A federal judge in New York has issued a temporary stay on parts of President Trump's executive order in immigration that halts the deportation of some individuals affected by the ban on refugees from certain countries.

The Hill:

The move appears to mark the first successful legal challenge to the Trump administration and affects those who have arrived in the U.S. with previously approved refugee applications or were in transit with valid visas. Similar rulings were later issued in Virginia, Massachusetts and Washington state.

U.S. District Court Judge Ann Donnelly ruled in favor of a habeas corpus petition filed by the American Civil Liberties Union (ACLU) on behalf of two Iraqi men who were detained at John F. Kennedy International Airport on Friday after Trump signed his order.

Donnelly, who was nominated by former President Barack Obama and confirmed to her judgeship in 2015, ruled in the Eastern District of New York that "there is imminent danger that, absent the stay of removal, there will be substantial and irreparable injury to refugees, visa-holders, and other individuals from nations subject" to Trump's order.

“This ruling preserves the status quo and ensures that people who have been granted permission to be in this country are not illegally removed off U.S. soil," said Lee Gelernt, deputy director of the ACLU’s Immigrants’ Rights Project.

The ruling deals with a portion of Trump's order handed down Friday, which bars Syrian refugees indefinitely and halts the resettlement of all refugees for four months as the administration reviews the vetting process.

The order also denies entry for 90 days for individuals from seven predominantly Muslims countries: Iraq, Iran, Somalia, Sudan, Syria, Libya and Yemen.

“Clearly the judge understood the possibility for irreparable harm to hundreds of immigrants and lawful visitors to this country," ACLU Executive Director Anthony D. Romero said in a statement.

"Our courts today worked as they should as bulwarks against government abuse or unconstitutional policies and orders. On week one, Donald Trump suffered his first loss in court.”

The order Saturday evening capped off a chaotic first day following Trump's directive, as the administration moved to implement his order, with reports emerging of individuals being detained at a number of airports across the country.

The ruling affects only those travelers who have approved visas or approval to enter the US as a refugee. The court's concern is that once issued, these documents can't be rescinded without due process. 

As has been pointed out elsewhere, there is nothing illegal about denying entry to refugees from specific countries. My concern is with legal US residents who may have been traveling overseas (or are planning an overseas trip) that are prevented from returning to the US. Also, there are US citizens who hold dual citizenship who are unable to return.

There is absolutely no reason for this and it appears that this interpretation of the executive order was not thought through. Banning the return of legal residents - even from Canada - is going to be the next part of the executive order that will be challenged.

When all is said and done, Trump's order will remain largely intact with a few tweaks to account for legal residents and those who have already been approved to travel to America. Meanwhile, DHS, the FBI, and immigration officials will come up with a better way to vet the refugees , improving on the Obama administration's procedures which everyone from the FBI director to those in the national security establishment believed wasn't good enough.