation.ts index 15c9efab2..358354faa 100644 --- a/shesmu-server-ui/src/simulation.ts +++ b/shesmu-server-ui/src/simulation.ts @@ -104,7 +104,7 @@ interface ExportDefine { parameters: string[]; /** If true, the definition is returning an “unmodified” data stream. * - * The data stream may actaully be modified through a Flatten or Require operation, but it is close enough to the original format to still compute signatures on. + * The data stream may actually be modified through a Flatten or Require operation, but it is close enough to the original format to still compute signatures on. */ isRoot: boolean; } @@ -778,9 +778,9 @@ export function initialiseSimulationDashboard( const spot = spotCounter((c) => { switch (c) { case 0: - return "No local defintions"; + return "No local definitions"; case 1: - return "One local defintion."; + return "One local definition."; default: return `${c} local definitions`; } diff --git a/shesmu-server-ui/src/stats.ts b/shesmu-server-ui/src/stats.ts index 11cf9b65a..981bb6c3c 100644 --- a/shesmu-server-ui/src/stats.ts +++ b/shesmu-server-ui/src/stats.ts @@ -478,7 +478,7 @@ function renderStat( * Produce a stats pane that can be fed filters to rebuild itself */ export function actionStats( - addPropertySeach: AddPropertySearch, + addPropertySearch: AddPropertySearch, addRangeSearch: AddRangeSearch, filenameFormatter: FilenameFormatter, exportSearches: ExportSearchCommand[] @@ -489,7 +489,7 @@ export function actionStats( const results = stats.map((stat) => renderStat( stat, - addPropertySeach, + addPropertySearch, addRangeSearch, filenameFormatter, exportSearches, diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/BaseOliveBuilder.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/BaseOliveBuilder.java index 0844a8232..293bc2928 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/BaseOliveBuilder.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/BaseOliveBuilder.java @@ -299,7 +299,7 @@ protected Type currentType() { protected abstract void emitSigner(SignatureDefinition name, Renderer renderer); /** - * Create a “Where” clause in a olive. + * Create a “Where” clause in an olive. * * @param capturedVariables A collection of variables that must be available in the filter clause. * These will be available in the resulting method @@ -688,7 +688,7 @@ public Renderer peek(String action, int line, int column, LoadableValue[] captur * @param max whether we are finding a maximum or a minimum * @param discriminators the stream variables over which the groups are constructed * @param capturedVariables any captures that are needed by the comparison expression - * @return a new method that must return a value to be compared for a input row + * @return a new method that must return a value to be compared for an input row */ public Renderer pick( int line, diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/BinaryOperation.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/BinaryOperation.java index 7b5327438..249c9a129 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/BinaryOperation.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/BinaryOperation.java @@ -23,7 +23,7 @@ import org.objectweb.asm.commons.Method; /** - * Describes how to perform an binary operation + * Describes how to perform a binary operation * *

The operation must be able to take exactly two arguments and know what to do based only on the * types of the operands. diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/CollectNode.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/CollectNode.java index a1506834a..16ff0ec64 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/CollectNode.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/CollectNode.java @@ -1,7 +1,7 @@ package ca.on.oicr.gsi.shesmu.compiler; import ca.on.oicr.gsi.Pair; -import ca.on.oicr.gsi.shesmu.compiler.CollectNodeConcatenate.ConcatentationType; +import ca.on.oicr.gsi.shesmu.compiler.CollectNodeConcatenate.ConcatenationType; import ca.on.oicr.gsi.shesmu.compiler.ListNode.Ordering; import ca.on.oicr.gsi.shesmu.compiler.Target.Flavour; import ca.on.oicr.gsi.shesmu.plugin.Parser; @@ -190,7 +190,7 @@ private interface OptionalConstructor { return result; }); } - for (final var concatType : ConcatentationType.values()) { + for (final var concatType : ConcatenationType.values()) { DISPATCH.addKeyword( concatType.syntax(), (p, o) -> { diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/CollectNodeConcatenate.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/CollectNodeConcatenate.java index 719e54977..5ad61f059 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/CollectNodeConcatenate.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/CollectNodeConcatenate.java @@ -16,12 +16,12 @@ public class CollectNodeConcatenate extends CollectNode { - public enum ConcatentationType { + public enum ConcatenationType { LEXICOGRAPHICAL("LexicalConcat"), PROVIDED("FixedConcat"); private final String syntax; - ConcatentationType(String syntax) { + ConcatenationType(String syntax) { this.syntax = syntax; } @@ -40,7 +40,7 @@ public String syntax() { private static final Method METHOD_STREAM__SORTED = new Method("sorted", A_STREAM_TYPE, new Type[] {}); - private final ConcatentationType concatentation; + private final ConcatenationType concatenation; private final ExpressionNode delimiter; private final ExpressionNode getter; @@ -49,11 +49,11 @@ public String syntax() { public CollectNodeConcatenate( int line, int column, - ConcatentationType concatentation, + ConcatenationType concatenation, ExpressionNode getter, ExpressionNode delimiter) { super(line, column); - this.concatentation = concatentation; + this.concatenation = concatenation; this.getter = getter; this.delimiter = delimiter; } @@ -72,7 +72,7 @@ public void collectPlugins(Set pluginFileNames) { @Override public final boolean orderingCheck(Ordering ordering, Consumer errorHandler) { - switch (concatentation) { + switch (concatenation) { case LEXICOGRAPHICAL: needsSort = true; return true; diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/Compiler.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/Compiler.java index 413bb789c..9b64bc739 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/Compiler.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/Compiler.java @@ -49,7 +49,7 @@ public abstract class Compiler { private static final Method METHOD_SERVICES_REQUIRED = new Method("services", Type.getType(Stream.class), new Type[0]); - private static final Handle SERVICES_REQURED_BSM = + private static final Handle SERVICES_REQUIRED_BSM = new Handle( Opcodes.H_INVOKESTATIC, Type.getInternalName(RuntimeSupport.class), @@ -187,7 +187,7 @@ protected ClassVisitor createClassVisitor() { methodGen.invokeDynamic( "services", Type.getMethodDescriptor(Type.getType(String[].class)), - SERVICES_REQURED_BSM, + SERVICES_REQUIRED_BSM, pluginFilenames.stream().map(Path::toString).toArray()); methodGen.invokeInterface(A_OLIVE_SERVICES, METHOD_OLIVE_SERVICES__IS_OVERLOADED_ARRAY); }); @@ -198,7 +198,7 @@ protected ClassVisitor createClassVisitor() { servicesMethodGen.invokeDynamic( "services", Type.getMethodDescriptor(Type.getType(String[].class)), - SERVICES_REQURED_BSM, + SERVICES_REQUIRED_BSM, pluginFilenames.stream().map(Path::toString).toArray()); servicesMethodGen.invokeStatic(A_ARRAYS_TYPE, METHOD_ARRAYS__STREAM); servicesMethodGen.returnValue(); diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/EcmaScriptRenderer.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/EcmaScriptRenderer.java index 890ee3395..02e7f77b4 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/EcmaScriptRenderer.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/EcmaScriptRenderer.java @@ -247,7 +247,7 @@ public String integer() { public String json() { // This may not be right as it assumes that all keys are in the same order, but we have // endeavoured to make that true, so YOLO? - return String.format("(JSON.stringfiy(%s) == JSON.stringify(%s))", left, right); + return String.format("(JSON.stringify(%s) == JSON.stringify(%s))", left, right); } @Override diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNode.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNode.java index 574f4c17e..5213983de 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNode.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNode.java @@ -958,7 +958,7 @@ private static Parser parseTupleOrObject( Parser parser, Consumer output, Function gangConstructor, - Function, ExpressionNode> objectContsructor, + Function, ExpressionNode> objectConstructor, Function, ExpressionNode> tupleConstructor) { final var gangParser = parser.whitespace().symbol("@"); if (gangParser.isGood()) { @@ -1003,7 +1003,7 @@ private static Parser parseTupleOrObject( } objectResult = objectResult.symbol("}").whitespace(); if (objectResult.isGood() && !fields.get().isEmpty()) { - output.accept(objectContsructor.apply(fields.get())); + output.accept(objectConstructor.apply(fields.get())); return objectResult; } diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNodeVariable.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNodeVariable.java index 59beb64ba..786b6cc0b 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNodeVariable.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNodeVariable.java @@ -54,7 +54,7 @@ public void collectFreeVariables(Set names, Predicate predicate names.add(target.unaliasedName()); } // We also need to get an accessor when in a Define olive and we need to lift the accessor - // along the way; in a other olives, this will just get ignored. + // along the way; in other olives, this will just get ignored. if (predicate.test(Flavour.CONSTANT)) { names.add(BaseOliveBuilder.SIGNER_ACCESSOR_NAME); } diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNodeWdlPair.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNodeWdlPair.java index 92ab4cd6a..1d7796264 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNodeWdlPair.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ExpressionNodeWdlPair.java @@ -45,7 +45,7 @@ public String renderEcma(EcmaScriptRenderer renderer) { public void render(Renderer renderer) { inner.render(renderer); - // Whether in the object or tuple form, Shemu's internal representation is a Tuple object and + // Whether in the object or tuple form, Shesmu's internal representation is a Tuple object and // since the fields are in the correct order, there is no need to do anything with the object. // This is zero cost. } diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/GroupNodeOptionalUnpack.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/GroupNodeOptionalUnpack.java index e2e24258d..f5a4c6d3b 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/GroupNodeOptionalUnpack.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/GroupNodeOptionalUnpack.java @@ -10,7 +10,7 @@ import java.util.function.Predicate; /** - * A only-if action in a “Group” clause + * An only-if action in a “Group” clause * *

Also usable as the variable definition for the result */ diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/OliveClauseNodeRequire.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/OliveClauseNodeRequire.java index 816d7e50b..72d1fc485 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/OliveClauseNodeRequire.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/OliveClauseNodeRequire.java @@ -106,7 +106,7 @@ public ClauseStreamOrder ensureRoot( expression.collectFreeVariables(signableNames, Flavour.STREAM_SIGNABLE::equals); copySignatures = true; } - // All though we technically manipulate the stream, we're only adding, so we can pretend the + // Although we technically manipulate the stream, we're only adding, so we can pretend the // stream is still pure. return state; } diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ProgramNode.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ProgramNode.java index 6e7ba60a4..e0d73225f 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ProgramNode.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/ProgramNode.java @@ -3,7 +3,7 @@ import ca.on.oicr.gsi.Pair; import ca.on.oicr.gsi.shesmu.compiler.definitions.*; import ca.on.oicr.gsi.shesmu.compiler.definitions.ConstantDefinition.AliasedConstantDefinition; -import ca.on.oicr.gsi.shesmu.compiler.definitions.SignatureDefinition.AliasedSignatureDefintion; +import ca.on.oicr.gsi.shesmu.compiler.definitions.SignatureDefinition.AliasedSignatureDefinition; import ca.on.oicr.gsi.shesmu.compiler.description.FileTable; import ca.on.oicr.gsi.shesmu.plugin.ErrorConsumer; import ca.on.oicr.gsi.shesmu.plugin.Parser; @@ -288,7 +288,7 @@ public RefillerDefinition refiller(String name) { @Override public Stream signatures() { - return stripImport(signatures.get(), AliasedSignatureDefintion::new); + return stripImport(signatures.get(), AliasedSignatureDefinition::new); } @Override diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/Target.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/Target.java index 1b125cf11..5cd3789f2 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/Target.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/Target.java @@ -15,7 +15,7 @@ enum Flavour { /** * A variable in a For operation * - *

May be be captured and should not be in scope to even worry about stream alteration + *

May be captured and should not be in scope to even worry about stream alteration */ LAMBDA(false), /** @@ -147,7 +147,7 @@ public Imyhat type() { /** What category of variables this one belongs to */ Flavour flavour(); - /** The Shemsu name for this variable */ + /** The Shesmu name for this variable */ String name(); /** Indicate that this variable is read */ diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/ActionDefinition.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/ActionDefinition.java index 87268bdc1..eba41fb36 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/ActionDefinition.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/ActionDefinition.java @@ -57,7 +57,7 @@ public Path filename() { /** * Write the bytecode to create a new instance of the action. * - *

This method should create an new instance of the action and leave it on the stack. If there + *

This method should create a new instance of the action and leave it on the stack. If there * is any hidden state (remote server addresses, workflow identifier), they must be handled at * this stage. * diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/ConstantDefinition.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/ConstantDefinition.java index 0ba7eae98..22e92bdd3 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/ConstantDefinition.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/ConstantDefinition.java @@ -287,7 +287,7 @@ public Type type() { * Create a new constant * * @param name the name of the constant, which must be valid Shesmu identifier - * @param type the Shemsu type of the constant + * @param type the Shesmu type of the constant */ public ConstantDefinition(String name, Imyhat type, String description, Path path) { super(); diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/SignatureDefinition.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/SignatureDefinition.java index b723eb243..fd2417880 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/SignatureDefinition.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/compiler/definitions/SignatureDefinition.java @@ -14,10 +14,10 @@ * input */ public abstract class SignatureDefinition implements Target { - public static class AliasedSignatureDefintion extends SignatureDefinition { + public static class AliasedSignatureDefinition extends SignatureDefinition { private final SignatureDefinition original; - public AliasedSignatureDefintion(SignatureDefinition original, String alias) { + public AliasedSignatureDefinition(SignatureDefinition original, String alias) { super(alias, original.storage(), original.type()); this.original = original; } diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/core/StandardDefinitions.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/core/StandardDefinitions.java index 77b5ef8b4..636a33433 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/core/StandardDefinitions.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/core/StandardDefinitions.java @@ -463,7 +463,7 @@ public Imyhat returnType() { String.join(Parser.NAMESPACE_SEPARATOR, "std", "path", "relativize"), "relativize", "Creates a new path of relativize one path as if in the directory of the other.", - "$runtime.pathRelativeize(%s, %s)", + "$runtime.pathRelativize(%s, %s)", Imyhat.PATH, new FunctionParameter("directory path", Imyhat.PATH), new FunctionParameter("path to relativize", Imyhat.PATH)), @@ -530,7 +530,7 @@ public Imyhat returnType() { String.join(Parser.NAMESPACE_SEPARATOR, "std", "string", "eq"), "equalsIgnoreCase", "Compares two strings ignoring case.", - "(%s.localeComapre(%s, undefined, {sensitivity:\"accent\"}) == 0)", + "(%s.localeCompare(%s, undefined, {sensitivity:\"accent\"}) == 0)", Imyhat.BOOLEAN, new FunctionParameter("first", Imyhat.STRING), new FunctionParameter("second", Imyhat.STRING)), diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/ActionGenerator.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/ActionGenerator.java index 5a09f589f..e6a6db45f 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/ActionGenerator.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/ActionGenerator.java @@ -83,7 +83,7 @@ protected final Gauge buildGauge(String metricName, String help, String[] labelN /** * Add all Prometheus monitoring for this program. * - *

Only one Shemsu script may be active at any time, but multiple may be loaded in memory as + *

Only one Shesmu script may be active at any time, but multiple may be loaded in memory as * part of compilation. Since duplicate Prometheus metrics are not permitted, Shesmu will {@link * #unregister()} the old {@link ActionGenerator} to remove its monitoring output, then connect * the new one using {@link #register()}. diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/CompiledGenerator.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/CompiledGenerator.java index 005b0d1ac..b58112c10 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/CompiledGenerator.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/CompiledGenerator.java @@ -803,7 +803,7 @@ public void function( } } - /** Bind to a exported function. */ + /** Bind to an exported function. */ public static CallSite bootstrap( MethodHandles.Lookup lookup, String methodName, MethodType type, String fileName) { final CallSite result = FUNCTION_REGISTRY.get(new Pair<>(fileName, methodName)); diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/RuntimeSupport.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/RuntimeSupport.java index 3ddfa1350..eedf5cc78 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/RuntimeSupport.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/runtime/RuntimeSupport.java @@ -549,7 +549,7 @@ public static Optional parseLong(String input) { * * @param input the stream of input items * @param hashCode the hashing for the grouping of interest over the input type - * @param equals a equality for the grouping of interest over the input type + * @param equals an equality for the grouping of interest over the input type * @param comparator the sorting operating to be performed on the grouped input */ @RuntimeInterop diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/BaseHotloadingCompiler.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/BaseHotloadingCompiler.java index 0ab544b6b..7aeacdd0f 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/BaseHotloadingCompiler.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/BaseHotloadingCompiler.java @@ -64,7 +64,7 @@ protected final ClassVisitor createClassVisitor() { } /** - * Create an instantiate a new instance of a just compiled class. + * Create and instantiate a new instance of a just compiled class. * *

This requires a zero-arguments constructor. * diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/BaseSimulateRequest.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/BaseSimulateRequest.java index b30dd1227..f56829918 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/BaseSimulateRequest.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/BaseSimulateRequest.java @@ -78,7 +78,7 @@ public abstract class BaseSimulateRequest { private static final Counter CACHE_REFRESH = Counter.build( "shesmu_simulate_refresh", - "The number of simulation requests and the cache freshess requested.") + "The number of simulation requests and the cache freshness requested.") .labelNames("mode", "format") .register(); diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/StaticActions.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/StaticActions.java index d33c6f204..3dec0b057 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/StaticActions.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/StaticActions.java @@ -99,7 +99,7 @@ public Optional update() { private static final Gauge processedCount = Gauge.build( "shesmu_static_actions_processed_count", - "The number of static actions defined in a file that were succsessfully added to the actions queue.") + "The number of static actions defined in a file that were successfully added to the actions queue.") .labelNames("filename") .register(); diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java index c3120882c..06b315b12 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java @@ -1854,7 +1854,7 @@ public static CallSite bootstrap( // Now we smash the instance from above with the method. We can create a // constant call site (i.e., one that can't be updated) because the method // called - // will never change but the instance is referenced through it's mutable call + // will never change but the instance is referenced through its mutable call // site, so we can update the instance. return new ConstantCallSite( MethodHandles.foldArguments(methodHandle, instance.dynamicInvoker())); @@ -1889,7 +1889,8 @@ public static CallSite bootstrapServices( collector, callsite.dynamicInvoker().asType(MethodType.methodType(RequiredServices.class))); } - // Now, we should have a method thats () → String[], which is what we wanted, so shove it in the + // Now, we should have a method that's () → String[], which is what we wanted, so shove it in + // the // olive return new ConstantCallSite(collector.asType(methodType)); } diff --git a/shesmu-server/src/main/resources/ca/on/oicr/gsi/shesmu/swagger.json b/shesmu-server/src/main/resources/ca/on/oicr/gsi/shesmu/swagger.json index 14017c765..5e2ae5619 100644 --- a/shesmu-server/src/main/resources/ca/on/oicr/gsi/shesmu/swagger.json +++ b/shesmu-server/src/main/resources/ca/on/oicr/gsi/shesmu/swagger.json @@ -539,7 +539,7 @@ "AlertFilterAnd": { "properties": { "filters": { - "description": "the filters which must be all be satisified", + "description": "the filters which must be all be satisfied", "items": { "$ref": "#/components/schemas/AlertFilter" }, @@ -605,7 +605,7 @@ "AlertFilterOr": { "properties": { "filters": { - "description": "the filters from which at least one must be satisified", + "description": "the filters from which at least one must be satisfied", "items": { "$ref": "#/components/schemas/AlertFilter" }, From 48916bcb8b640282890da1e894e5635bad6c3531 Mon Sep 17 00:00:00 2001 From: avarsava <17747491+avarsava@users.noreply.github.com> Date: Fri, 10 May 2024 08:45:49 -0400 Subject: [PATCH 2/4] Typo in shesmu-server-ui/src/histogram.ts Co-authored-by: Michael Laszloffy --- shesmu-server-ui/src/histogram.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shesmu-server-ui/src/histogram.ts b/shesmu-server-ui/src/histogram.ts index 3ae238212..fcf7f9f08 100644 --- a/shesmu-server-ui/src/histogram.ts +++ b/shesmu-server-ui/src/histogram.ts @@ -25,7 +25,7 @@ export interface HistogramRow { */ selectionDisplay(start: number, end: number): string; /** - * A callback inidicating that the user has selected this range of the histogram. + * A callback indicating that the user has selected this range of the histogram. * * It is guaranteed that start will be less than end. */ From 88e1182b755b86c0a1295f880442b3c84bac17e0 Mon Sep 17 00:00:00 2001 From: avarsava <17747491+avarsava@users.noreply.github.com> Date: Fri, 10 May 2024 08:46:03 -0400 Subject: [PATCH 3/4] Line breaks in shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java Co-authored-by: Michael Laszloffy --- .../ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java index 06b315b12..4d9fcaa4c 100644 --- a/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java +++ b/shesmu-server/src/main/java/ca/on/oicr/gsi/shesmu/server/plugins/PluginManager.java @@ -1890,7 +1890,7 @@ public static CallSite bootstrapServices( callsite.dynamicInvoker().asType(MethodType.methodType(RequiredServices.class))); } // Now, we should have a method that's () → String[], which is what we wanted, so shove it in - // the + // the olive // olive return new ConstantCallSite(collector.asType(methodType)); } From 5eae6e2242878552125702f56288de873dd617f5 Mon Sep 17 00:00:00 2001 From: Alexis Varsava Date: Tue, 14 May 2024 12:13:35 -0400 Subject: [PATCH 4/4] another mistake --- docs/faq.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/faq.md b/docs/faq.md index b5dbb2499..86f497f89 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -61,4 +61,4 @@ No worries, this isn't much harder: You can click almost any cell header or value and then use the buttons at the bottom to act on the subset of actions. Use the _Add Filter_ button to slice and dice the actions displayed. ## Can I see how some data is propagating through this olive? -Not quite, but you can go to the _Olives_ page and select the olive, and click _Edit in Simulator_ to have the source code for that file show up in the simulation dashboard. Add a _Where_ or _Dump_ clauses to filter the data of interest and simulate it to see what's going on. +Not quite, but you can go to the _Olives_ page and select the olive, and click _Edit in Simulator_ to have the source code for that file show up in the simulation dashboard. Add a _Where_ or _Dump_ clause to filter the data of interest and simulate it to see what's going on.